=============================================================================== About this build: this rebuild has been done as part of reproduce.debian.net where we aim to reproduce Debian binary packages distributed via ftp.debian.org, by rebuilding using the exact same packages as the original build on the buildds, as described in the relevant .buildinfo file from buildinfos.debian.net. For more information please go to https://reproduce.debian.net or join #debian-reproducible on irc.debian.org =============================================================================== Preparing download of sources for /srv/rebuilderd/tmp/rebuilderd3HfAy5/inputs/rdkit_202503.1-4_all.buildinfo Source: rdkit Version: 202503.1-4 rebuilderd-worker node: ionos17-amd64 +------------------------------------------------------------------------------+ | Downloading sources Mon, 28 Jul 2025 09:06:34 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [168 kB] Get:2 https://deb.debian.org/debian sid InRelease [213 kB] Get:3 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:4 https://deb.debian.org/debian sid/main Sources [11.0 MB] Fetched 21.9 MB in 1s (15.2 MB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/r/rdkit/rdkit_202503.1-4.dsc' rdkit_202503.1-4.dsc 3081 SHA256:bef3fda91aa5bd06459bc6641b2efb4d9f26d5ab090848d1e89c3b132595e629 'https://deb.debian.org/debian/pool/main/r/rdkit/rdkit_202503.1.orig.tar.xz' rdkit_202503.1.orig.tar.xz 63530544 SHA256:1c4cca2eef824f77d7dd1421f5a35f700fa66b83dbdd79a43116af29b564a0df 'https://deb.debian.org/debian/pool/main/r/rdkit/rdkit_202503.1-4.debian.tar.xz' rdkit_202503.1-4.debian.tar.xz 47576 SHA256:71154d2ebc03ce8c99bf562ef27981a1289f63ff5f10bedb15311ba1f1fd0f88 1c4cca2eef824f77d7dd1421f5a35f700fa66b83dbdd79a43116af29b564a0df rdkit_202503.1.orig.tar.xz 71154d2ebc03ce8c99bf562ef27981a1289f63ff5f10bedb15311ba1f1fd0f88 rdkit_202503.1-4.debian.tar.xz bef3fda91aa5bd06459bc6641b2efb4d9f26d5ab090848d1e89c3b132595e629 rdkit_202503.1-4.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Mon, 28 Jul 2025 09:06:37 +0000 | +------------------------------------------------------------------------------+ + nice /usr/bin/debrebuildRebuilding rdkit=202503.1-4 in /srv/rebuilderd/tmp/rebuilderd3HfAy5/inputs now. --buildresult=/srv/rebuilderd/tmp/rebuilderd3HfAy5/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderd3HfAy5/inputs/rdkit_202503.1-4_all.buildinfo /srv/rebuilderd/tmp/rebuilderd3HfAy5/inputs/rdkit_202503.1-4_all.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/rdkit-202503.1 I: verifying dsc... successful! Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid InRelease [205 kB] Get:2 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 Packages [10.1 MB] Fetched 10.3 MB in 1s (7447 kB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20250501T203212Z/dists/sid/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Fetched 538 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphmzq36n7/libcairo2_1.18.4-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-sphinx all 8.1.3-5 [468 kB] Fetched 468 kB in 0s (41.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5c8mgqvt/python3-sphinx_8.1.3-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 passwd amd64 1:4.17.4-2 [1229 kB] Fetched 1229 kB in 0s (89.1 MB/s) dpkg-name: info: moved 'passwd_1%3a4.17.4-2_amd64.deb' to '/srv/rebuilderd/tmp/tmpygo29n6y/passwd_4.17.4-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-4.2 [261 kB] Fetched 261 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmputb334dk/libboost-iostreams1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcc1-0 amd64 14.2.0-19 [42.8 kB] Fetched 42.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbk83eu42/libcc1-0_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Fetched 98.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsoo4rwp3/xtrans-dev_1.4.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 x11proto-dev all 2024.1-1 [603 kB] Fetched 603 kB in 0s (55.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj2fhgddj/x11proto-dev_2024.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libtiff6 amd64 4.7.0-3 [346 kB] Fetched 346 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpps_ur7pk/libtiff6_4.7.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-atomic1.83-dev amd64 1.83.0-4.2 [236 kB] Fetched 236 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprqen2du8/libboost-atomic1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libio-pty-perl amd64 1:1.20-1+b3 [34.3 kB] Fetched 34.3 kB in 0s (0 B/s) dpkg-name: info: moved 'libio-pty-perl_1%3a1.20-1+b3_amd64.deb' to '/srv/rebuilderd/tmp/tmpeex0e6j6/libio-pty-perl_1.20-1+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libblkid1 amd64 2.41-4 [171 kB] Fetched 171 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp19s7thm1/libblkid1_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Fetched 33.0 kB in 1s (52.2 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5okkbaew/libkrb5support0_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Fetched 109 kB in 0s (331 kB/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.46-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpwis2ffk2/libmagic1t64_5.46-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Fetched 4540 kB in 1s (3728 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbcs1pij1/fonts-lmodern_2.005-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-python1.83.0 amd64 1.83.0-4.2 [306 kB] Fetched 306 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9stkjih4/libboost-python1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 base-files amd64 13.7 [73.0 kB] Fetched 73.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoqm07y1o/base-files_13.7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpango-1.0-0 amd64 1.56.3-1 [226 kB] Fetched 226 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph0vgpfj5/libpango-1.0-0_1.56.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Fetched 10.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg3_6z24o/sgml-base_1.31+nmu1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Fetched 81.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphntqdaux/libk5crypto3_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libc-bin amd64 2.41-7 [636 kB] Fetched 636 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw6ej6v7b/libc-bin_2.41-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Fetched 90.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgniua_89/python3-typing-extensions_4.13.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 ssl-cert all 1.1.3 [16.8 kB] Fetched 16.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmv6c8xe0/ssl-cert_1.1.3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 imagemagick amd64 8:7.1.1.47+dfsg1-1 [20.1 kB] Fetched 20.1 kB in 0s (159 kB/s) dpkg-name: info: moved 'imagemagick_8%3a7.1.1.47+dfsg1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpm4vwh79i/imagemagick_7.1.1.47+dfsg1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Fetched 75.2 kB in 0s (1147 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpryjqpv10/libgdbm6t64_1.24-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-4.2 [254 kB] Fetched 254 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqnqy8oj9/libboost-iostreams1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB] Fetched 125 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6q5qinij/python3-charset-normalizer_3.4.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Fetched 109 kB in 0s (10.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnhy5g3bt/libidn2-0_2.3.8-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Fetched 23.3 kB in 0s (409 kB/s) dpkg-name: info: moved 'libfontenc1_1%3a1.1.8-1+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpil5cu8py/libfontenc1_1.1.8-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libssl3t64 amd64 3.5.0-1 [2432 kB] Fetched 2432 kB in 0s (21.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmgr_7yav/libssl3t64_3.5.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 catch2 all 3.7.1-0.5 [5144 B] Fetched 5144 B in 0s (130 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7onff606/catch2_3.7.1-0.5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libobjc-14-dev amd64 14.2.0-19 [173 kB] Fetched 173 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkkdy5hwh/libobjc-14-dev_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxmu6 amd64 2:1.1.3-3+b4 [59.0 kB] Fetched 59.0 kB in 0s (3412 kB/s) dpkg-name: info: moved 'libxmu6_2%3a1.1.3-3+b4_amd64.deb' to '/srv/rebuilderd/tmp/tmpkjlzhw6r/libxmu6_1.1.3-3+b4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libc6-dev amd64 2.41-7 [1992 kB] Fetched 1992 kB in 0s (131 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq1l7o_jy/libc6-dev_2.41-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-19 [11.0 MB] Fetched 11.0 MB in 0s (192 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvs2fo9in/cpp-14-x86-64-linux-gnu_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Fetched 128 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc7zsppip/docutils-common_0.21.2+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Fetched 459 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq1_q9oyv/pandoc-data_3.1.11.1-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-6 [157 kB] Fetched 157 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp77es92tf/libkpathsea6_2024.20240313.70630+ds-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 util-linux amd64 2.41-4 [1234 kB] Fetched 1234 kB in 0s (103 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfkcyuxax/util-linux_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Fetched 307 kB in 0s (6525 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3fbuajgc/libbrotli1_1.1.0-2+b7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcrypt1 amd64 1:4.4.38-1 [90.1 kB] Fetched 90.1 kB in 0s (0 B/s) dpkg-name: info: moved 'libcrypt1_1%3a4.4.38-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpgsaa2ikt/libcrypt1_4.4.38-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Fetched 20.4 kB in 0s (174 kB/s) dpkg-name: info: moved 'libxau6_1%3a1.0.11-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpxk0qvpi0/libxau6_1.0.11-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-sqlalchemy all 2.0.40+ds1-1 [1210 kB] Fetched 1210 kB in 0s (43.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2v3nzld2/python3-sqlalchemy_2.0.40+ds1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libmount-dev amd64 2.41-4 [30.5 kB] Fetched 30.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpusb36d5d/libmount-dev_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [55.6 kB] Fetched 55.6 kB in 0s (398 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbk5a1eik/libpangoft2-1.0-0_1.56.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libobjc4 amd64 14.2.0-19 [43.3 kB] Fetched 43.3 kB in 0s (1371 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3bj5hz0t/libobjc4_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libuuid1 amd64 2.41-4 [37.6 kB] Fetched 37.6 kB in 1s (74.5 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn9wje1wu/libuuid1_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Fetched 105 kB in 0s (420 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe0n4snkd/libncurses6_6.5+20250216-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Fetched 62.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc0cu4_0g/t1utils_1.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Fetched 452 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq43rrr17/libfreetype6_2.13.3+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Fetched 815 kB in 0s (79.6 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmppfyop8c9/libx11-6_1.8.12-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 tex-common all 6.19 [29.4 kB] Fetched 29.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7xx8it3u/tex-common_6.19_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 bsdutils amd64 1:2.41-4 [110 kB] Fetched 110 kB in 0s (1896 kB/s) dpkg-name: info: moved 'bsdutils_1%3a2.41-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp40kk3d2k/bsdutils_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (414 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwdxv66d9/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpython3.13-minimal amd64 3.13.3-2 [861 kB] Fetched 861 kB in 0s (75.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9nz94oie/libpython3.13-minimal_3.13.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpcre2-dev amd64 10.45-1 [853 kB] Fetched 853 kB in 0s (77.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwtcfh1k3/libpcre2-dev_10.45-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 llvm-19-linker-tools amd64 1:19.1.7-3 [1260 kB] Fetched 1260 kB in 0s (102 MB/s) dpkg-name: info: moved 'llvm-19-linker-tools_1%3a19.1.7-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp00_i8bnp/llvm-19-linker-tools_19.1.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Fetched 144 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkjl6hovi/libxcb1_1.17.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-9 [4595 kB] Fetched 4595 kB in 0s (41.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9sufvfjm/python3-pandas-lib_2.2.3+dfsg-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsepol2 amd64 3.8.1-1 [296 kB] Fetched 296 kB in 0s (12.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7yavz8u3/libsepol2_3.8.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpaper2 amd64 2.2.5-0.3+b2 [16.7 kB] Fetched 16.7 kB in 0s (363 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5gcct4a4/libpaper2_2.2.5-0.3+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsystemd0 amd64 257.5-2 [453 kB] Fetched 453 kB in 0s (8347 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4nrurdk5/libsystemd0_257.5-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libmpfr6 amd64 4.2.2-1 [729 kB] Fetched 729 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwk5wiqyz/libmpfr6_4.2.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libseccomp2 amd64 2.6.0-2 [51.7 kB] Fetched 51.7 kB in 0s (4444 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_bb_gg_4/libseccomp2_2.6.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libnettle8t64 amd64 3.10.1-1 [305 kB] Fetched 305 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwrswc5rx/libnettle8t64_3.10.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxpm4 amd64 1:3.5.17-1+b3 [56.2 kB] Fetched 56.2 kB in 0s (0 B/s) dpkg-name: info: moved 'libxpm4_1%3a3.5.17-1+b3_amd64.deb' to '/srv/rebuilderd/tmp/tmp1g3nrsqj/libxpm4_3.5.17-1+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 imagemagick-7-common all 8:7.1.1.47+dfsg1-1 [67.5 kB] Fetched 67.5 kB in 0s (0 B/s) dpkg-name: info: moved 'imagemagick-7-common_8%3a7.1.1.47+dfsg1-1_all.deb' to '/srv/rebuilderd/tmp/tmpg275k29m/imagemagick-7-common_7.1.1.47+dfsg1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcurl4t64 amd64 8.13.0-5 [382 kB] Fetched 382 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp76r_df83/libcurl4t64_8.13.0-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 x11-common all 1:7.7+24 [217 kB] Fetched 217 kB in 0s (0 B/s) dpkg-name: info: moved 'x11-common_1%3a7.7+24_all.deb' to '/srv/rebuilderd/tmp/tmpzxu9f37a/x11-common_7.7+24_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Fetched 101 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4a93x_26/libipc-run-perl_20231003.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 dash amd64 0.5.12-12 [98.5 kB] Fetched 98.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp116si4w2/dash_0.5.12-12_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libdebconfclient0 amd64 0.278 [10.5 kB] Fetched 10.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo_gz_l7o/libdebconfclient0_0.278_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxrender-dev amd64 1:0.9.12-1 [39.0 kB] Fetched 39.0 kB in 0s (0 B/s) dpkg-name: info: moved 'libxrender-dev_1%3a0.9.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpwxozmjyu/libxrender-dev_0.9.12-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Fetched 135 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzo684js3/libncursesw6_6.5+20250216-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpixman-1-dev amd64 0.44.0-3 [11.4 kB] Fetched 11.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpihmxp_up/libpixman-1-dev_0.44.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Fetched 30.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_4bi1swv/pkgconf-bin_1.8.1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsm-dev amd64 2:1.2.6-1 [39.7 kB] Fetched 39.7 kB in 0s (0 B/s) dpkg-name: info: moved 'libsm-dev_2%3a1.2.6-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp0gpf_j3i/libsm-dev_1.2.6-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-jinja2 all 3.1.6-1 [107 kB] Fetched 107 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph8mzz0e1/python3-jinja2_3.1.6-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB] Fetched 55.1 kB in 0s (124 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpib01h0v2/liblzo2-2_2.10-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Fetched 489 kB in 0s (1168 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpanwc1j6g/fonts-dejavu-mono_2.37-8_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libstdc++6 amd64 14.2.0-19 [714 kB] Fetched 714 kB in 1s (709 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprl0pxdso/libstdc++6_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libmd0 amd64 1.1.0-2+b1 [36.3 kB] Fetched 36.3 kB in 0s (75.9 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8puizel8/libmd0_1.1.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-numpy-dev amd64 1.83.0.2+b2 [3644 B] Fetched 3644 B in 1s (5485 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf4c_yaqd/libboost-numpy-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Fetched 8560 kB in 1s (14.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpucpfit8x/libz3-4_4.13.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 gcc amd64 4:14.2.0-1 [5136 B] Fetched 5136 B in 1s (9025 B/s) dpkg-name: info: moved 'gcc_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpb11t8v2l/gcc_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 native-architecture all 0.2.6 [2264 B] Fetched 2264 B in 0s (4628 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphek2d4x8/native-architecture_0.2.6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Fetched 248 kB in 0s (597 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsuca_qgm/po-debconf_1.0.21+nmu1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libnuma1 amd64 2.0.19-1 [22.2 kB] Fetched 22.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpptwhz352/libnuma1_2.0.19-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Fetched 63.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpffdrmt2o/rpcsvc-proto_1.4.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-6 [8446 kB] Fetched 8446 kB in 0s (243 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3xloqrmm/texlive-binaries_2024.20240313.70630+ds-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Fetched 31.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdi4hqzb1/libbz2-dev_1.0.8-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 dpkg-dev all 1.22.18 [1338 kB] Fetched 1338 kB in 0s (105 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcn6da1ia/dpkg-dev_1.22.18_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libudev1 amd64 257.5-2 [151 kB] Fetched 151 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppn304moh/libudev1_257.5-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpcre2-16-0 amd64 10.45-1 [281 kB] Fetched 281 kB in 0s (7237 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0oj5sf0m/libpcre2-16-0_10.45-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Fetched 6396 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptshi8gdc/python3-iniconfig_1.1.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 adduser all 3.150 [187 kB] Fetched 187 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8couekx6/adduser_3.150_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 binutils-common amd64 2.44-3 [2509 kB] Fetched 2509 kB in 0s (152 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3im55_35/binutils-common_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 liblsan0 amd64 14.2.0-19 [1204 kB] Fetched 1204 kB in 0s (103 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg2l3slwk/liblsan0_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 cmake amd64 3.31.6-2 [12.0 MB] Fetched 12.0 MB in 0s (259 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplu096sn4/cmake_3.31.6-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libjansson4 amd64 2.14-2+b3 [39.8 kB] Fetched 39.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_xgdrvs2/libjansson4_2.14-2+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libctf0 amd64 2.44-3 [88.6 kB] Fetched 88.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_xcy5r9p/libctf0_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-6 [62.9 kB] Fetched 62.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp88du23ss/libsynctex2_2024.20240313.70630+ds-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 clang-19 amd64 1:19.1.7-3 [116 kB] Fetched 116 kB in 0s (0 B/s) dpkg-name: info: moved 'clang-19_1%3a19.1.7-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpljziw0oq/clang-19_19.1.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Fetched 126 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpokr_20tr/libwebpmux3_1.5.0-0.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Fetched 127 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9s016y4t/libfmt10_10.1.1+ds1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libhwasan0 amd64 14.2.0-19 [1488 kB] Fetched 1488 kB in 0s (112 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyg56vx6d/libhwasan0_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 g++ amd64 4:14.2.0-1 [1344 B] Fetched 1344 B in 0s (0 B/s) dpkg-name: info: moved 'g++_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpbkww9cxw/g++_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 latexmk all 1:4.86~ds-1 [507 kB] Fetched 507 kB in 0s (0 B/s) dpkg-name: info: moved 'latexmk_1%3a4.86~ds-1_all.deb' to '/srv/rebuilderd/tmp/tmpl01urzpu/latexmk_4.86~ds-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Fetched 90.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk3zhl84m/libdebhelper-perl_13.24.2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-19 [12.1 MB] Fetched 12.1 MB in 0s (248 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp50mmaqz4/g++-14-x86-64-linux-gnu_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Fetched 24.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5wa22lb4/libffi8_3.4.8-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libmount1 amd64 2.41-4 [209 kB] Fetched 209 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph7robrmx/libmount1_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-markdown-it all 3.0.0-2 [62.5 kB] Fetched 62.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph_ui5n_k/python3-markdown-it_3.0.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libhogweed6t64 amd64 3.10.1-1 [335 kB] Fetched 335 kB in 0s (27.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphdv050bl/libhogweed6t64_3.10.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 gettext amd64 0.23.1-2 [1680 kB] Fetched 1680 kB in 0s (134 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpawieu5tl/gettext_0.23.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 postgresql-common-dev all 277 [72.2 kB] Fetched 72.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt0pevvec/postgresql-common-dev_277_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Fetched 38.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphqlfrfvr/libdatrie1_0.2.13-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libmagickwand-7.q16-10 amd64 8:7.1.1.47+dfsg1-1 [343 kB] Fetched 343 kB in 0s (0 B/s) dpkg-name: info: moved 'libmagickwand-7.q16-10_8%3a7.1.1.47+dfsg1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpm7jdd4vx/libmagickwand-7.q16-10_7.1.1.47+dfsg1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 bison amd64 2:3.8.2+dfsg-1+b2 [1170 kB] Fetched 1170 kB in 0s (87.7 MB/s) dpkg-name: info: moved 'bison_2%3a3.8.2+dfsg-1+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpzu_jfi44/bison_3.8.2+dfsg-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-9 [704 kB] Fetched 704 kB in 0s (68.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2autp9i1/libdb5.3t64_5.3.28+dfsg2-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Fetched 30.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi1lxzyvr/libjs-sphinxdoc_8.1.3-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libheif1 amd64 1.19.8-1 [520 kB] Fetched 520 kB in 0s (50.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz4279rco/libheif1_1.19.8-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Fetched 245 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvjba63n4/libssh2-1t64_1.11.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3.13 amd64 3.13.3-2 [751 kB] Fetched 751 kB in 0s (55.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmtainpbp/python3.13_3.13.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 bsdextrautils amd64 2.41-4 [94.6 kB] Fetched 94.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphzos4h4e/bsdextrautils_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsemanage-common all 3.8.1-1 [7812 B] Fetched 7812 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprp5uygqu/libsemanage-common_3.8.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-mdurl all 0.1.2-1 [9444 B] Fetched 9444 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw85115tu/python3-mdurl_0.1.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 xml-core all 0.19 [20.1 kB] Fetched 20.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps2hmtqdx/xml-core_0.19_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 hostname amd64 3.25 [11.0 kB] Fetched 11.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps2gpdfgm/hostname_3.25_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Fetched 50.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb7xcx8a5/libgdbm-compat4t64_1.24-2_amd64.deb' Downloading dependency 1 of 495: libcairo2:amd64=1.18.4-1+b1 Downloading dependency 2 of 495: python3-sphinx:amd64=8.1.3-5 Downloading dependency 3 of 495: passwd:amd64=1:4.17.4-2 Downloading dependency 4 of 495: libboost-iostreams1.83-dev:amd64=1.83.0-4.2 Downloading dependency 5 of 495: libcc1-0:amd64=14.2.0-19 Downloading dependency 6 of 495: xtrans-dev:amd64=1.4.0-1 Downloading dependency 7 of 495: x11proto-dev:amd64=2024.1-1 Downloading dependency 8 of 495: libtiff6:amd64=4.7.0-3 Downloading dependency 9 of 495: libboost-atomic1.83-dev:amd64=1.83.0-4.2 Downloading dependency 10 of 495: libio-pty-perl:amd64=1:1.20-1+b3 Downloading dependency 11 of 495: libblkid1:amd64=2.41-4 Downloading dependency 12 of 495: libkrb5support0:amd64=1.21.3-5 Downloading dependency 13 of 495: libmagic1t64:amd64=1:5.46-5 Downloading dependency 14 of 495: fonts-lmodern:amd64=2.005-1 Downloading dependency 15 of 495: 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Downloading dependency 31 of 495: libobjc-14-dev:amd64=14.2.0-19 Downloading dependency 32 of 495: libxmu6:amd64=2:1.1.3-3+b4 Downloading dependency 33 of 495: libc6-dev:amd64=2.41-7 Downloading dependency 34 of 495: cpp-14-x86-64-linux-gnu:amd64=14.2.0-19 Downloading dependency 35 of 495: docutils-common:amd64=0.21.2+dfsg-2 Downloading dependency 36 of 495: pandoc-data:amd64=3.1.11.1-3 Downloading dependency 37 of 495: libkpathsea6:amd64=2024.20240313.70630+ds-6 Downloading dependency 38 of 495: util-linux:amd64=2.41-4 Downloading dependency 39 of 495: libbrotli1:amd64=1.1.0-2+b7 Downloading dependency 40 of 495: libcrypt1:amd64=1:4.4.38-1 Downloading dependency 41 of 495: libxau6:amd64=1:1.0.11-1 Downloading dependency 42 of 495: python3-sqlalchemy:amd64=2.0.40+ds1-1 Downloading dependency 43 of 495: libmount-dev:amd64=2.41-4 Downloading dependency 44 of 495: libpangoft2-1.0-0:amd64=1.56.3-1 Downloading dependency 45 of 495: libobjc4:amd64=14.2.0-19 Downloading dependency 46 of 495: libuuid1:amd64=2.41-4 Downloading dependency 47 of 495: libncurses6:amd64=6.5+20250216-2 Downloading dependency 48 of 495: t1utils:amd64=1.41-4 Downloading dependency 49 of 495: libfreetype6:amd64=2.13.3+dfsg-1 Downloading dependency 50 of 495: libx11-6:amd64=2:1.8.12-1 Downloading dependency 51 of 495: tex-common:amd64=6.19 Downloading dependency 52 of 495: bsdutils:amd64=1:2.41-4 Downloading dependency 53 of 495: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 54 of 495: libpython3.13-minimal:amd64=3.13.3-2 Downloading dependency 55 of 495: libpcre2-dev:amd64=10.45-1 Downloading dependency 56 of 495: llvm-19-linker-tools:amd64=1:19.1.7-3 Downloading dependency 57 of 495: libxcb1:amd64=1.17.0-2+b1 Downloading dependency 58 of 495: python3-pandas-lib:amd64=2.2.3+dfsg-9 Downloading dependency 59 of 495: libsepol2:amd64=3.8.1-1 Downloading dependency 60 of 495: libpaper2:amd64=2.2.5-0.3+b2 Downloading dependency 61 of 495: libsystemd0:amd64=257.5-2 Downloading dependency 62 of 495: libmpfr6:amd64=4.2.2-1 Downloading dependency 63 of 495: libseccomp2:amd64=2.6.0-2 Downloading dependency 64 of 495: libnettle8t64:amd64=3.10.1-1 Downloading dependency 65 of 495: libxpm4:amd64=1:3.5.17-1+b3 Downloading dependency 66 of 495: imagemagick-7-common:amd64=8:7.1.1.47+dfsg1-1 Downloading dependency 67 of 495: libcurl4t64:amd64=8.13.0-5 Downloading dependency 68 of 495: x11-common:amd64=1:7.7+24 Downloading dependency 69 of 495: libipc-run-perl:amd64=20231003.0-2 Downloading dependency 70 of 495: dash:amd64=0.5.12-12 Downloading dependency 71 of 495: libdebconfclient0:amd64=0.278 Downloading dependency 72 of 495: libxrender-dev:amd64=1:0.9.12-1 Downloading dependency 73 of 495: libncursesw6:amd64=6.5+20250216-2 Downloading dependency 74 of 495: libpixman-1-dev:amd64=0.44.0-3 Downloading dependency 75 of 495: pkgconf-bin:amd64=1.8.1-4 Downloading dependency 76 of 495: libsm-dev:amd64=2:1.2.6-1 Downloading dependency 77 of 495: python3-jinja2:amd64=3.1.6-1 Downloading dependency 78 of 495: liblzo2-2:amd64=2.10-3+b1 Downloading dependency 79 of 495: fonts-dejavu-mono:amd64=2.37-8 Downloading dependency 80 of 495: libstdc++6:amd64=14.2.0-19 Downloading dependency 81 of 495: libmd0:amd64=1.1.0-2+b1 Downloading dependency 82 of 495: libboost-numpy-dev:amd64=1.83.0.2+b2 Downloading dependency 83 of 495: libz3-4:amd64=4.13.3-1 Downloading dependency 84 of 495: gcc:amd64=4:14.2.0-1 Downloading dependency 85 of 495: native-architecture:amd64=0.2.6 Downloading dependency 86 of 495: po-debconf:amd64=1.0.21+nmu1 Downloading dependency 87 of 495: libnuma1:amd64=2.0.19-1 Downloading dependency 88 of 495: rpcsvc-proto:amd64=1.4.3-1 Downloading dependency 89 of 495: texlive-binaries:amd64=2024.20240313.70630+ds-6 Downloading dependency 90 of 495: libbz2-dev:amd64=1.0.8-6 Downloading dependency 91 of 495: dpkg-dev:amd64=1.22.18 Downloading dependency 92 of 495: libudev1:amd64=257.5-2 Downloading dependency 93 of 495: libpcre2-16-0:amd64=10.45-1 Downloading dependency 94 of 495: python3-iniconfig:amd64=1.1.1-2 Downloading dependency 95 of 495: adduser:amd64=3.150 Downloading dependency 96 of 495: binutils-common:amd64=2.44-3 Downloading dependency 97 of 495: liblsan0:amd64=14.2.0-19 Downloading dependency 98 of 495: cmake:amd64=3.31.6-2 Downloading dependency 99 of 495: libjansson4:amd64=2.14-2+b3 Downloading dependency 100 of 495: libctf0:amd64=2.44-3 Downloading dependency 101 of 495: libsynctex2:amd64=2024.20240313.70630+ds-6 Downloading dependency 102 of 495: clang-19:amd64=1:19.1.7-3 Downloading dependency 103 of 495: libwebpmux3:amd64=1.5.0-0.1 Downloading dependency 104 of 495: libfmt10:amd64=10.1.1+ds1-4 Downloading dependency 105 of 495: libhwasan0:amd64=14.2.0-19 Downloading dependency 106 of 495: g++:amd64=4:14.2.0-1 Downloading dependency 107 of 495: latexmk:amd64=1:4.86~ds-1 Downloading dependency 108 of 495: libdebhelper-perl:amd64=13.24.2 Downloading dependency 109 of 495: g++-14-x86-64-linux-gnu:amd64=14.2.0-19 Downloading dependency 110 of 495: libffi8:amd64=3.4.8-2 Downloading dependency 111 of 495: libmount1:amd64=2.41-4 Downloading dependency 112 of 495: python3-markdown-it:amd64=3.0.0-2 Downloading dependency 113 of 495: libhogweed6t64:amd64=3.10.1-1 Downloading dependency 114 of 495: gettext:amd64=0.23.1-2 Downloading dependency 115 of 495: postgresql-common-dev:amd64=277 Downloading dependency 116 of 495: libdatrie1:amd64=0.2.13-3+b1 Downloading dependency 117 of 495: libmagickwand-7.q16-10:amd64=8:7.1.1.47+dfsg1-1 Downloading dependency 118 of 495: bison:amd64=2:3.8.2+dfsg-1+b2 Downloading dependency 119 of 495: libdb5.3t64:amd64=5.3.28+dfsg2-9 Downloading dependency 120 of 495: libjs-sphinxdoc:amd64=8.1.3-5 Downloading dependency 121 of 495: libheif1:amd64=1.19.8-1 Downloading dependency 122 of 495: libssh2-1t64:amd64=1.11.1-1 Downloading dependency 123 of 495: python3.13:amd64=3.13.3-2 Downloading dependency 124 of 495: bsdextrautils:amd64=2.41-4 Downloading dependency 125 of 495: libsemanage-common:amd64=3.8.1-1 Downloading dependency 126 of 495: python3-mdurl:amd64=0.1.2-1 Downloading dependency 127 of 495: xml-core:amd64=0.19 Downloading dependency 128 of 495: hostname:amd64=3.25 Downloading dependency 129 of 495: libgdbm-compat4t64:amd64=1.24-2 Downloading dependency 130 of 495: fontconfig:amd64=2.15.0-2.3Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 fontconfig amd64 2.15.0-2.3 [463 kB] Fetched 463 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4cfk674t/fontconfig_2.15.0-2.3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 openssl amd64 3.5.0-1 [1491 kB] Fetched 1491 kB in 0s (121 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkbniyfi1/openssl_3.5.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 icu-devtools amd64 76.1-3 [215 kB] Fetched 215 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkfd9rflz/icu-devtools_76.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 m4 amd64 1.4.19-8 [294 kB] Fetched 294 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqr66rvcl/m4_1.4.19-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Fetched 78.9 kB in 0s (0 B/s) dpkg-name: info: moved 'libxi6_2%3a1.8.2-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpp2kmy4c1/libxi6_1.8.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libctf-nobfd0 amd64 2.44-3 [156 kB] Fetched 156 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6eaa9muk/libctf-nobfd0_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB] Fetched 25.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd4h550zn/libpotrace0_1.16-2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libisl23 amd64 0.27-1 [659 kB] Fetched 659 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd_f_uu9g/libisl23_0.27-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw1bn2w3n/libexpat1_2.7.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 texlive-latex-base all 2024.20250309-1 [1294 kB] Fetched 1294 kB in 0s (97.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxns6gkts/texlive-latex-base_2024.20250309-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 texlive-fonts-recommended all 2024.20250309-1 [4989 kB] Fetched 4989 kB in 0s (208 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpry8rday5/texlive-fonts-recommended_2024.20250309-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-system1.83.0 amd64 1.83.0-4.2 [231 kB] Fetched 231 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp75y8m26o/libboost-system1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 dpkg amd64 1.22.18 [1545 kB] Fetched 1545 kB in 0s (129 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcv3es9ah/dpkg_1.22.18_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Fetched 75.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqc7ti2xa/libgraphite2-3_1.3.14-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-urllib3 all 2.3.0-2 [114 kB] Fetched 114 kB in 0s (10.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2msfs6ti/python3-urllib3_2.3.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcoordgen3 amd64 3.0.2-1+b2 [225 kB] Fetched 225 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplk5mi2xd/libcoordgen3_3.0.2-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 patch amd64 2.8-1 [134 kB] Fetched 134 kB in 0s (309 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwfesyu38/patch_2.8-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libglib2.0-dev-bin amd64 2.84.1-2 [53.0 kB] Fetched 53.0 kB in 1s (83.1 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp87a6f4od/libglib2.0-dev-bin_2.84.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpcre2-posix3 amd64 10.45-1 [63.5 kB] Fetched 63.5 kB in 0s (153 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp63jlq7hf/libpcre2-posix3_10.45-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpq5 amd64 17.4-2 [227 kB] Fetched 227 kB in 1s (392 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp73f9rch6/libpq5_17.4-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Fetched 81.7 kB in 1s (140 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb8b8iym0/libjsoncpp26_1.9.6-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-system1.83-dev amd64 1.83.0-4.2 [232 kB] Fetched 232 kB in 0s (1113 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5k93eslo/libboost-system1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Fetched 1041 kB in 0s (5996 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphxl_2jw0/libeigen3-dev_3.4.0-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libglib2.0-dev amd64 2.84.1-2 [53.7 kB] Fetched 53.7 kB in 0s (1990 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpukbnc2pn/libglib2.0-dev_2.84.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Fetched 37.3 kB in 0s (371 kB/s) dpkg-name: info: moved 'libsm6_2%3a1.2.6-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpdq63il59/libsm6_1.2.6-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 gcc-14 amd64 14.2.0-19 [540 kB] Fetched 540 kB in 0s (4529 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpktzpukum/gcc-14_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsframe1 amd64 2.44-3 [78.4 kB] Fetched 78.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsnc62kj0/libsframe1_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3.13-minimal amd64 3.13.3-2 [2212 kB] Fetched 2212 kB in 0s (38.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5tetdzna/python3.13-minimal_3.13.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 cmake-data all 3.31.6-2 [2268 kB] Fetched 2268 kB in 0s (49.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqv_3s36r/cmake-data_3.31.6-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxapian30 amd64 1.4.29-2 [1165 kB] Fetched 1165 kB in 0s (96.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplxcsqiot/libxapian30_1.4.29-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Fetched 212 kB in 0s (0 B/s) dpkg-name: info: moved 'libxaw7_2%3a1.0.16-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp5chgu6le/libxaw7_1.0.16-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgio-2.0-dev-bin amd64 2.84.1-2 [165 kB] Fetched 165 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp05fj86pp/libgio-2.0-dev-bin_2.84.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Fetched 49.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp221y7h1j/libthai0_0.1.29-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libc6 amd64 2.41-7 [2847 kB] Fetched 2847 kB in 0s (54.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfkxprd6p/libc6_2.41-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcairo-gobject2 amd64 1.18.4-1+b1 [130 kB] Fetched 130 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptauj6dih/libcairo-gobject2_1.18.4-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libasan8 amd64 14.2.0-19 [2725 kB] Fetched 2725 kB in 0s (144 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfm0uv2_r/libasan8_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Fetched 559 kB in 0s (50.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8qdun3fs/libdav1d7_1.5.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 ncurses-base all 6.5+20250216-2 [273 kB] Fetched 273 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1umqqwn9/ncurses-base_6.5+20250216-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Fetched 9476 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr7har7h0/libtext-charwidth-perl_0.04-11+b4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-6 [49.3 kB] Fetched 49.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi_mn2seb/libptexenc1_2024.20240313.70630+ds-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgcc-14-dev amd64 14.2.0-19 [2672 kB] Fetched 2672 kB in 0s (148 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxvlcyswn/libgcc-14-dev_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.4 [793 kB] Fetched 793 kB in 0s (70.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7h3no5rl/libxml2-dev_2.12.7+dfsg+really2.9.14-0.4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprytvt3fk/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libitm1 amd64 14.2.0-19 [26.0 kB] Fetched 26.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7th7vo8_/libitm1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 girepository-tools amd64 2.84.1-2 [148 kB] Fetched 148 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaw6ilssu/girepository-tools_2.84.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-chrono1.83-dev amd64 1.83.0-4.2 [246 kB] Fetched 246 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp76mgp6l2/libboost-chrono1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libglib2.0-0t64 amd64 2.84.1-2 [1514 kB] Fetched 1514 kB in 0s (115 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplwk_o91e/libglib2.0-0t64_2.84.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libssl-dev amd64 3.5.0-1 [2949 kB] Fetched 2949 kB in 0s (173 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpozom2uhr/libssl-dev_3.5.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-thread1.83-dev amd64 1.83.0-4.2 [277 kB] Fetched 277 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptpryycyl/libboost-thread1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-pandas all 2.2.3+dfsg-9 [3097 kB] Fetched 3097 kB in 0s (165 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpldexdg3f/python3-pandas_2.2.3+dfsg-9_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Fetched 211 kB in 0s (0 B/s) dpkg-name: info: moved 'libfontbox-java_1%3a1.8.16-5_all.deb' to '/srv/rebuilderd/tmp/tmp3ochk72j/libfontbox-java_1.8.16-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libinchi-dev amd64 1.07.3+dfsg-1 [19.6 kB] Fetched 19.6 kB in 0s (135 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1q87jztx/libinchi-dev_1.07.3+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libselinux1 amd64 3.8.1-1 [84.7 kB] Fetched 84.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp4yjf1bf/libselinux1_3.8.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libltdl7 amd64 2.5.4-4 [416 kB] Fetched 416 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphyu5tdob/libltdl7_2.5.4-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB] Fetched 73.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libice-dev_2%3a1.1.1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpptylb3fy/libice-dev_1.1.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libbinutils amd64 2.44-3 [534 kB] Fetched 534 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppm9fsgqh/libbinutils_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 postgresql-server-dev-17 amd64 17.4-2 [1319 kB] Fetched 1319 kB in 0s (103 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp011y5qe2/postgresql-server-dev-17_17.4-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Fetched 1185 kB in 0s (107 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmc713abi/groff-base_1.23.0-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 liblqr-1-0 amd64 0.4.2-2.1+b2 [29.5 kB] Fetched 29.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcks6u2v2/liblqr-1-0_0.4.2-2.1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Fetched 479 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnzghnrn3/libharfbuzz0b_10.2.0-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Fetched 168 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2em6q36k/libthai-data_0.1.29-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 debconf all 1.5.91 [121 kB] Fetched 121 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpte4ngfbg/debconf_1.5.91_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libtool all 2.5.4-4 [539 kB] Fetched 539 kB in 0s (51.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq0mc9vvk/libtool_2.5.4-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpython3-dev amd64 3.13.3-1 [10.4 kB] Fetched 10.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk778450u/libpython3-dev_3.13.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 llvm-19-runtime amd64 1:19.1.7-3 [551 kB] Fetched 551 kB in 0s (12.9 MB/s) dpkg-name: info: moved 'llvm-19-runtime_1%3a19.1.7-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpa115iri7/llvm-19-runtime_19.1.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB] Fetched 760 kB in 0s (69.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2nnokf72/shared-mime-info_2.4-5+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 openssl-provider-legacy amd64 3.5.0-1 [307 kB] Fetched 307 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8f0xmwmp/openssl-provider-legacy_3.5.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Fetched 57.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw9__mlv6/libsasl2-2_2.1.28+dfsg1-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Fetched 9456 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_tznask4/libkeyutils1_1.6.3-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Fetched 52.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeuugr56p/libyaml-0-2_0.2.5-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsepol-dev amd64 3.8.1-1 [373 kB] Fetched 373 kB in 0s (3207 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprh7ap591/libsepol-dev_3.8.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-dev amd64 3.13.3-1 [26.1 kB] Fetched 26.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpevxprlg5/python3-dev_3.13.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Fetched 116 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwqsnoleh/libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 diffutils amd64 1:3.10-4 [387 kB] Fetched 387 kB in 0s (0 B/s) dpkg-name: info: moved 'diffutils_1%3a3.10-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp305916yn/diffutils_3.10-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Fetched 11.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa5y5iyqu/hicolor-icon-theme_0.18-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Fetched 189 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpji7xjjbg/libelf1t64_0.192-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 ncurses-bin amd64 6.5+20250216-2 [438 kB] Fetched 438 kB in 0s (35.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6srsgca9/ncurses-bin_6.5+20250216-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libzstd1 amd64 1.5.7+dfsg-1 [304 kB] Fetched 304 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5oj0ypip/libzstd1_1.5.7+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 netbase all 6.5 [12.4 kB] Fetched 12.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp53ni1zqt/netbase_6.5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Fetched 75.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpemgsts7i/xdg-utils_1.2.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Fetched 115 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdr7ijk_m/libxcb-render0_1.17.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 readline-common all 8.2-6 [69.4 kB] Fetched 69.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4vi3sqzx/readline-common_8.2-6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-python1.83-dev amd64 1.83.0-4.2 [328 kB] Fetched 328 kB in 0s (31.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5egd3bm_/libboost-python1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxext-dev amd64 2:1.3.4-1+b3 [104 kB] Fetched 104 kB in 0s (0 B/s) dpkg-name: info: moved 'libxext-dev_2%3a1.3.4-1+b3_amd64.deb' to '/srv/rebuilderd/tmp/tmpcra_zzlh/libxext-dev_1.3.4-1+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-serialization1.83-dev amd64 1.83.0-4.2 [373 kB] Fetched 373 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiytzvbvy/libboost-serialization1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-regex1.83-dev amd64 1.83.0-4.2 [346 kB] Fetched 346 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6t1on36d/libboost-regex1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libglib2.0-data all 2.84.1-2 [1284 kB] Fetched 1284 kB in 0s (96.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg75id1t9/libglib2.0-data_2.84.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3 amd64 3.13.3-1 [28.2 kB] Fetched 28.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpngr0mj7f/python3_3.13.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB] Fetched 140 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp76kos08i/libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 findutils amd64 4.10.0-3 [700 kB] Fetched 700 kB in 0s (58.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyzetuvvw/findutils_4.10.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libmaeparser-dev amd64 1.3.1-1+b2 [13.7 kB] Fetched 13.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfj5ifytv/libmaeparser-dev_1.3.1-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-babel all 2.17.0-1 [117 kB] Fetched 117 kB in 0s (1320 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp20ozj4fm/python3-babel_2.17.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-idna all 3.10-1 [42.0 kB] Fetched 42.0 kB in 0s (1638 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzgsuazy7/python3-idna_3.10-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxxhash0 amd64 0.8.3-2 [27.1 kB] Fetched 27.1 kB in 0s (346 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph1cx4u9p/libxxhash0_0.8.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Fetched 13.9 kB in 0s (216 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1x1qpasm/libraqm0_0.10.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-requests all 2.32.3+dfsg-5 [72.2 kB] Fetched 72.2 kB in 0s (617 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqplpwm73/python3-requests_2.32.3+dfsg-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsysprof-capture-4-dev amd64 48.0-2 [49.9 kB] Fetched 49.9 kB in 0s (471 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgenoc27_/libsysprof-capture-4-dev_48.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libtsan2 amd64 14.2.0-19 [2460 kB] Fetched 2460 kB in 0s (18.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp68ucmd7k/libtsan2_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libclang1-19 amd64 1:19.1.7-3 [7638 kB] Fetched 7638 kB in 0s (48.5 MB/s) dpkg-name: info: moved 'libclang1-19_1%3a19.1.7-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpbamad81i/libclang1-19_19.1.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-pytz all 2025.2-2 [151 kB] Fetched 151 kB in 0s (2227 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6m8gm3vf/python3-pytz_2025.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-3 [560 kB] Fetched 560 kB in 0s (0 B/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpobfsjo6b/libgmp10_6.3.0+dfsg-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libraw23t64 amd64 0.21.4-2 [390 kB] Fetched 390 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9pexzbaj/libraw23t64_0.21.4-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB] Fetched 392 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvxvjumq7/libfontconfig1_2.15.0-2.3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Fetched 139 kB in 0s (0 B/s) dpkg-name: info: moved 'python3-numpy-dev_1%3a2.2.4+ds-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpzcj1d_hk/python3-numpy-dev_2.2.4+ds-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Fetched 87.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpshi_1wyv/libjson-perl_4.10000-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libfreetype-dev amd64 2.13.3+dfsg-1 [622 kB] Fetched 622 kB in 0s (61.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz_x8bt8a/libfreetype-dev_2.13.3+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.2 [347 kB] Fetched 347 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpduwqtvxa/libboost-program-options1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 llvm-19-tools amd64 1:19.1.7-3 [511 kB] Fetched 511 kB in 0s (2846 kB/s) dpkg-name: info: moved 'llvm-19-tools_1%3a19.1.7-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpu5to26a_/llvm-19-tools_19.1.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Fetched 188 kB in 0s (0 B/s) dpkg-name: info: moved 'libxt6t64_1%3a1.2.1-1.2+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmp5m3gcldy/libxt6t64_1.2.1-1.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libexpat1-dev amd64 2.7.1-1 [161 kB] Fetched 161 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp196nefuv/libexpat1-dev_2.7.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpam-modules amd64 1.7.0-3 [177 kB] Fetched 177 kB in 0s (1250 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg2b17voy/libpam-modules_1.7.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 postgresql-common all 277 [112 kB] Fetched 112 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpel25q7tq/postgresql-common_277_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Fetched 47.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpktz9ao49/libdeflate0_1.23-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 media-types all 13.0.0 [29.3 kB] Fetched 29.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_aobnbbg/media-types_13.0.0_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Fetched 183 kB in 0s (8881 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfgg01qbe/liblerc4_4.0.0+ds-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Fetched 343 kB in 0s (0 B/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.12-1_all.deb' to '/srv/rebuilderd/tmp/tmp26r8b4t4/libx11-data_1.8.12-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 grep amd64 3.11-4 [431 kB] Fetched 431 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr2x6omyp/grep_3.11-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libbsd0 amd64 0.12.2-2 [131 kB] Fetched 131 kB in 0s (2070 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc5slt891/libbsd0_0.12.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libfontconfig-dev amd64 2.15.0-2.3 [414 kB] Fetched 414 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpssh5zo7m/libfontconfig-dev_2.15.0-2.3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 file amd64 1:5.46-5 [43.6 kB] Fetched 43.6 kB in 0s (0 B/s) dpkg-name: info: moved 'file_1%3a5.46-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp7h0dacnc/file_5.46-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Fetched 27.8 kB in 0s (56.5 kB/s) dpkg-name: info: moved 'libxdmcp6_1%3a1.1.5-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpz0buaeey/libxdmcp6_1.1.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Fetched 577 kB in 0s (0 B/s) dpkg-name: info: moved 'xfonts-encodings_1%3a1.0.4-2.2_all.deb' to '/srv/rebuilderd/tmp/tmptawlsil0/xfonts-encodings_1.0.4-2.2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Fetched 154 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3j7totw1/libuv1t64_1.50.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libheif-plugin-dav1d amd64 1.19.8-1 [11.7 kB] Fetched 11.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwp90gyx0/libheif-plugin-dav1d_1.19.8-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Fetched 168 kB in 0s (0 B/s) dpkg-name: info: moved 'libjpeg62-turbo_1%3a2.1.5-3.1_amd64.deb' to '/srv/rebuilderd/tmp/tmp2hgunxz5/libjpeg62-turbo_2.1.5-3.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Fetched 44.3 kB in 0s (0 B/s) dpkg-name: info: moved 'libxdmcp-dev_1%3a1.1.5-1_amd64.deb' to '/srv/rebuilderd/tmp/tmprb_woaix/libxdmcp-dev_1.1.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Fetched 76.0 kB in 0s (2074 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiq87f_rp/libnghttp2-14_1.64.0-1.1_amd64.deb' Downloading dependency 131 of 495: openssl:amd64=3.5.0-1 Downloading dependency 132 of 495: icu-devtools:amd64=76.1-3 Downloading dependency 133 of 495: m4:amd64=1.4.19-8 Downloading dependency 134 of 495: libxi6:amd64=2:1.8.2-1 Downloading dependency 135 of 495: libctf-nobfd0:amd64=2.44-3 Downloading dependency 136 of 495: libpotrace0:amd64=1.16-2+b2 Downloading dependency 137 of 495: libisl23:amd64=0.27-1 Downloading dependency 138 of 495: libexpat1:amd64=2.7.1-1 Downloading dependency 139 of 495: texlive-latex-base:amd64=2024.20250309-1 Downloading dependency 140 of 495: texlive-fonts-recommended:amd64=2024.20250309-1 Downloading dependency 141 of 495: libboost-system1.83.0:amd64=1.83.0-4.2 Downloading dependency 142 of 495: dpkg:amd64=1.22.18 Downloading dependency 143 of 495: libgraphite2-3:amd64=1.3.14-2+b1 Downloading dependency 144 of 495: python3-urllib3:amd64=2.3.0-2 Downloading dependency 145 of 495: libcoordgen3:amd64=3.0.2-1+b2 Downloading dependency 146 of 495: patch:amd64=2.8-1 Downloading dependency 147 of 495: libglib2.0-dev-bin:amd64=2.84.1-2 Downloading dependency 148 of 495: libpcre2-posix3:amd64=10.45-1 Downloading dependency 149 of 495: libpq5:amd64=17.4-2 Downloading dependency 150 of 495: libjsoncpp26:amd64=1.9.6-3 Downloading dependency 151 of 495: libboost-system1.83-dev:amd64=1.83.0-4.2 Downloading dependency 152 of 495: libeigen3-dev:amd64=3.4.0-4 Downloading dependency 153 of 495: libglib2.0-dev:amd64=2.84.1-2 Downloading dependency 154 of 495: libsm6:amd64=2:1.2.6-1 Downloading dependency 155 of 495: gcc-14:amd64=14.2.0-19 Downloading dependency 156 of 495: libsframe1:amd64=2.44-3 Downloading dependency 157 of 495: python3.13-minimal:amd64=3.13.3-2 Downloading dependency 158 of 495: cmake-data:amd64=3.31.6-2 Downloading dependency 159 of 495: libxapian30:amd64=1.4.29-2 Downloading dependency 160 of 495: libxaw7:amd64=2:1.0.16-1 Downloading dependency 161 of 495: libgio-2.0-dev-bin:amd64=2.84.1-2 Downloading dependency 162 of 495: libthai0:amd64=0.1.29-2+b1 Downloading dependency 163 of 495: libc6:amd64=2.41-7 Downloading dependency 164 of 495: libcairo-gobject2:amd64=1.18.4-1+b1 Downloading dependency 165 of 495: libasan8:amd64=14.2.0-19 Downloading dependency 166 of 495: libdav1d7:amd64=1.5.1-1 Downloading dependency 167 of 495: ncurses-base:amd64=6.5+20250216-2 Downloading dependency 168 of 495: libtext-charwidth-perl:amd64=0.04-11+b4 Downloading dependency 169 of 495: libptexenc1:amd64=2024.20240313.70630+ds-6 Downloading dependency 170 of 495: libgcc-14-dev:amd64=14.2.0-19 Downloading dependency 171 of 495: libxml2-dev:amd64=2.12.7+dfsg+really2.9.14-0.4 Downloading dependency 172 of 495: libarchive-zip-perl:amd64=1.68-1 Downloading dependency 173 of 495: libitm1:amd64=14.2.0-19 Downloading dependency 174 of 495: girepository-tools:amd64=2.84.1-2 Downloading dependency 175 of 495: libboost-chrono1.83-dev:amd64=1.83.0-4.2 Downloading dependency 176 of 495: libglib2.0-0t64:amd64=2.84.1-2 Downloading dependency 177 of 495: libssl-dev:amd64=3.5.0-1 Downloading dependency 178 of 495: libboost-thread1.83-dev:amd64=1.83.0-4.2 Downloading dependency 179 of 495: python3-pandas:amd64=2.2.3+dfsg-9 Downloading dependency 180 of 495: libfontbox-java:amd64=1:1.8.16-5 Downloading dependency 181 of 495: libinchi-dev:amd64=1.07.3+dfsg-1 Downloading dependency 182 of 495: libselinux1:amd64=3.8.1-1 Downloading dependency 183 of 495: libltdl7:amd64=2.5.4-4 Downloading dependency 184 of 495: libice-dev:amd64=2:1.1.1-1 Downloading dependency 185 of 495: libbinutils:amd64=2.44-3 Downloading dependency 186 of 495: postgresql-server-dev-17:amd64=17.4-2 Downloading dependency 187 of 495: groff-base:amd64=1.23.0-7 Downloading dependency 188 of 495: liblqr-1-0:amd64=0.4.2-2.1+b2 Downloading dependency 189 of 495: libharfbuzz0b:amd64=10.2.0-1+b1 Downloading dependency 190 of 495: libthai-data:amd64=0.1.29-2 Downloading dependency 191 of 495: debconf:amd64=1.5.91 Downloading dependency 192 of 495: libtool:amd64=2.5.4-4 Downloading dependency 193 of 495: libpython3-dev:amd64=3.13.3-1 Downloading dependency 194 of 495: llvm-19-runtime:amd64=1:19.1.7-3 Downloading dependency 195 of 495: shared-mime-info:amd64=2.4-5+b2 Downloading dependency 196 of 495: openssl-provider-legacy:amd64=3.5.0-1 Downloading dependency 197 of 495: libsasl2-2:amd64=2.1.28+dfsg1-9 Downloading dependency 198 of 495: libkeyutils1:amd64=1.6.3-6 Downloading dependency 199 of 495: libyaml-0-2:amd64=0.2.5-2 Downloading dependency 200 of 495: libsepol-dev:amd64=3.8.1-1 Downloading dependency 201 of 495: python3-dev:amd64=3.13.3-1 Downloading dependency 202 of 495: libjs-underscore:amd64=1.13.4~dfsg+~1.11.4-3 Downloading dependency 203 of 495: diffutils:amd64=1:3.10-4 Downloading dependency 204 of 495: hicolor-icon-theme:amd64=0.18-2 Downloading dependency 205 of 495: libelf1t64:amd64=0.192-4 Downloading dependency 206 of 495: ncurses-bin:amd64=6.5+20250216-2 Downloading dependency 207 of 495: libzstd1:amd64=1.5.7+dfsg-1 Downloading dependency 208 of 495: netbase:amd64=6.5 Downloading dependency 209 of 495: xdg-utils:amd64=1.2.1-2 Downloading dependency 210 of 495: libxcb-render0:amd64=1.17.0-2+b1 Downloading dependency 211 of 495: readline-common:amd64=8.2-6 Downloading dependency 212 of 495: 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dependency 227 of 495: libtsan2:amd64=14.2.0-19 Downloading dependency 228 of 495: libclang1-19:amd64=1:19.1.7-3 Downloading dependency 229 of 495: python3-pytz:amd64=2025.2-2 Downloading dependency 230 of 495: libgmp10:amd64=2:6.3.0+dfsg-3 Downloading dependency 231 of 495: libraw23t64:amd64=0.21.4-2 Downloading dependency 232 of 495: libfontconfig1:amd64=2.15.0-2.3 Downloading dependency 233 of 495: python3-numpy-dev:amd64=1:2.2.4+ds-1 Downloading dependency 234 of 495: libjson-perl:amd64=4.10000-1 Downloading dependency 235 of 495: libfreetype-dev:amd64=2.13.3+dfsg-1 Downloading dependency 236 of 495: libboost-program-options1.83.0:amd64=1.83.0-4.2 Downloading dependency 237 of 495: llvm-19-tools:amd64=1:19.1.7-3 Downloading dependency 238 of 495: libxt6t64:amd64=1:1.2.1-1.2+b2 Downloading dependency 239 of 495: libexpat1-dev:amd64=2.7.1-1 Downloading dependency 240 of 495: libpam-modules:amd64=1.7.0-3 Downloading dependency 241 of 495: postgresql-common:amd64=277 Downloading dependency 242 of 495: libdeflate0:amd64=1.23-2 Downloading dependency 243 of 495: media-types:amd64=13.0.0 Downloading dependency 244 of 495: liblerc4:amd64=4.0.0+ds-5 Downloading dependency 245 of 495: libx11-data:amd64=2:1.8.12-1 Downloading dependency 246 of 495: grep:amd64=3.11-4 Downloading dependency 247 of 495: libbsd0:amd64=0.12.2-2 Downloading dependency 248 of 495: libfontconfig-dev:amd64=2.15.0-2.3 Downloading dependency 249 of 495: file:amd64=1:5.46-5 Downloading dependency 250 of 495: libxdmcp6:amd64=1:1.1.5-1 Downloading dependency 251 of 495: xfonts-encodings:amd64=1:1.0.4-2.2 Downloading dependency 252 of 495: libuv1t64:amd64=1.50.0-2 Downloading dependency 253 of 495: libheif-plugin-dav1d:amd64=1.19.8-1 Downloading dependency 254 of 495: libjpeg62-turbo:amd64=1:2.1.5-3.1 Downloading dependency 255 of 495: libxdmcp-dev:amd64=1:1.1.5-1 Downloading dependency 256 of 495: libnghttp2-14:amd64=1.64.0-1.1 Downloading dependency 257 of 495: libsqlite3-dev:amd64=3.46.1-3Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsqlite3-dev amd64 3.46.1-3 [1107 kB] Fetched 1107 kB in 0s (86.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx2pniyo1/libsqlite3-dev_3.46.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 doxygen amd64 1.9.8+ds-2.1 [5017 kB] Fetched 5017 kB in 0s (197 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuo7auyzk/doxygen_1.9.8+ds-2.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 login.defs all 1:4.17.4-2 [186 kB] Fetched 186 kB in 0s (0 B/s) dpkg-name: info: moved 'login.defs_1%3a4.17.4-2_all.deb' to '/srv/rebuilderd/tmp/tmpw1n3bpth/login.defs_4.17.4-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libapache-pom-java all 33-2 [5852 B] Fetched 5852 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7oqow46d/libapache-pom-java_33-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpython3.13 amd64 3.13.3-2 [2156 kB] Fetched 2156 kB in 0s (137 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwku537lj/libpython3.13_3.13.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libproc2-0 amd64 2:4.0.4-8 [65.4 kB] Fetched 65.4 kB in 0s (0 B/s) dpkg-name: info: moved 'libproc2-0_2%3a4.0.4-8_amd64.deb' to '/srv/rebuilderd/tmp/tmp5omfykmc/libproc2-0_4.0.4-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 texlive-latex-recommended all 2024.20250309-1 [8745 kB] Fetched 8745 kB in 0s (247 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk3wjwzar/texlive-latex-recommended_2024.20250309-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 man-db amd64 2.13.0-1 [1420 kB] Fetched 1420 kB in 0s (118 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxx2oco89/man-db_2.13.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Fetched 326 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp412w9zpb/libkrb5-3_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B] Fetched 3736 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk1i6goe_/libboost-system-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 flex amd64 2.6.4-8.2+b4 [423 kB] Fetched 423 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8g6wcxk3/flex_2.6.4-8.2+b4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpfm4 amd64 4.13.0+git99-gc5587f9-1 [371 kB] Fetched 371 kB in 0s (10.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoze4znwu/libpfm4_4.13.0+git99-gc5587f9-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 postgresql-client-17 amd64 17.4-2 [2037 kB] Fetched 2037 kB in 0s (141 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbxp5g8z2/postgresql-client-17_17.4-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-19 [21.4 MB] Fetched 21.4 MB in 0s (67.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvdnqscgc/gcc-14-x86-64-linux-gnu_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3 [1014 kB] Fetched 1014 kB in 0s (81.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphb4462bm/binutils-x86-64-linux-gnu_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Fetched 26.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_hwjvnef/pkgconf_1.8.1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3.13-dev amd64 3.13.3-2 [508 kB] Fetched 508 kB in 0s (48.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd1ka01yn/python3.13-dev_3.13.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Fetched 836 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4ddlqj97/libgfortran5_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 postgresql-server-dev-all all 277 [13.9 kB] Fetched 13.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5gezbs_s/postgresql-server-dev-all_277_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 base-passwd amd64 3.6.7 [53.7 kB] Fetched 53.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr35hmnbu/base-passwd_3.6.7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1 [1200 B] Fetched 1200 B in 0s (0 B/s) dpkg-name: info: moved 'g++-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp88rs6bz8/g++-x86-64-linux-gnu_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Fetched 26.4 MB in 0s (152 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp59owitbf/pandoc_3.1.11.1+ds-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Fetched 9308 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppnkgsvah/libatomic1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Fetched 248 kB in 0s (14.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkxl8r4hd/libpixman-1-0_0.44.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 dwz amd64 0.15-1+b1 [110 kB] Fetched 110 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxgjn3nah/dwz_0.15-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Fetched 3580 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppz_vlbk4/libboost-iostreams-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Fetched 2452 kB in 0s (162 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2kzw0901/liblapack3_3.12.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b1 [88.9 kB] Fetched 88.9 kB in 0s (0 B/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpy81gm11c/zlib1g_1.3.dfsg+really1.3.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 librsvg2-bin amd64 2.60.0+dfsg-1 [1967 kB] Fetched 1967 kB in 0s (137 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuo1wk39s/librsvg2-bin_2.60.0+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpython3-stdlib amd64 3.13.3-1 [10.2 kB] Fetched 10.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk1r0mm3c/libpython3-stdlib_3.13.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Fetched 840 kB in 0s (80.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb2d690d_/fonts-dejavu-core_2.37-8_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1 [1436 B] Fetched 1436 B in 0s (0 B/s) dpkg-name: info: moved 'gcc-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpicstiz41/gcc-x86-64-linux-gnu_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Fetched 10.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4vv_1oj4/libcommons-parent-java_56-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Fetched 3612 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1pt9hps3/libboost-program-options-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpam-runtime all 1.7.0-3 [248 kB] Fetched 248 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7o8weyma/libpam-runtime_1.7.0-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Fetched 243 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpffur9pij/gettext-base_0.23.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Fetched 50.4 kB in 0s (0 B/s) dpkg-name: info: moved 'libxext6_2%3a1.3.4-1+b3_amd64.deb' to '/srv/rebuilderd/tmp/tmpr_5of91o/libxext6_1.3.4-1+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 llvm-19 amd64 1:19.1.7-3 [16.4 MB] Fetched 16.4 MB in 0s (66.5 MB/s) dpkg-name: info: moved 'llvm-19_1%3a19.1.7-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpryw5yl9o/llvm-19_19.1.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libperl5.40 amd64 5.40.1-3 [4320 kB] Fetched 4320 kB in 0s (190 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpse80zpqb/libperl5.40_5.40.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-regex-dev amd64 1.83.0.2+b2 [3864 B] Fetched 3864 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkbmgkffs/libboost-regex-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 liblzma5 amd64 5.8.1-1 [309 kB] Fetched 309 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb389ypqy/liblzma5_5.8.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 xz-utils amd64 5.8.1-1 [660 kB] Fetched 660 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp1mlcmo9/xz-utils_5.8.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 tar amd64 1.35+dfsg-3.1 [815 kB] Fetched 815 kB in 0s (65.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbtezhp6x/tar_1.35+dfsg-3.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libbz2-1.0 amd64 1.0.8-6 [37.9 kB] Fetched 37.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj74ie185/libbz2-1.0_1.0.8-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpam0g amd64 1.7.0-3 [69.7 kB] Fetched 69.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjhrqyp6q/libpam0g_1.7.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 perl-modules-5.40 all 5.40.1-3 [3021 kB] Fetched 3021 kB in 0s (173 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgjf2bmd1/perl-modules-5.40_5.40.1-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Fetched 160 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv2_77gvc/liblcms2-2_2.16-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 texlive-base all 2024.20250309-1 [23.1 MB] Fetched 23.1 MB in 0s (279 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_vg96z1c/texlive-base_2024.20250309-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-recommonmark all 0.7.1+ds-8 [17.6 kB] Fetched 17.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9u2sp805/python3-recommonmark_0.7.1+ds-8_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 dh-python all 6.20250414 [116 kB] Fetched 116 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6v9zbx9n/dh-python_6.20250414_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] Fetched 353 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpixvgiyvb/libncurses-dev_6.5+20250216-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Fetched 27.9 kB in 0s (0 B/s) dpkg-name: info: moved 'libxrender1_1%3a0.9.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmptuz_0ltm/libxrender1_0.9.12-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libquadmath0 amd64 14.2.0-19 [145 kB] Fetched 145 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpws2qm0ja/libquadmath0_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Fetched 137 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplsqugt00/libgomp1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 debhelper all 13.24.2 [919 kB] Fetched 919 kB in 0s (85.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg838rzpv/debhelper_13.24.2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Fetched 3892 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm3l_rkzz/libboost-python-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-myst-parser all 4.0.1-1 [78.8 kB] Fetched 78.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi392u9wd/python3-myst-parser_4.0.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libarchive13t64 amd64 3.7.4-3 [349 kB] Fetched 349 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplccv0zwa/libarchive13t64_3.7.4-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpq-dev amd64 17.4-2 [149 kB] Fetched 149 kB in 0s (5744 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8btywlmr/libpq-dev_17.4-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Fetched 1464 kB in 0s (113 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjy4sdjln/libgnutls30t64_3.8.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libattr1 amd64 1:2.5.2-3 [22.9 kB] Fetched 22.9 kB in 0s (0 B/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpsio1dryb/libattr1_2.5.2-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Fetched 57.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfc5edwys/libpsl5t64_0.21.2-1.1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libc-dev-bin amd64 2.41-7 [57.3 kB] Fetched 57.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpffla4qgi/libc-dev-bin_2.41-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libz3-dev amd64 4.13.3-1 [107 kB] Fetched 107 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuvwxdw2o/libz3-dev_4.13.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-yaml amd64 6.0.2-1+b2 [136 kB] Fetched 136 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp99o3qxjh/python3-yaml_6.0.2-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Fetched 113 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo814wb4d/libwebpdemux2_1.5.0-0.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libmaeparser1 amd64 1.3.1-1+b2 [94.0 kB] Fetched 94.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph3ngqrsn/libmaeparser1_1.3.1-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 dh-autoreconf all 20 [17.1 kB] Fetched 17.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcwpf6k6n/dh-autoreconf_20_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpam-modules-bin amd64 1.7.0-3 [48.9 kB] Fetched 48.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcr1rg9dz/libpam-modules-bin_1.7.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 bash amd64 5.2.37-2 [1500 kB] Fetched 1500 kB in 0s (112 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo2n15jcw/bash_5.2.37-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcap2 amd64 1:2.75-7 [28.1 kB] Fetched 28.1 kB in 0s (0 B/s) dpkg-name: info: moved 'libcap2_1%3a2.75-7_amd64.deb' to '/srv/rebuilderd/tmp/tmpoxajmc03/libcap2_2.75-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 llvm-19-dev amd64 1:19.1.7-3 [43.1 MB] Fetched 43.1 MB in 0s (286 MB/s) dpkg-name: info: moved 'llvm-19-dev_1%3a19.1.7-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpfiefi62o/llvm-19-dev_19.1.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 bzip2 amd64 1.0.8-6 [40.5 kB] Fetched 40.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfi4hzo9l/bzip2_1.0.8-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.4 [98.1 kB] Fetched 98.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2cjsts3h/rapidjson-dev_1.1.0+dfsg2-7.4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Fetched 160 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpremosfy0/libblas3_3.12.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcairo2-dev amd64 1.18.4-1+b1 [43.4 kB] Fetched 43.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx2x8tkar/libcairo2-dev_1.18.4-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcairo-script-interpreter2 amd64 1.18.4-1+b1 [59.3 kB] Fetched 59.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxkb2pkq0/libcairo-script-interpreter2_1.18.4-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 920 kB in 0s (84.7 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmptaq4ssy2/zlib1g-dev_1.3.dfsg+really1.3.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libacl1 amd64 2.3.2-2+b1 [32.9 kB] Fetched 32.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqthb3h3j/libacl1_2.3.2-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Fetched 169 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbih5a9m6/libreadline8t64_8.2-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] Fetched 35.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3fojo3lc/libmpfi0_1.5.4+ds-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Fetched 116 kB in 0s (1039 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_h889mqc/libsharpyuv0_1.5.0-0.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Fetched 27.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwfgm1h82/python3-alabaster_0.7.16-0.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcatch2-dev amd64 3.7.1-0.5 [613 kB] Fetched 613 kB in 0s (59.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjtzdh667/libcatch2-dev_3.7.1-0.5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsemanage2 amd64 3.8.1-1 [95.3 kB] Fetched 95.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnc7b_9oy/libsemanage2_3.8.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libclang-cpp19 amd64 1:19.1.7-3 [13.2 MB] Fetched 13.2 MB in 0s (236 MB/s) dpkg-name: info: moved 'libclang-cpp19_1%3a19.1.7-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpv9c37068/libclang-cpp19_19.1.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcrypt-dev amd64 1:4.4.38-1 [119 kB] Fetched 119 kB in 0s (0 B/s) dpkg-name: info: moved 'libcrypt-dev_1%3a4.4.38-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpxi7ql87s/libcrypt-dev_4.4.38-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-numpy1.83.0 amd64 1.83.0-4.2 [242 kB] Fetched 242 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzs62thgt/libboost-numpy1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Fetched 5096 kB in 0s (204 MB/s) dpkg-name: info: moved 'python3-numpy_1%3a2.2.4+ds-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpfo2_bt_k/python3-numpy_2.2.4+ds-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Fetched 79.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp76wa1pue/python3-dateutil_2.9.0-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Fetched 26.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjn7_wgur/python3-pluggy_1.5.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 gcc-14-base amd64 14.2.0-19 [49.4 kB] Fetched 49.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpofz8y9u1/gcc-14-base_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpython3.13-stdlib amd64 3.13.3-2 [1953 kB] Fetched 1953 kB in 1s (2865 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjnvjvcah/libpython3.13-stdlib_3.13.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpython3.13-dev amd64 3.13.3-2 [5015 kB] Fetched 5015 kB in 1s (9611 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw6tyxbzr/libpython3.13-dev_3.13.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 coreutils amd64 9.7-2 [3024 kB] Fetched 3024 kB in 0s (8432 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcodt1cx6/coreutils_9.7-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Fetched 58.0 kB in 0s (360 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkl79tihi/python3-snowballstemmer_2.2.0-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Fetched 132 kB in 0s (1061 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpko8snmlh/librhash1_1.4.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-greenlet amd64 3.1.0-1+b2 [165 kB] Fetched 165 kB in 0s (890 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9mvcbtka/python3-greenlet_3.1.0-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-4.2 [240 kB] Fetched 240 kB in 0s (643 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsqwncbau/libboost-chrono1.83.0t64_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 autoconf all 2.72-3.1 [494 kB] Fetched 494 kB in 1s (933 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphudlm8cm/autoconf_2.72-3.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libglib2.0-bin amd64 2.84.1-2 [129 kB] Fetched 129 kB in 0s (321 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptlpsrqqg/libglib2.0-bin_2.84.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 liblua5.4-0 amd64 5.4.7-1+b2 [147 kB] Fetched 147 kB in 0s (387 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdotfr6vm/liblua5.4-0_5.4.7-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 perl-base amd64 5.40.1-3 [1665 kB] Fetched 1665 kB in 1s (2936 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkezv3441/perl-base_5.40.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Fetched 19.8 kB in 0s (41.5 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0w79959o/libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1 [4840 B] Fetched 4840 B in 0s (10.3 kB/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp_nvzy7wt/cpp-x86-64-linux-gnu_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Fetched 49.9 kB in 0s (152 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpicvhxoht/libtasn1-6_4.20.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 liblz4-1 amd64 1.10.0-4 [63.9 kB] Fetched 63.9 kB in 0s (292 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9dss7est/liblz4-1_1.10.0-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Fetched 14.0 kB in 0s (28.5 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6co6fyom/python3-markupsafe_2.1.5-1+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Fetched 326 kB in 1s (596 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp43x77nyk/libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Fetched 68.9 kB in 1s (112 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5g1jbjp9/libuchardet0_0.0.8-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsqlite3-0 amd64 3.46.1-3 [913 kB] Fetched 913 kB in 0s (4062 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu7h7046j/libsqlite3-0_3.46.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [35.7 kB] Fetched 35.7 kB in 0s (107 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph72x5__q/libpangocairo-1.0-0_1.56.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxcb-shm0-dev amd64 1.17.0-2+b1 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0figcz57/libxcb-shm0-dev_1.17.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libaudit1 amd64 1:4.0.2-2+b2 [55.1 kB] Fetched 55.1 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit1_1%3a4.0.2-2+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpdwc35_re/libaudit1_4.0.2-2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 gzip amd64 1.13-1 [138 kB] Fetched 138 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnpbohpep/gzip_1.13-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgprofng0 amd64 2.44-3 [808 kB] Fetched 808 kB in 0s (74.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj18w00vo/libgprofng0_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Fetched 22.1 kB in 0s (0 B/s) dpkg-name: info: moved 'xorg-sgml-doctools_1%3a1.11-1.1_all.deb' to '/srv/rebuilderd/tmp/tmpeaszgrtk/xorg-sgml-doctools_1.11-1.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 binutils amd64 2.44-3 [265 kB] Fetched 265 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpebl55w1u/binutils_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Fetched 316 kB in 0s (27.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplg1ykd9o/libbrotli-dev_1.1.0-2+b7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Fetched 43.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp87dhsdva/python3-defusedxml_0.7.1-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Fetched 403 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5nlukgu3/python3-docutils_0.21.2+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libblkid-dev amd64 2.41-4 [208 kB] Fetched 208 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprn6h4met/libblkid-dev_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libstdc++-14-dev amd64 14.2.0-19 [2376 kB] Fetched 2376 kB in 0s (155 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd5kuv8r7/libstdc++-14-dev_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB] Fetched 10.6 MB in 0s (236 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3z0bvi2o/libboost1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.1 [59.0 kB] Fetched 59.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2ne0c7th/libzzip-0-13t64_0.13.78+dfsg.1-0.1_amd64.deb' Downloading dependency 258 of 495: doxygen:amd64=1.9.8+ds-2.1 Downloading dependency 259 of 495: login.defs:amd64=1:4.17.4-2 Downloading dependency 260 of 495: libapache-pom-java:amd64=33-2 Downloading dependency 261 of 495: libpython3.13:amd64=3.13.3-2 Downloading dependency 262 of 495: libproc2-0:amd64=2:4.0.4-8 Downloading dependency 263 of 495: texlive-latex-recommended:amd64=2024.20250309-1 Downloading dependency 264 of 495: man-db:amd64=2.13.0-1 Downloading dependency 265 of 495: libkrb5-3:amd64=1.21.3-5 Downloading dependency 266 of 495: libboost-system-dev:amd64=1.83.0.2+b2 Downloading dependency 267 of 495: flex:amd64=2.6.4-8.2+b4 Downloading dependency 268 of 495: libpfm4:amd64=4.13.0+git99-gc5587f9-1 Downloading dependency 269 of 495: postgresql-client-17:amd64=17.4-2 Downloading dependency 270 of 495: gcc-14-x86-64-linux-gnu:amd64=14.2.0-19 Downloading dependency 271 of 495: 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dependency 317 of 495: libattr1:amd64=1:2.5.2-3 Downloading dependency 318 of 495: libpsl5t64:amd64=0.21.2-1.1+b1 Downloading dependency 319 of 495: libc-dev-bin:amd64=2.41-7 Downloading dependency 320 of 495: libz3-dev:amd64=4.13.3-1 Downloading dependency 321 of 495: python3-yaml:amd64=6.0.2-1+b2 Downloading dependency 322 of 495: libwebpdemux2:amd64=1.5.0-0.1 Downloading dependency 323 of 495: libmaeparser1:amd64=1.3.1-1+b2 Downloading dependency 324 of 495: dh-autoreconf:amd64=20 Downloading dependency 325 of 495: libpam-modules-bin:amd64=1.7.0-3 Downloading dependency 326 of 495: bash:amd64=5.2.37-2 Downloading dependency 327 of 495: libcap2:amd64=1:2.75-7 Downloading dependency 328 of 495: llvm-19-dev:amd64=1:19.1.7-3 Downloading dependency 329 of 495: bzip2:amd64=1.0.8-6 Downloading dependency 330 of 495: rapidjson-dev:amd64=1.1.0+dfsg2-7.4 Downloading dependency 331 of 495: libblas3:amd64=3.12.1-2 Downloading dependency 332 of 495: libcairo2-dev:amd64=1.18.4-1+b1 Downloading dependency 333 of 495: libcairo-script-interpreter2:amd64=1.18.4-1+b1 Downloading dependency 334 of 495: zlib1g-dev:amd64=1:1.3.dfsg+really1.3.1-1+b1 Downloading dependency 335 of 495: libacl1:amd64=2.3.2-2+b1 Downloading dependency 336 of 495: libreadline8t64:amd64=8.2-6 Downloading dependency 337 of 495: libmpfi0:amd64=1.5.4+ds-4 Downloading dependency 338 of 495: libsharpyuv0:amd64=1.5.0-0.1 Downloading dependency 339 of 495: python3-alabaster:amd64=0.7.16-0.1 Downloading dependency 340 of 495: libcatch2-dev:amd64=3.7.1-0.5 Downloading dependency 341 of 495: libsemanage2:amd64=3.8.1-1 Downloading dependency 342 of 495: libclang-cpp19:amd64=1:19.1.7-3 Downloading dependency 343 of 495: libcrypt-dev:amd64=1:4.4.38-1 Downloading dependency 344 of 495: libboost-numpy1.83.0:amd64=1.83.0-4.2 Downloading dependency 345 of 495: python3-numpy:amd64=1:2.2.4+ds-1 Downloading dependency 346 of 495: python3-dateutil:amd64=2.9.0-4 Downloading dependency 347 of 495: python3-pluggy:amd64=1.5.0-1 Downloading dependency 348 of 495: gcc-14-base:amd64=14.2.0-19 Downloading dependency 349 of 495: libpython3.13-stdlib:amd64=3.13.3-2 Downloading dependency 350 of 495: libpython3.13-dev:amd64=3.13.3-2 Downloading dependency 351 of 495: coreutils:amd64=9.7-2 Downloading dependency 352 of 495: python3-snowballstemmer:amd64=2.2.0-4 Downloading dependency 353 of 495: librhash1:amd64=1.4.5-1 Downloading dependency 354 of 495: python3-greenlet:amd64=3.1.0-1+b2 Downloading dependency 355 of 495: libboost-chrono1.83.0t64:amd64=1.83.0-4.2 Downloading dependency 356 of 495: autoconf:amd64=2.72-3.1 Downloading dependency 357 of 495: libglib2.0-bin:amd64=2.84.1-2 Downloading dependency 358 of 495: liblua5.4-0:amd64=5.4.7-1+b2 Downloading dependency 359 of 495: perl-base:amd64=5.40.1-3 Downloading dependency 360 of 495: libsasl2-modules-db:amd64=2.1.28+dfsg1-9 Downloading dependency 361 of 495: cpp-x86-64-linux-gnu:amd64=4:14.2.0-1 Downloading dependency 362 of 495: libtasn1-6:amd64=4.20.0-2 Downloading dependency 363 of 495: liblz4-1:amd64=1.10.0-4 Downloading dependency 364 of 495: python3-markupsafe:amd64=2.1.5-1+b3 Downloading dependency 365 of 495: libjs-jquery:amd64=3.6.1+dfsg+~3.5.14-1 Downloading dependency 366 of 495: libuchardet0:amd64=0.0.8-1+b2 Downloading dependency 367 of 495: libsqlite3-0:amd64=3.46.1-3 Downloading dependency 368 of 495: libpangocairo-1.0-0:amd64=1.56.3-1 Downloading dependency 369 of 495: libxcb-shm0-dev:amd64=1.17.0-2+b1 Downloading dependency 370 of 495: libaudit1:amd64=1:4.0.2-2+b2 Downloading dependency 371 of 495: gzip:amd64=1.13-1 Downloading dependency 372 of 495: libgprofng0:amd64=2.44-3 Downloading dependency 373 of 495: xorg-sgml-doctools:amd64=1:1.11-1.1 Downloading dependency 374 of 495: binutils:amd64=2.44-3 Downloading dependency 375 of 495: libbrotli-dev:amd64=1.1.0-2+b7 Downloading dependency 376 of 495: python3-defusedxml:amd64=0.7.1-3 Downloading dependency 377 of 495: python3-docutils:amd64=0.21.2+dfsg-2 Downloading dependency 378 of 495: libblkid-dev:amd64=2.41-4 Downloading dependency 379 of 495: libstdc++-14-dev:amd64=14.2.0-19 Downloading dependency 380 of 495: libboost1.83-dev:amd64=1.83.0-4.2 Downloading dependency 381 of 495: libzzip-0-13t64:amd64=0.13.78+dfsg.1-0.1 Downloading dependency 382 of 495: python3-minimal:amd64=3.13.3-1Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-minimal amd64 3.13.3-1 [27.2 kB] Fetched 27.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2jndel5q/python3-minimal_3.13.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 autotools-dev all 20240727.1 [60.2 kB] Fetched 60.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_w4wr65a/autotools-dev_20240727.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 init-system-helpers all 1.68 [38.7 kB] Fetched 38.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp94ze3u19/init-system-helpers_1.68_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB] Fetched 24.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv87qq9ub/libcom-err2_1.47.2-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libde265-0 amd64 1.0.15-1+b3 [189 kB] Fetched 189 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpncv18d3a/libde265-0_1.0.15-1+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 postgresql-client-common all 277 [47.0 kB] Fetched 47.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmporo7y2pk/postgresql-client-common_277_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 g++-14 amd64 14.2.0-19 [22.5 kB] Fetched 22.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpziu6r3wo/g++-14_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 liblastlog2-2 amd64 2.41-4 [28.4 kB] Fetched 28.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpprnzjc96/liblastlog2-2_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Fetched 93.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgl7pp3zm/libedit2_3.1-20250104-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Fetched 35.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu_8enmg3/libimagequant0_2.18.0-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Fetched 8808 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2h5fi31u/libtext-wrapi18n-perl_0.06-10_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Fetched 181 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphj0_5qp8/libxcb1-dev_1.17.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 procps amd64 2:4.0.4-8 [881 kB] Fetched 881 kB in 0s (77.2 MB/s) dpkg-name: info: moved 'procps_2%3a4.0.4-8_amd64.deb' to '/srv/rebuilderd/tmp/tmp9nan6xfu/procps_4.0.4-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgc1 amd64 1:8.2.8-1 [247 kB] Fetched 247 kB in 0s (0 B/s) dpkg-name: info: moved 'libgc1_1%3a8.2.8-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp0ey1rd7j/libgc1_8.2.8-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Fetched 93.3 kB in 0s (0 B/s) dpkg-name: info: moved 'xfonts-utils_1%3a7.7+7_amd64.deb' to '/srv/rebuilderd/tmp/tmpk65zlsae/xfonts-utils_7.7+7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Fetched 338 kB in 0s (0 B/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.46-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp0t9xethy/libmagic-mgc_5.46-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Fetched 425 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprhlzrsex/libp11-kit0_0.25.5-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 librsvg2-2 amd64 2.60.0+dfsg-1 [1789 kB] Fetched 1789 kB in 0s (131 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp05hqoujq/librsvg2-2_2.60.0+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgirepository-2.0-0 amd64 2.84.1-2 [141 kB] Fetched 141 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplzv8i4y1/libgirepository-2.0-0_2.84.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 cpp-14 amd64 14.2.0-19 [1280 B] Fetched 1280 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp91vu9m6n/cpp-14_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpcre2-32-0 amd64 10.45-1 [268 kB] Fetched 268 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2jk57lrz/libpcre2-32-0_10.45-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcap-ng0 amd64 0.8.5-4+b1 [17.6 kB] Fetched 17.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1dhfc6ft/libcap-ng0_0.8.5-4+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Fetched 32.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdgec_9ou/libjbig0_2.1-6.1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 mawk amd64 1.3.4.20250131-1 [141 kB] Fetched 141 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdwlce70w/mawk_1.3.4.20250131-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB] Fetched 341 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa0e81nnf/libteckit0_2.5.12+ds1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 tzdata all 2025b-2 [260 kB] Fetched 260 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb9szafw1/tzdata_2025b-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libicu-dev amd64 76.1-3 [10.8 MB] Fetched 10.8 MB in 0s (254 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppar8g9kj/libicu-dev_76.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Fetched 67.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2mxwvmy4/libnghttp3-9_1.8.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.2 [270 kB] Fetched 270 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0ndxy81p/libboost-thread1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libmpc3 amd64 1.3.1-1+b3 [52.2 kB] Fetched 52.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzz_d4a5s/libmpc3_1.3.1-1+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 make amd64 4.4.1-2 [463 kB] Fetched 463 kB in 0s (43.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb5w9dbph/make_4.4.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxcb-render0-dev amd64 1.17.0-2+b1 [118 kB] Fetched 118 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp55svuyf0/libxcb-render0-dev_1.17.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-packaging all 25.0-1 [56.6 kB] Fetched 56.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxzyb9ux2/python3-packaging_25.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-pytest all 8.3.5-2 [250 kB] Fetched 250 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7kz1vsc2/python3-pytest_8.3.5-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Fetched 311 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5j84byu7/libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 preview-latex-style all 13.2-1 [350 kB] Fetched 350 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdfq66vq5/preview-latex-style_13.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libunistring5 amd64 1.3-2 [477 kB] Fetched 477 kB in 0s (12.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwt1mc4cv/libunistring5_1.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 build-essential amd64 12.12 [4624 B] Fetched 4624 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6sgkxzqf/build-essential_12.12_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Fetched 698 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8ajy565f/libxml2_2.12.7+dfsg+really2.9.14-0.4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Fetched 781 kB in 0s (71.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzdi3vtf_/libfftw3-double3_3.3.10-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Fetched 23.6 kB in 0s (0 B/s) dpkg-name: info: moved 'libxau-dev_1%3a1.0.11-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpwmzufp59/libxau-dev_1.0.11-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB] Fetched 513 kB in 0s (44.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu666hu9g/python3-pil_11.1.0-5+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpng-dev amd64 1.6.47-1.1 [366 kB] Fetched 366 kB in 0s (33.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8e4l5q2e/libpng-dev_1.6.47-1.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Fetched 8620 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0f6p48lc/dh-strip-nondeterminism_1.14.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 sed amd64 4.9-2 [329 kB] Fetched 329 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_j8t5gf4/sed_4.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libaudit-common all 1:4.0.2-2 [12.7 kB] Fetched 12.7 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit-common_1%3a4.0.2-2_all.deb' to '/srv/rebuilderd/tmp/tmp2zh3yyr4/libaudit-common_4.0.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcoordgen-dev amd64 3.0.2-1+b2 [46.9 kB] Fetched 46.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1b0f06w7/libcoordgen-dev_3.0.2-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB] Fetched 194 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpztg_65dr/libldap2_2.6.9+dfsg-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgcc-s1 amd64 14.2.0-19 [72.8 kB] Fetched 72.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjqn6v1d9/libgcc-s1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmperdwzoy4/python3-chardet_5.2.0+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 ucf all 3.0051 [42.8 kB] Fetched 42.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9y1fui4h/ucf_3.0051_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-regex1.83.0 amd64 1.83.0-4.2 [330 kB] Fetched 330 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2uc4b_yz/libboost-regex1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libmagickcore-7.q16-10 amd64 8:7.1.1.47+dfsg1-1 [1846 kB] Fetched 1846 kB in 0s (127 MB/s) dpkg-name: info: moved 'libmagickcore-7.q16-10_8%3a7.1.1.47+dfsg1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmph6pk14s5/libmagickcore-7.q16-10_7.1.1.47+dfsg1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libsmartcols1 amd64 2.41-4 [143 kB] Fetched 143 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqqc22i7n/libsmartcols1_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-mdit-py-plugins all 0.4.2-1 [32.4 kB] Fetched 32.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3rg6u162/python3-mdit-py-plugins_0.4.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpaper-utils amd64 2.2.5-0.3+b2 [16.5 kB] Fetched 16.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb5mreeyl/libpaper-utils_2.2.5-0.3+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Fetched 26.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn3gy7zl0/libfribidi0_1.0.16-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Fetched 3624 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8e284j47/libboost-thread-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-date-time1.83-dev amd64 1.83.0-4.2 [239 kB] Fetched 239 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp09pbhqot/libboost-date-time1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Fetched 65.4 kB in 0s (329 kB/s) dpkg-name: info: moved 'libice6_2%3a1.1.1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp7wo3vccr/libice6_1.1.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libubsan1 amd64 14.2.0-19 [1074 kB] Fetched 1074 kB in 0s (29.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeoz0azpu/libubsan1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libx11-dev amd64 2:1.8.12-1 [894 kB] Fetched 894 kB in 0s (21.7 MB/s) dpkg-name: info: moved 'libx11-dev_2%3a1.8.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp6wwt0mll/libx11-dev_1.8.12-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 texlive-pictures all 2024.20250309-1 [17.0 MB] Fetched 17.0 MB in 0s (91.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpylx3_kx7/texlive-pictures_2024.20250309-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-atomic1.83.0 amd64 1.83.0-4.2 [234 kB] Fetched 234 kB in 0s (644 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr9zis6k_/libboost-atomic1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Fetched 36.4 kB in 0s (215 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjcg_6x1e/libpkgconf3_1.8.1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4.2 [333 kB] Fetched 333 kB in 1s (541 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2dd_vaaj/libboost-serialization1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Fetched 6050 kB in 0s (50.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1e84ey6_/python-babel-localedata_2.17.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-roman all 5.0-1 [10.6 kB] Fetched 10.6 kB in 0s (127 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp94tat8c9/python3-roman_5.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 uuid-dev amd64 2.41-4 [48.8 kB] Fetched 48.8 kB in 0s (454 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfmqrlbf9/uuid-dev_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 sensible-utils all 0.0.25 [25.0 kB] Fetched 25.0 kB in 0s (1443 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9j8b9m7l/sensible-utils_0.0.25_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libtinfo6 amd64 6.5+20250216-2 [348 kB] Fetched 348 kB in 0s (25.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsq2r9k8i/libtinfo6_6.5+20250216-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-date-time1.83.0 amd64 1.83.0-4.2 [230 kB] Fetched 230 kB in 0s (18.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0gjt7_5k/libboost-date-time1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libdpkg-perl all 1.22.18 [649 kB] Fetched 649 kB in 0s (12.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk3_j8r53/libdpkg-perl_1.22.18_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libclang-common-19-dev amd64 1:19.1.7-3 [740 kB] Fetched 740 kB in 0s (70.4 MB/s) dpkg-name: info: moved 'libclang-common-19-dev_1%3a19.1.7-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp2ed0xr24/libclang-common-19-dev_19.1.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Fetched 19.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7ly3svvt/libfile-stripnondeterminism-perl_1.14.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB] Fetched 318 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxs_ig1lg/fontconfig-config_2.15.0-2.3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Fetched 9652 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnk8mzts8/python3-certifi_2025.1.31+ds-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Fetched 42.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgx3eo7xj/libpipeline1_1.5.8-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libffi-dev amd64 3.4.8-2 [61.1 kB] Fetched 61.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp3pwokv9/libffi-dev_3.4.8-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Fetched 318 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptbdu7j26/libwebp7_1.5.0-0.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libllvm19 amd64 1:19.1.7-3 [26.0 MB] Fetched 26.0 MB in 1s (39.6 MB/s) dpkg-name: info: moved 'libllvm19_1%3a19.1.7-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpnevpf5_6/libllvm19_19.1.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libopenjp2-7 amd64 2.5.3-2 [204 kB] Fetched 204 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpazzjrr8s/libopenjp2-7_2.5.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libicu76 amd64 76.1-3 [9721 kB] Fetched 9721 kB in 0s (221 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkb0npe67/libicu76_76.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-program-options1.83-dev amd64 1.83.0-4.2 [375 kB] Fetched 375 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpczglicwo/libboost-program-options1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-commonmark all 0.9.1-8 [45.5 kB] Fetched 45.5 kB in 0s (230 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl8s_bhcz/python3-commonmark_0.9.1-8_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgio-2.0-dev amd64 2.84.1-2 [1685 kB] Fetched 1685 kB in 0s (114 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptdh8sexo/libgio-2.0-dev_2.84.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Fetched 3836 B in 0s (377 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzmo5z5tc/libboost-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [282 kB] Fetched 282 kB in 0s (25.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxuumexb9/libpng16-16t64_1.6.47-1.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Fetched 6688 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqt6o8xuf/python3-imagesize_1.4.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 autopoint all 0.23.1-2 [770 kB] Fetched 770 kB in 0s (72.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6u0ist00/autopoint_0.23.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 automake all 1:1.17-4 [862 kB] Fetched 862 kB in 0s (73.3 MB/s) dpkg-name: info: moved 'automake_1%3a1.17-4_all.deb' to '/srv/rebuilderd/tmp/tmpfblw6nah/automake_1.17-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Fetched 58.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4v6m9d99/librtmp1_2.4+20151223.gitfa8646d.1-2+b5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 perl amd64 5.40.1-3 [267 kB] Fetched 267 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpztt5soda/perl_5.40.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Fetched 105 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpozd6y5sm/libxcb-shm0_1.17.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 debianutils amd64 5.22 [92.2 kB] Fetched 92.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpda2xud0j/debianutils_5.22_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libboost-numpy1.83-dev amd64 1.83.0-4.2 [246 kB] Fetched 246 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprhedya_j/libboost-numpy1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 ca-certificates all 20250419 [162 kB] Fetched 162 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzsq07n_n/ca-certificates_20250419_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libinchi1.07 amd64 1.07.3+dfsg-1 [557 kB] Fetched 557 kB in 0s (50.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5gv2pkfk/libinchi1.07_1.07.3+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 sysvinit-utils amd64 3.14-4 [34.1 kB] Fetched 34.1 kB in 0s (174 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6ldh6492/sysvinit-utils_3.14-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Fetched 138 kB in 0s (13.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnbfum432/libgssapi-krb5-2_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-6 [114 kB] Fetched 114 kB in 0s (528 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdkrgv5ee/libtexlua53-5_2024.20240313.70630+ds-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Fetched 836 kB in 0s (3195 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppb0rv166/python3-pygments_2.18.0+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 linux-libc-dev all 6.12.25-1 [2565 kB] Fetched 2565 kB in 0s (161 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpterk1itv/linux-libc-dev_6.12.25-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Fetched 5527 kB in 0s (12.3 MB/s) dpkg-name: info: moved 'libpdfbox-java_1%3a1.8.16-5_all.deb' to '/srv/rebuilderd/tmp/tmp3npvpnoi/libpdfbox-java_1.8.16-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Fetched 68.6 kB in 0s (175 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprbuo08ks/libcommons-logging-java_1.3.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libpcre2-8-0 amd64 10.45-1 [298 kB] Fetched 298 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo8nmxm0d/libpcre2-8-0_10.45-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libselinux1-dev amd64 3.8.1-1 [169 kB] Fetched 169 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqysq__zc/libselinux1-dev_3.8.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 tex-gyre all 20180621-6 [6209 kB] Fetched 6209 kB in 0s (77.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn9q9cic0/tex-gyre_20180621-6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 architecture-properties amd64 0.2.6 [2336 B] Fetched 2336 B in 0s (54.2 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5etr6pf0/architecture-properties_0.2.6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 imagemagick-7.q16 amd64 8:7.1.1.47+dfsg1-1 [726 kB] Fetched 726 kB in 0s (65.6 MB/s) dpkg-name: info: moved 'imagemagick-7.q16_8%3a7.1.1.47+dfsg1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpcigbobml/imagemagick-7.q16_7.1.1.47+dfsg1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 cpp amd64 4:14.2.0-1 [1568 B] Fetched 1568 B in 0s (0 B/s) dpkg-name: info: moved 'cpp_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpt2d6lzhd/cpp_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 sphinx-common all 8.1.3-5 [617 kB] Fetched 617 kB in 0s (60.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1a6w9e0y/sphinx-common_8.1.3-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 libheif-plugin-libde265 amd64 1.19.8-1 [15.3 kB] Fetched 15.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph_onq6i0/libheif-plugin-libde265_1.19.8-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250501T203212Z sid/main amd64 texlive-latex-extra all 2024.20250309-2 [25.2 MB] Fetched 25.2 MB in 0s (276 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppn2vvxbb/texlive-latex-extra_2024.20250309-2_all.deb' dpkg-buildpackage: info: source package debootsnap-dummy dpkg-buildpackage: info: source version 1.0 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Equivs Dummy Package Generator dpkg-buildpackage: info: host architecture amd64 dpkg-source --before-build . debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/debootsnap-dummy/ dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'debootsnap-dummy' in '../debootsnap-dummy_1.0_all.deb'. dpkg-genbuildinfo --build=binary -O../debootsnap-dummy_1.0_amd64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) The package has been created. Attention, the package has been created in the /srv/rebuilderd/tmp/tmpof8u1oma/cache directory, not in ".." as indicated by the message above! I: automatically chosen mode: unshare I: chroot architecture amd64 is equal to the host's architecture I: using /srv/rebuilderd/tmp/mmdebstrap.MNljpK0jYE as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.MNljpK0jYE 127.0.0.1 - - [28/Jul/2025 09:09:19] code 404, message File not found 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:35819 ./ InRelease 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:35819 ./ Release [462 B] 127.0.0.1 - - [28/Jul/2025 09:09:19] code 404, message File not found 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:35819 ./ Release.gpg 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:35819 ./ Packages [765 kB] Fetched 765 kB in 0s (32.8 MB/s) Reading package lists... usr-is-merged found but not real -- not running merged-usr setup hook I: skipping apt-get update because it was already run I: downloading packages with apt... 127.0.0.1 - 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127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./libattr1_2.5.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./libgmp10_6.3.0%2bdfsg-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./libpcre2-8-0_10.45-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./libselinux1_3.8.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./libzstd1_1.5.7%2bdfsg-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./zlib1g_1.3.dfsg%2breally1.3.1-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./libssl3t64_3.5.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./openssl-provider-legacy_3.5.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./coreutils_9.7-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./dash_0.5.12-12_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 09:09:19] "GET /./diffutils_3.10-4_amd64.deb HTTP/1.1" 200 - 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- [28/Jul/2025 09:09:20] "GET /./ncurses-base_6.5%2b20250216-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 09:09:20] "GET /./sysvinit-utils_3.14-4_amd64.deb HTTP/1.1" 200 - I: extracting archives... I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.MNljpK0jYE 127.0.0.1 - - [28/Jul/2025 09:09:22] code 404, message File not found 127.0.0.1 - - [28/Jul/2025 09:09:22] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:35819 ./ InRelease 127.0.0.1 - - [28/Jul/2025 09:09:22] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:35819 ./ Release 127.0.0.1 - - [28/Jul/2025 09:09:22] code 404, message File not found 127.0.0.1 - - [28/Jul/2025 09:09:22] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:35819 ./ Release.gpg Reading package lists... usr-is-merged found but not real -- not running merged-usr extract hook I: installing essential packages... 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Building dependency tree... Reading state information... libcairo2 is already the newest version (1.18.4-1+b1). libcairo2 set to manually installed. python3-sphinx is already the newest version (8.1.3-5). python3-sphinx set to manually installed. passwd is already the newest version (1:4.17.4-2). passwd set to manually installed. libboost-iostreams1.83-dev is already the newest version (1.83.0-4.2). libboost-iostreams1.83-dev set to manually installed. libcc1-0 is already the newest version (14.2.0-19). libcc1-0 set to manually installed. xtrans-dev is already the newest version (1.4.0-1). xtrans-dev set to manually installed. x11proto-dev is already the newest version (2024.1-1). x11proto-dev set to manually installed. libtiff6 is already the newest version (4.7.0-3). libtiff6 set to manually installed. libboost-atomic1.83-dev is already the newest version (1.83.0-4.2). libboost-atomic1.83-dev set to manually installed. libio-pty-perl is already the newest version (1:1.20-1+b3). libio-pty-perl set to manually installed. libblkid1 is already the newest version (2.41-4). libkrb5support0 is already the newest version (1.21.3-5). libkrb5support0 set to manually installed. libmagic1t64 is already the newest version (1:5.46-5). libmagic1t64 set to manually installed. fonts-lmodern is already the newest version (2.005-1). fonts-lmodern set to manually installed. libboost-python1.83.0 is already the newest version (1.83.0-4.2). libboost-python1.83.0 set to manually installed. base-files is already the newest version (13.7). libpango-1.0-0 is already the newest version (1.56.3-1). libpango-1.0-0 set to manually installed. sgml-base is already the newest version (1.31+nmu1). sgml-base set to manually installed. libk5crypto3 is already the newest version (1.21.3-5). libk5crypto3 set to manually installed. libc-bin is already the newest version (2.41-7). python3-typing-extensions is already the newest version (4.13.2-1). python3-typing-extensions set to manually installed. ssl-cert is already the newest version (1.1.3). ssl-cert set to manually installed. imagemagick is already the newest version (8:7.1.1.47+dfsg1-1). imagemagick set to manually installed. libgdbm6t64 is already the newest version (1.24-2). libgdbm6t64 set to manually installed. libboost-iostreams1.83.0 is already the newest version (1.83.0-4.2). libboost-iostreams1.83.0 set to manually installed. python3-charset-normalizer is already the newest version (3.4.1-1+b1). python3-charset-normalizer set to manually installed. libidn2-0 is already the newest version (2.3.8-2). libidn2-0 set to manually installed. libfontenc1 is already the newest version (1:1.1.8-1+b2). libfontenc1 set to manually installed. libssl3t64 is already the newest version (3.5.0-1). catch2 is already the newest version (3.7.1-0.5). catch2 set to manually installed. libobjc-14-dev is already the newest version (14.2.0-19). libobjc-14-dev set to manually installed. libxmu6 is already the newest version (2:1.1.3-3+b4). libxmu6 set to manually installed. libc6-dev is already the newest version (2.41-7). libc6-dev set to manually installed. cpp-14-x86-64-linux-gnu is already the newest version (14.2.0-19). cpp-14-x86-64-linux-gnu set to manually installed. docutils-common is already the newest version (0.21.2+dfsg-2). docutils-common set to manually installed. pandoc-data is already the newest version (3.1.11.1-3). pandoc-data set to manually installed. libkpathsea6 is already the newest version (2024.20240313.70630+ds-6). libkpathsea6 set to manually installed. util-linux is already the newest version (2.41-4). libbrotli1 is already the newest version (1.1.0-2+b7). libbrotli1 set to manually installed. libcrypt1 is already the newest version (1:4.4.38-1). libxau6 is already the newest version (1:1.0.11-1). libxau6 set to manually installed. python3-sqlalchemy is already the newest version (2.0.40+ds1-1). python3-sqlalchemy set to manually installed. libmount-dev is already the newest version (2.41-4). libmount-dev set to manually installed. libpangoft2-1.0-0 is already the newest version (1.56.3-1). libpangoft2-1.0-0 set to manually installed. libobjc4 is already the newest version (14.2.0-19). libobjc4 set to manually installed. libuuid1 is already the newest version (2.41-4). libncurses6 is already the newest version (6.5+20250216-2). libncurses6 set to manually installed. t1utils is already the newest version (1.41-4). t1utils set to manually installed. libfreetype6 is already the newest version (2.13.3+dfsg-1). libfreetype6 set to manually installed. libx11-6 is already the newest version (2:1.8.12-1). libx11-6 set to manually installed. tex-common is already the newest version (6.19). tex-common set to manually installed. bsdutils is already the newest version (1:2.41-4). intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. libpython3.13-minimal is already the newest version (3.13.3-2). libpython3.13-minimal set to manually installed. libpcre2-dev is already the newest version (10.45-1). libpcre2-dev set to manually installed. llvm-19-linker-tools is already the newest version (1:19.1.7-3). llvm-19-linker-tools set to manually installed. libxcb1 is already the newest version (1.17.0-2+b1). libxcb1 set to manually installed. python3-pandas-lib is already the newest version (2.2.3+dfsg-9). python3-pandas-lib set to manually installed. libsepol2 is already the newest version (3.8.1-1). libsepol2 set to manually installed. libpaper2 is already the newest version (2.2.5-0.3+b2). libpaper2 set to manually installed. libsystemd0 is already the newest version (257.5-2). libmpfr6 is already the newest version (4.2.2-1). libmpfr6 set to manually installed. libseccomp2 is already the newest version (2.6.0-2). libseccomp2 set to manually installed. libnettle8t64 is already the newest version (3.10.1-1). libnettle8t64 set to manually installed. libxpm4 is already the newest version (1:3.5.17-1+b3). libxpm4 set to manually 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installed. python3-jinja2 is already the newest version (3.1.6-1). python3-jinja2 set to manually installed. liblzo2-2 is already the newest version (2.10-3+b1). liblzo2-2 set to manually installed. fonts-dejavu-mono is already the newest version (2.37-8). fonts-dejavu-mono set to manually installed. libstdc++6 is already the newest version (14.2.0-19). libstdc++6 set to manually installed. libmd0 is already the newest version (1.1.0-2+b1). libboost-numpy-dev is already the newest version (1.83.0.2+b2). libboost-numpy-dev set to manually installed. libz3-4 is already the newest version (4.13.3-1). libz3-4 set to manually installed. gcc is already the newest version (4:14.2.0-1). gcc set to manually installed. native-architecture is already the newest version (0.2.6). native-architecture set to manually installed. po-debconf is already the newest version (1.0.21+nmu1). po-debconf set to manually installed. libnuma1 is already the newest version (2.0.19-1). libnuma1 set to manually 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libjansson4 is already the newest version (2.14-2+b3). libjansson4 set to manually installed. libctf0 is already the newest version (2.44-3). libctf0 set to manually installed. libsynctex2 is already the newest version (2024.20240313.70630+ds-6). libsynctex2 set to manually installed. clang-19 is already the newest version (1:19.1.7-3). clang-19 set to manually installed. libwebpmux3 is already the newest version (1.5.0-0.1). libwebpmux3 set to manually installed. libfmt10 is already the newest version (10.1.1+ds1-4). libfmt10 set to manually installed. libhwasan0 is already the newest version (14.2.0-19). libhwasan0 set to manually installed. g++ is already the newest version (4:14.2.0-1). g++ set to manually installed. latexmk is already the newest version (1:4.86~ds-1). latexmk set to manually installed. libdebhelper-perl is already the newest version (13.24.2). libdebhelper-perl set to manually installed. g++-14-x86-64-linux-gnu is already the newest version (14.2.0-19). g++-14-x86-64-linux-gnu set to manually installed. libffi8 is already the newest version (3.4.8-2). libffi8 set to manually installed. libmount1 is already the newest version (2.41-4). python3-markdown-it is already the newest version (3.0.0-2). python3-markdown-it set to manually installed. libhogweed6t64 is already the newest version (3.10.1-1). libhogweed6t64 set to manually installed. gettext is already the newest version (0.23.1-2). gettext set to manually installed. postgresql-common-dev is already the newest version (277). postgresql-common-dev set to manually installed. libdatrie1 is already the newest version (0.2.13-3+b1). libdatrie1 set to manually installed. libmagickwand-7.q16-10 is already the newest version (8:7.1.1.47+dfsg1-1). libmagickwand-7.q16-10 set to manually installed. bison is already the newest version (2:3.8.2+dfsg-1+b2). bison set to manually installed. libdb5.3t64 is already the newest version (5.3.28+dfsg2-9). libjs-sphinxdoc is already the newest version 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openssl set to manually installed. icu-devtools is already the newest version (76.1-3). icu-devtools set to manually installed. m4 is already the newest version (1.4.19-8). m4 set to manually installed. libxi6 is already the newest version (2:1.8.2-1). libxi6 set to manually installed. libctf-nobfd0 is already the newest version (2.44-3). libctf-nobfd0 set to manually installed. libpotrace0 is already the newest version (1.16-2+b2). libpotrace0 set to manually installed. libisl23 is already the newest version (0.27-1). libisl23 set to manually installed. libexpat1 is already the newest version (2.7.1-1). libexpat1 set to manually installed. texlive-latex-base is already the newest version (2024.20250309-1). texlive-latex-base set to manually installed. texlive-fonts-recommended is already the newest version (2024.20250309-1). texlive-fonts-recommended set to manually installed. libboost-system1.83.0 is already the newest version (1.83.0-4.2). libboost-system1.83.0 set to manually installed. dpkg is already the newest version (1.22.18). libgraphite2-3 is already the newest version (1.3.14-2+b1). libgraphite2-3 set to manually installed. python3-urllib3 is already the newest version (2.3.0-2). python3-urllib3 set to manually installed. libcoordgen3 is already the newest version (3.0.2-1+b2). libcoordgen3 set to manually installed. patch is already the newest version (2.8-1). patch set to manually installed. libglib2.0-dev-bin is already the newest version (2.84.1-2). libglib2.0-dev-bin set to manually installed. libpcre2-posix3 is already the newest version (10.45-1). libpcre2-posix3 set to manually installed. libpq5 is already the newest version (17.4-2). libpq5 set to manually installed. libjsoncpp26 is already the newest version (1.9.6-3). libjsoncpp26 set to manually installed. libboost-system1.83-dev is already the newest version (1.83.0-4.2). libboost-system1.83-dev set to manually installed. libeigen3-dev is already the newest version (3.4.0-4). libeigen3-dev set to manually installed. libglib2.0-dev is already the newest version (2.84.1-2). libglib2.0-dev set to manually installed. libsm6 is already the newest version (2:1.2.6-1). libsm6 set to manually installed. gcc-14 is already the newest version (14.2.0-19). gcc-14 set to manually installed. libsframe1 is already the newest version (2.44-3). libsframe1 set to manually installed. python3.13-minimal is already the newest version (3.13.3-2). python3.13-minimal set to manually installed. cmake-data is already the newest version (3.31.6-2). cmake-data set to manually installed. libxapian30 is already the newest version (1.4.29-2). libxapian30 set to manually installed. libxaw7 is already the newest version (2:1.0.16-1). libxaw7 set to manually installed. libgio-2.0-dev-bin is already the newest version (2.84.1-2). libgio-2.0-dev-bin set to manually installed. libthai0 is already the newest version (0.1.29-2+b1). libthai0 set to manually installed. libc6 is already the newest version (2.41-7). libcairo-gobject2 is already the newest version (1.18.4-1+b1). libcairo-gobject2 set to manually installed. libasan8 is already the newest version (14.2.0-19). libasan8 set to manually installed. libdav1d7 is already the newest version (1.5.1-1). libdav1d7 set to manually installed. ncurses-base is already the newest version (6.5+20250216-2). libtext-charwidth-perl is already the newest version (0.04-11+b4). libtext-charwidth-perl set to manually installed. libptexenc1 is already the newest version (2024.20240313.70630+ds-6). libptexenc1 set to manually installed. libgcc-14-dev is already the newest version (14.2.0-19). libgcc-14-dev set to manually installed. libxml2-dev is already the newest version (2.12.7+dfsg+really2.9.14-0.4). libxml2-dev set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libitm1 is already the newest version (14.2.0-19). libitm1 set to manually installed. 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already the newest version (2:1.1.1-1). libice-dev set to manually installed. libbinutils is already the newest version (2.44-3). libbinutils set to manually installed. postgresql-server-dev-17 is already the newest version (17.4-2). postgresql-server-dev-17 set to manually installed. groff-base is already the newest version (1.23.0-7). groff-base set to manually installed. liblqr-1-0 is already the newest version (0.4.2-2.1+b2). liblqr-1-0 set to manually installed. libharfbuzz0b is already the newest version (10.2.0-1+b1). libharfbuzz0b set to manually installed. libthai-data is already the newest version (0.1.29-2). libthai-data set to manually installed. debconf is already the newest version (1.5.91). libtool is already the newest version (2.5.4-4). libtool set to manually installed. libpython3-dev is already the newest version (3.13.3-1). libpython3-dev set to manually installed. llvm-19-runtime is already the newest version (1:19.1.7-3). llvm-19-runtime set to manually installed. 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installed. libtsan2 is already the newest version (14.2.0-19). libtsan2 set to manually installed. libclang1-19 is already the newest version (1:19.1.7-3). libclang1-19 set to manually installed. python3-pytz is already the newest version (2025.2-2). python3-pytz set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-3). libraw23t64 is already the newest version (0.21.4-2). libraw23t64 set to manually installed. libfontconfig1 is already the newest version (2.15.0-2.3). libfontconfig1 set to manually installed. python3-numpy-dev is already the newest version (1:2.2.4+ds-1). python3-numpy-dev set to manually installed. libjson-perl is already the newest version (4.10000-1). libjson-perl set to manually installed. libfreetype-dev is already the newest version (2.13.3+dfsg-1). libfreetype-dev set to manually installed. libboost-program-options1.83.0 is already the newest version (1.83.0-4.2). libboost-program-options1.83.0 set to manually installed. llvm-19-tools 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libatomic1 is already the newest version (14.2.0-19). libatomic1 set to manually installed. libpixman-1-0 is already the newest version (0.44.0-3). libpixman-1-0 set to manually installed. dwz is already the newest version (0.15-1+b1). dwz set to manually installed. libboost-iostreams-dev is already the newest version (1.83.0.2+b2). libboost-iostreams-dev set to manually installed. liblapack3 is already the newest version (3.12.1-2). liblapack3 set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). librsvg2-bin is already the newest version (2.60.0+dfsg-1). librsvg2-bin set to manually installed. libpython3-stdlib is already the newest version (3.13.3-1). libpython3-stdlib set to manually installed. fonts-dejavu-core is already the newest version (2.37-8). fonts-dejavu-core set to manually installed. gcc-x86-64-linux-gnu is already the newest version (4:14.2.0-1). gcc-x86-64-linux-gnu set to manually installed. libcommons-parent-java is already 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installed. libboost-python-dev is already the newest version (1.83.0.2+b2). libboost-python-dev set to manually installed. python3-myst-parser is already the newest version (4.0.1-1). python3-myst-parser set to manually installed. libarchive13t64 is already the newest version (3.7.4-3). libarchive13t64 set to manually installed. libpq-dev is already the newest version (17.4-2). libpq-dev set to manually installed. libgnutls30t64 is already the newest version (3.8.9-2). libgnutls30t64 set to manually installed. libattr1 is already the newest version (1:2.5.2-3). libpsl5t64 is already the newest version (0.21.2-1.1+b1). libpsl5t64 set to manually installed. libc-dev-bin is already the newest version (2.41-7). libc-dev-bin set to manually installed. libz3-dev is already the newest version (4.13.3-1). libz3-dev set to manually installed. python3-yaml is already the newest version (6.0.2-1+b2). python3-yaml set to manually installed. libwebpdemux2 is already the newest version (1.5.0-0.1). libwebpdemux2 set to manually installed. libmaeparser1 is already the newest version (1.3.1-1+b2). libmaeparser1 set to manually installed. dh-autoreconf is already the newest version (20). dh-autoreconf set to manually installed. libpam-modules-bin is already the newest version (1.7.0-3). bash is already the newest version (5.2.37-2). libcap2 is already the newest version (1:2.75-7). llvm-19-dev is already the newest version (1:19.1.7-3). llvm-19-dev set to manually installed. bzip2 is already the newest version (1.0.8-6). bzip2 set to manually installed. rapidjson-dev is already the newest version (1.1.0+dfsg2-7.4). rapidjson-dev set to manually installed. libblas3 is already the newest version (3.12.1-2). libblas3 set to manually installed. libcairo2-dev is already the newest version (1.18.4-1+b1). libcairo2-dev set to manually installed. libcairo-script-interpreter2 is already the newest version (1.18.4-1+b1). libcairo-script-interpreter2 set to manually installed. zlib1g-dev is 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libboost-numpy1.83.0 set to manually installed. python3-numpy is already the newest version (1:2.2.4+ds-1). python3-numpy set to manually installed. python3-dateutil is already the newest version (2.9.0-4). python3-dateutil set to manually installed. python3-pluggy is already the newest version (1.5.0-1). python3-pluggy set to manually installed. gcc-14-base is already the newest version (14.2.0-19). libpython3.13-stdlib is already the newest version (3.13.3-2). libpython3.13-stdlib set to manually installed. libpython3.13-dev is already the newest version (3.13.3-2). libpython3.13-dev set to manually installed. coreutils is already the newest version (9.7-2). python3-snowballstemmer is already the newest version (2.2.0-4). python3-snowballstemmer set to manually installed. librhash1 is already the newest version (1.4.5-1). librhash1 set to manually installed. python3-greenlet is already the newest version (3.1.0-1+b2). python3-greenlet set to manually installed. libboost-chrono1.83.0t64 is already the newest version (1.83.0-4.2). libboost-chrono1.83.0t64 set to manually installed. autoconf is already the newest version (2.72-3.1). autoconf set to manually installed. libglib2.0-bin is already the newest version (2.84.1-2). libglib2.0-bin set to manually installed. liblua5.4-0 is already the newest version (5.4.7-1+b2). liblua5.4-0 set to manually installed. perl-base is already the newest version (5.40.1-3). libsasl2-modules-db is already the newest version (2.1.28+dfsg1-9). libsasl2-modules-db set to manually installed. cpp-x86-64-linux-gnu is already the newest version (4:14.2.0-1). cpp-x86-64-linux-gnu set to manually installed. libtasn1-6 is already the newest version (4.20.0-2). libtasn1-6 set to manually installed. liblz4-1 is already the newest version (1.10.0-4). liblz4-1 set to manually installed. python3-markupsafe is already the newest version (2.1.5-1+b3). python3-markupsafe set to manually installed. libjs-jquery is already the newest version (3.6.1+dfsg+~3.5.14-1). libjs-jquery set to manually installed. libuchardet0 is already the newest version (0.0.8-1+b2). libuchardet0 set to manually installed. libsqlite3-0 is already the newest version (3.46.1-3). libpangocairo-1.0-0 is already the newest version (1.56.3-1). libpangocairo-1.0-0 set to manually installed. libxcb-shm0-dev is already the newest version (1.17.0-2+b1). libxcb-shm0-dev set to manually installed. libaudit1 is already the newest version (1:4.0.2-2+b2). gzip is already the newest version (1.13-1). libgprofng0 is already the newest version (2.44-3). libgprofng0 set to manually installed. xorg-sgml-doctools is already the newest version (1:1.11-1.1). xorg-sgml-doctools set to manually installed. binutils is already the newest version (2.44-3). binutils set to manually installed. libbrotli-dev is already the newest version (1.1.0-2+b7). libbrotli-dev set to manually installed. python3-defusedxml is already the newest version (0.7.1-3). python3-defusedxml set to manually installed. python3-docutils is already the newest version (0.21.2+dfsg-2). python3-docutils set to manually installed. libblkid-dev is already the newest version (2.41-4). libblkid-dev set to manually installed. libstdc++-14-dev is already the newest version (14.2.0-19). libstdc++-14-dev set to manually installed. libboost1.83-dev is already the newest version (1.83.0-4.2). libboost1.83-dev set to manually installed. libzzip-0-13t64 is already the newest version (0.13.78+dfsg.1-0.1). libzzip-0-13t64 set to manually installed. python3-minimal is already the newest version (3.13.3-1). python3-minimal set to manually installed. autotools-dev is already the newest version (20240727.1). autotools-dev set to manually installed. init-system-helpers is already the newest version (1.68). libcom-err2 is already the newest version (1.47.2-1+b1). libcom-err2 set to manually installed. libde265-0 is already the newest version (1.0.15-1+b3). libde265-0 set to manually installed. postgresql-client-common is already the newest version (277). postgresql-client-common set to manually installed. g++-14 is already the newest version (14.2.0-19). g++-14 set to manually installed. liblastlog2-2 is already the newest version (2.41-4). libedit2 is already the newest version (3.1-20250104-1). libedit2 set to manually installed. libimagequant0 is already the newest version (2.18.0-1+b2). libimagequant0 set to manually installed. libtext-wrapi18n-perl is already the newest version (0.06-10). libtext-wrapi18n-perl set to manually installed. libxcb1-dev is already the newest version (1.17.0-2+b1). libxcb1-dev set to manually installed. procps is already the newest version (2:4.0.4-8). procps set to manually installed. libgc1 is already the newest version (1:8.2.8-1). libgc1 set to manually installed. xfonts-utils is already the newest version (1:7.7+7). xfonts-utils set to manually installed. libmagic-mgc is already the newest version (1:5.46-5). libmagic-mgc set to manually installed. libp11-kit0 is already the newest version (0.25.5-3). libp11-kit0 set to manually installed. librsvg2-2 is already the newest version (2.60.0+dfsg-1). librsvg2-2 set to manually installed. libgirepository-2.0-0 is already the newest version (2.84.1-2). libgirepository-2.0-0 set to manually installed. cpp-14 is already the newest version (14.2.0-19). cpp-14 set to manually installed. libpcre2-32-0 is already the newest version (10.45-1). libpcre2-32-0 set to manually installed. libcap-ng0 is already the newest version (0.8.5-4+b1). libjbig0 is already the newest version (2.1-6.1+b2). libjbig0 set to manually installed. mawk is already the newest version (1.3.4.20250131-1). libteckit0 is already the newest version (2.5.12+ds1-1+b1). libteckit0 set to manually installed. tzdata is already the newest version (2025b-2). tzdata set to manually installed. libicu-dev is already the newest version (76.1-3). libicu-dev set to manually installed. libnghttp3-9 is already the newest version (1.8.0-1). libnghttp3-9 set to manually installed. libboost-thread1.83.0 is already the newest version (1.83.0-4.2). libboost-thread1.83.0 set to manually installed. libmpc3 is already the newest version (1.3.1-1+b3). libmpc3 set to manually installed. make is already the newest version (4.4.1-2). make set to manually installed. libxcb-render0-dev is already the newest version (1.17.0-2+b1). libxcb-render0-dev set to manually installed. python3-packaging is already the newest version (25.0-1). python3-packaging set to manually installed. python3-pytest is already the newest version (8.3.5-2). python3-pytest set to manually installed. libgdk-pixbuf2.0-common is already the newest version (2.42.12+dfsg-2). libgdk-pixbuf2.0-common set to manually installed. preview-latex-style is already the newest version (13.2-1). preview-latex-style set to manually installed. libunistring5 is already the newest version (1.3-2). libunistring5 set to manually 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manually installed. libgcc-s1 is already the newest version (14.2.0-19). python3-chardet is already the newest version (5.2.0+dfsg-2). python3-chardet set to manually installed. ucf is already the newest version (3.0051). ucf set to manually installed. libboost-regex1.83.0 is already the newest version (1.83.0-4.2). libboost-regex1.83.0 set to manually installed. libmagickcore-7.q16-10 is already the newest version (8:7.1.1.47+dfsg1-1). libmagickcore-7.q16-10 set to manually installed. libsmartcols1 is already the newest version (2.41-4). python3-mdit-py-plugins is already the newest version (0.4.2-1). python3-mdit-py-plugins set to manually installed. libpaper-utils is already the newest version (2.2.5-0.3+b2). libpaper-utils set to manually installed. libfribidi0 is already the newest version (1.0.16-1). libfribidi0 set to manually installed. libboost-thread-dev is already the newest version (1.83.0.2+b2). libboost-thread-dev set to manually installed. libboost-date-time1.83-dev is already the newest version (1.83.0-4.2). libboost-date-time1.83-dev set to manually installed. libice6 is already the newest version (2:1.1.1-1). libice6 set to manually installed. libubsan1 is already the newest version (14.2.0-19). libubsan1 set to manually installed. libx11-dev is already the newest version (2:1.8.12-1). libx11-dev set to manually installed. texlive-pictures is already the newest version (2024.20250309-1). texlive-pictures set to manually installed. libboost-atomic1.83.0 is already the newest version (1.83.0-4.2). libboost-atomic1.83.0 set to manually installed. libpkgconf3 is already the newest version (1.8.1-4). libpkgconf3 set to manually installed. libboost-serialization1.83.0 is already the newest version (1.83.0-4.2). libboost-serialization1.83.0 set to manually installed. python-babel-localedata is already the newest version (2.17.0-1). python-babel-localedata set to manually installed. python3-roman is already the newest version (5.0-1). python3-roman set to manually installed. uuid-dev is already the newest version (2.41-4). uuid-dev set to manually installed. sensible-utils is already the newest version (0.0.25). sensible-utils set to manually installed. libtinfo6 is already the newest version (6.5+20250216-2). libboost-date-time1.83.0 is already the newest version (1.83.0-4.2). libboost-date-time1.83.0 set to manually installed. libdpkg-perl is already the newest version (1.22.18). libdpkg-perl set to manually installed. libclang-common-19-dev is already the newest version (1:19.1.7-3). libclang-common-19-dev set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.14.1-2). libfile-stripnondeterminism-perl set to manually installed. fontconfig-config is already the newest version (2.15.0-2.3). fontconfig-config set to manually installed. python3-certifi is already the newest version (2025.1.31+ds-1). python3-certifi set to manually installed. libpipeline1 is already the newest version (1.5.8-1). libpipeline1 set to manually installed. libffi-dev is already the newest version (3.4.8-2). libffi-dev set to manually installed. libwebp7 is already the newest version (1.5.0-0.1). libwebp7 set to manually installed. libllvm19 is already the newest version (1:19.1.7-3). libllvm19 set to manually installed. libopenjp2-7 is already the newest version (2.5.3-2). libopenjp2-7 set to manually installed. libicu76 is already the newest version (76.1-3). libicu76 set to manually installed. libboost-program-options1.83-dev is already the newest version (1.83.0-4.2). libboost-program-options1.83-dev set to manually installed. python3-commonmark is already the newest version (0.9.1-8). python3-commonmark set to manually installed. libgio-2.0-dev is already the newest version (2.84.1-2). libgio-2.0-dev set to manually installed. libboost-dev is already the newest version (1.83.0.2+b2). libboost-dev set to manually installed. libpng16-16t64 is already the newest version (1.6.47-1.1). libpng16-16t64 set to manually installed. python3-imagesize is already the newest version (1.4.1-1). python3-imagesize set to manually installed. autopoint is already the newest version (0.23.1-2). autopoint set to manually installed. automake is already the newest version (1:1.17-4). automake set to manually installed. librtmp1 is already the newest version (2.4+20151223.gitfa8646d.1-2+b5). librtmp1 set to manually installed. perl is already the newest version (5.40.1-3). perl set to manually installed. libxcb-shm0 is already the newest version (1.17.0-2+b1). libxcb-shm0 set to manually installed. debianutils is already the newest version (5.22). libboost-numpy1.83-dev is already the newest version (1.83.0-4.2). libboost-numpy1.83-dev set to manually installed. ca-certificates is already the newest version (20250419). ca-certificates set to manually installed. libinchi1.07 is already the newest version (1.07.3+dfsg-1). libinchi1.07 set to manually installed. sysvinit-utils is already the newest version (3.14-4). libgssapi-krb5-2 is already the newest version (1.21.3-5). libgssapi-krb5-2 set to manually installed. libtexlua53-5 is already the newest version (2024.20240313.70630+ds-6). libtexlua53-5 set to manually installed. python3-pygments is already the newest version (2.18.0+dfsg-2). python3-pygments set to manually installed. linux-libc-dev is already the newest version (6.12.25-1). linux-libc-dev set to manually installed. libpdfbox-java is already the newest version (1:1.8.16-5). libpdfbox-java set to manually installed. libcommons-logging-java is already the newest version (1.3.0-1). libcommons-logging-java set to manually installed. libpcre2-8-0 is already the newest version (10.45-1). libselinux1-dev is already the newest version (3.8.1-1). libselinux1-dev set to manually installed. tex-gyre is already the newest version (20180621-6). tex-gyre set to manually installed. architecture-properties is already the newest version (0.2.6). architecture-properties set to manually installed. imagemagick-7.q16 is already the newest version (8:7.1.1.47+dfsg1-1). imagemagick-7.q16 set to manually installed. cpp is already the newest version (4:14.2.0-1). cpp set to manually installed. sphinx-common is already the newest version (8.1.3-5). sphinx-common set to manually installed. libheif-plugin-libde265 is already the newest version (1.19.8-1). libheif-plugin-libde265 set to manually installed. texlive-latex-extra is already the newest version (2024.20250309-2). texlive-latex-extra set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg -r debootsnap-dummy' exec /srv/rebuilderd/tmp/mmdebstrap.MNljpK0jYE (Reading database ... 80345 files and directories currently installed.) Removing debootsnap-dummy (1.0) ... I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg-query --showformat '${binary:Package}=${Version}\n' --show > "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.MNljpK0jYE I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.MNljpK0jYE I: running special hook: upload sources.list /etc/apt/sources.list I: waiting for background processes to finish... I: cleaning package lists and apt cache... I: skipping cleanup/reproducible as requested I: creating tarball... I: done I: removing tempdir /srv/rebuilderd/tmp/mmdebstrap.MNljpK0jYE... 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--chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=rdkit-202503.1 /srv/rebuilderd/tmp/rebuilderd3HfAy5/inputs/rdkit_202503.1-4.dsc I: consider moving your ~/.sbuildrc to /srv/rebuilderd/.config/sbuild/config.pl The Debian buildds switched to the "unshare" backend and sbuild will default to it in the future. To start using "unshare" add this to your `~/.config/sbuild/config.pl`: $chroot_mode = "unshare"; If you want to keep the old "schroot" mode even in the future, add the following to your `~/.config/sbuild/config.pl`: $chroot_mode = "schroot"; $schroot = "schroot"; sbuild (Debian sbuild) 0.89.3 (07 June 2025) on ionos17-amd64 +==============================================================================+ | rdkit 202503.1-4 (amd64) Mon, 28 Jul 2025 09:14:36 +0000 | +==============================================================================+ Package: rdkit Version: 202503.1-4 Source Version: 202503.1-4 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: all I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/diskspace/rebuilderd_tmp/debrebuildfw5Som/debrebuild.tar.WqGAWGOPp5s_ to /srv/rebuilderd/tmp/tmp.sbuild.bMA5fUTBze... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Mon, 28 Jul 2025 09:15:23 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderd3HfAy5/inputs/rdkit_202503.1-4.dsc exists in /srv/rebuilderd/tmp/rebuilderd3HfAy5/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 28 Jul 2025 09:15:26 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: architecture-is-64-bit, architecture-is-little-endian, bison, catch2, cmake, debhelper-compat (= 13), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, libboost-iostreams-dev, libboost-numpy-dev, libboost-program-options-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libcairo2-dev, libcoordgen-dev, libeigen3-dev, libfreetype-dev, libinchi-dev (>= 1.07.1+dfsg-2), libmaeparser-dev, librsvg2-bin, libsqlite3-dev, pandoc, postgresql-server-dev-all, python3-dev, python3-myst-parser, python3-numpy, python3-pandas, python3-pil | python3-imaging, python3-pytest, python3-recommonmark, python3-sphinx, python3-sqlalchemy, rapidjson-dev, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended, build-essential Filtered Build-Depends: architecture-is-64-bit, architecture-is-little-endian, bison, catch2, cmake, debhelper-compat (= 13), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, libboost-iostreams-dev, libboost-numpy-dev, libboost-program-options-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libcairo2-dev, libcoordgen-dev, libeigen3-dev, libfreetype-dev, libinchi-dev (>= 1.07.1+dfsg-2), libmaeparser-dev, librsvg2-bin, libsqlite3-dev, pandoc, postgresql-server-dev-all, python3-dev, python3-myst-parser, python3-numpy, python3-pandas, python3-pil, python3-pytest, python3-recommonmark, python3-sphinx, python3-sqlalchemy, rapidjson-dev, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-dpWh4M/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Mon, 28 Jul 2025 09:15:34 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Mon, 28 Jul 2025 09:15:35 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.38+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.38-1 (2025-07-16) amd64 (x86_64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.18 g++-14_14.2.0-19 gcc-14_14.2.0-19 libc6-dev_2.41-7 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 linux-libc-dev_6.12.25-1 Package versions: adduser_3.150 architecture-properties_0.2.6 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_13.7 base-passwd_3.6.7 bash_5.2.37-2 binutils_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bison_2:3.8.2+dfsg-1+b2 bsdextrautils_2.41-4 bsdutils_1:2.41-4 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20250419 catch2_3.7.1-0.5 clang-19_1:19.1.7-3 cmake_3.31.6-2 cmake-data_3.31.6-2 coreutils_9.7-2 cpp_4:14.2.0-1 cpp-14_14.2.0-19 cpp-14-x86-64-linux-gnu_14.2.0-19 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debianutils_5.22 dh-autoreconf_20 dh-python_6.20250414 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 docutils-common_0.21.2+dfsg-2 doxygen_1.9.8+ds-2.1 dpkg_1.22.18 dpkg-dev_1.22.18 dwz_0.15-1+b1 file_1:5.46-5 findutils_4.10.0-3 flex_2.6.4-8.2+b4 fontconfig_2.15.0-2.3 fontconfig-config_2.15.0-2.3 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-lmodern_2.005-1 g++_4:14.2.0-1 g++-14_14.2.0-19 g++-14-x86-64-linux-gnu_14.2.0-19 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-19 gcc-14-base_14.2.0-19 gcc-14-x86-64-linux-gnu_14.2.0-19 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2 gettext-base_0.23.1-2 girepository-tools_2.84.1-2 grep_3.11-4 groff-base_1.23.0-7 gzip_1.13-1 hicolor-icon-theme_0.18-2 hostname_3.25 icu-devtools_76.1-3 imagemagick_8:7.1.1.47+dfsg1-1 imagemagick-7-common_8:7.1.1.47+dfsg1-1 imagemagick-7.q16_8:7.1.1.47+dfsg1-1 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 latexmk_1:4.86~ds-1 libacl1_2.3.2-2+b1 libapache-pom-java_33-2 libarchive-zip-perl_1.68-1 libarchive13t64_3.7.4-3 libasan8_14.2.0-19 libatomic1_14.2.0-19 libattr1_1:2.5.2-3 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b2 libbinutils_2.44-3 libblas3_3.12.1-2 libblkid-dev_2.41-4 libblkid1_2.41-4 libboost-atomic1.83-dev_1.83.0-4.2 libboost-atomic1.83.0_1.83.0-4.2 libboost-chrono1.83-dev_1.83.0-4.2 libboost-chrono1.83.0t64_1.83.0-4.2 libboost-date-time1.83-dev_1.83.0-4.2 libboost-date-time1.83.0_1.83.0-4.2 libboost-dev_1.83.0.2+b2 libboost-iostreams-dev_1.83.0.2+b2 libboost-iostreams1.83-dev_1.83.0-4.2 libboost-iostreams1.83.0_1.83.0-4.2 libboost-numpy-dev_1.83.0.2+b2 libboost-numpy1.83-dev_1.83.0-4.2 libboost-numpy1.83.0_1.83.0-4.2 libboost-program-options-dev_1.83.0.2+b2 libboost-program-options1.83-dev_1.83.0-4.2 libboost-program-options1.83.0_1.83.0-4.2 libboost-python-dev_1.83.0.2+b2 libboost-python1.83-dev_1.83.0-4.2 libboost-python1.83.0_1.83.0-4.2 libboost-regex-dev_1.83.0.2+b2 libboost-regex1.83-dev_1.83.0-4.2 libboost-regex1.83.0_1.83.0-4.2 libboost-serialization1.83-dev_1.83.0-4.2 libboost-serialization1.83.0_1.83.0-4.2 libboost-system-dev_1.83.0.2+b2 libboost-system1.83-dev_1.83.0-4.2 libboost-system1.83.0_1.83.0-4.2 libboost-thread-dev_1.83.0.2+b2 libboost-thread1.83-dev_1.83.0-4.2 libboost-thread1.83.0_1.83.0-4.2 libboost1.83-dev_1.83.0-4.2 libbrotli-dev_1.1.0-2+b7 libbrotli1_1.1.0-2+b7 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.41-7 libc-dev-bin_2.41-7 libc6_2.41-7 libc6-dev_2.41-7 libcairo-gobject2_1.18.4-1+b1 libcairo-script-interpreter2_1.18.4-1+b1 libcairo2_1.18.4-1+b1 libcairo2-dev_1.18.4-1+b1 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-7 libcatch2-dev_3.7.1-0.5 libcc1-0_14.2.0-19 libclang-common-19-dev_1:19.1.7-3 libclang-cpp19_1:19.1.7-3 libclang1-19_1:19.1.7-3 libcom-err2_1.47.2-1+b1 libcommons-logging-java_1.3.0-1 libcommons-parent-java_56-1 libcoordgen-dev_3.0.2-1+b2 libcoordgen3_3.0.2-1+b2 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libcurl4t64_8.13.0-5 libdatrie1_0.2.13-3+b1 libdav1d7_1.5.1-1 libdb5.3t64_5.3.28+dfsg2-9 libde265-0_1.0.15-1+b3 libdebconfclient0_0.278 libdebhelper-perl_13.24.2 libdeflate0_1.23-2 libdpkg-perl_1.22.18 libedit2_3.1-20250104-1 libeigen3-dev_3.4.0-4 libelf1t64_0.192-4 libexpat1_2.7.1-1 libexpat1-dev_2.7.1-1 libffi-dev_3.4.8-2 libffi8_3.4.8-2 libfftw3-double3_3.3.10-2+b1 libfile-stripnondeterminism-perl_1.14.1-2 libfmt10_10.1.1+ds1-4 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python3-sqlalchemy_2.0.40+ds1-1 python3-typing-extensions_4.13.2-1 python3-urllib3_2.3.0-2 python3-yaml_6.0.2-1+b2 python3.13_3.13.3-2 python3.13-dev_3.13.3-2 python3.13-minimal_3.13.3-2 rapidjson-dev_1.1.0+dfsg2-7.4 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sed_4.9-2 sensible-utils_0.0.25 sgml-base_1.31+nmu1 shared-mime-info_2.4-5+b2 sphinx-common_8.1.3-5 ssl-cert_1.1.3 sysvinit-utils_3.14-4 t1utils_1.41-4 tar_1.35+dfsg-3.1 tex-common_6.19 tex-gyre_20180621-6 texlive-base_2024.20250309-1 texlive-binaries_2024.20240313.70630+ds-6 texlive-fonts-recommended_2024.20250309-1 texlive-latex-base_2024.20250309-1 texlive-latex-extra_2024.20250309-2 texlive-latex-recommended_2024.20250309-1 texlive-pictures_2024.20250309-1 tzdata_2025b-2 ucf_3.0051 util-linux_2.41-4 uuid-dev_2.41-4 x11-common_1:7.7+24 x11proto-dev_2024.1-1 xdg-utils_1.2.1-2 xfonts-encodings_1:1.0.4-2.2 xfonts-utils_1:7.7+7 xml-core_0.19 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Mon, 28 Jul 2025 09:15:35 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rdkit Binary: python3-rdkit, rdkit-doc, rdkit-data, librdkit1t64, librdkit-dev, postgresql-17-rdkit Architecture: any all Version: 202503.1-4 Maintainer: Debichem Team Uploaders: Michael Banck , Andrius Merkys Homepage: http://www.rdkit.org Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/debichem-team/rdkit Vcs-Git: https://salsa.debian.org/debichem-team/rdkit.git Testsuite: autopkgtest Testsuite-Triggers: dpkg-dev, make Build-Depends: architecture-is-64-bit, architecture-is-little-endian, bison, catch2, cmake, debhelper-compat (= 13), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, 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dpkg-source: info: applying postgres_cmakelists_fixes.patch dpkg-source: info: applying disable_pgsql_test.patch dpkg-source: info: applying fix_inchi_linking.patch dpkg-source: info: applying disable_inchi_test.patch dpkg-source: info: applying disable_python_test.patch dpkg-source: info: applying disable_riscv64_timeout_tests.patch dpkg-source: info: applying better_enums.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=6 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh SOURCE_DATE_EPOCH=1745933237 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -A dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202503.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . debian/rules clean pg_buildext checkcontrol dh clean --with python3 --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' find /build/reproducible-path/rdkit-202503.1 -name "*.pyc" | xargs rm -f rm -f -r Projects/DbCLI/testData/bzr/ rdkit/Chem/inchi.py rm -f -r Docs/Book/_build Code/docs rdkit/docs Code/doxygen_sqlite3.db rm -f \ Code/ForceField/MMFF/test_data/MMFF94_dative_min.sdf \ Code/ForceField/MMFF/test_data/MMFF94_dative_min_from_SMILES.sdf \ Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min.sdf \ Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min_from_SMILES.sdf \ Code/ForceField/MMFF/test_data/MMFF94_reference.log \ Code/ForceField/MMFF/test_data/MMFF94s_reference.log \ Code/ForceField/MMFF/test_data/testMMFFForceField.log \ Code/GraphMol/Depictor/test_data/cis_trans_cpp.out.sdf \ Code/GraphMol/Depictor/test_data/collisions.out.sdf \ Code/GraphMol/Depictor/test_data/first_200.out.sdf \ Code/GraphMol/Depictor/test_data/test1.out.sdf \ Code/GraphMol/FileParsers/test_data/blah.sdf \ Code/GraphMol/FileParsers/test_data/cdk2_stereo.sdf \ Code/GraphMol/FileParsers/test_data/outNCI_few.sdf \ Code/GraphMol/FileParsers/test_data/outNCI_few.tdt \ Code/GraphMol/FileParsers/test_data/outNCI_first_200.props.sdf \ Code/GraphMol/FileParsers/test_data/outSmiles.csv \ Code/GraphMol/ForceFieldHelpers/UFF/test_data/Issue62.sdf \ Code/GraphMol/MolAlign/test_data/ref_e2_pyCrippenO3A.sdf \ Code/GraphMol/SLNParse/lex.yysln.cpp \ Code/GraphMol/SLNParse/sln.tab.cpp \ Code/GraphMol/SLNParse/sln.tab.hpp \ Code/GraphMol/SmilesParse/lex.yysmarts.cpp \ Code/GraphMol/SmilesParse/lex.yysmiles.cpp \ Code/GraphMol/SmilesParse/smarts.tab.cpp \ Code/GraphMol/SmilesParse/smarts.tab.hpp \ Code/GraphMol/SmilesParse/smiles.tab.cpp \ Code/GraphMol/SmilesParse/smiles.tab.hpp \ Code/GraphMol/Wrap/test_data/outNCI_few.sdf \ Code/GraphMol/Wrap/test_data/outSmiles.txt \ Code/RDGeneral/versions.cpp \ Docs/Book/Cartridge.rst \ Docs/Book/Install.rst \ Docs/Book/Overview.rst \ rdkit/ML/Data/test_data/testgeneral.dat.pkl \ rdkit/ML/Data/test_data/testquant.qdat.pkl rm -f Code/RDGeneral/versions.h rdkit/sping/tests/testallps.ps dh_auto_clean rm -f -rf /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-* make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary-indep dh binary-indep --with python3 --buildsystem=cmake dh_update_autotools_config -i -O--buildsystem=cmake dh_autoreconf -i -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' dh_auto_configure -- -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_THREADSAFE_SSS=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DRDK_INSTALL_COMIC_FONTS=OFF -DRDK_BUILD_CAIRO_SUPPORT=ON -DRDK_BUILD_PUBCHEMSHAPE_SUPPORT=OFF -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DRDK_BUILD_PGSQL=ON -DRDK_PGSQL_STATIC=OFF -DPostgreSQL_CONFIG=/usr/bin/pg_config -DPostgreSQL_TYPE_INCLUDE_DIR="/usr/include/postgresql/17/server" -DPYTHON_EXECUTABLE=/usr/bin/python3.13 ../ cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_THREADSAFE_SSS=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DRDK_INSTALL_COMIC_FONTS=OFF -DRDK_BUILD_CAIRO_SUPPORT=ON -DRDK_BUILD_PUBCHEMSHAPE_SUPPORT=OFF -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DRDK_BUILD_PGSQL=ON -DRDK_PGSQL_STATIC=OFF -DPostgreSQL_CONFIG=/usr/bin/pg_config -DPostgreSQL_TYPE_INCLUDE_DIR=/usr/include/postgresql/17/server -DPYTHON_EXECUTABLE=/usr/bin/python3.13 ../ .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Inchi: /usr/lib/x86_64-linux-gnu/libinchi.so -- Found Python3: /usr/bin/python3 (found version "3.13.3") found components: Interpreter Development.Module NumPy Python Install directory /usr/lib/python3.13/site-packages nbval not found, disabling the jupyter tests -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found PostgreSQL: /usr/lib/x86_64-linux-gnu/libpq.so (found version "17.4") == Using strict rotor definition -- maeparser include dir set as '/usr/include' -- maeparser libraries set as '/usr/lib/x86_64-linux-gnu/libmaeparser.so' -- coordgen include dir set as /usr/include -- coordgen libraries set as '/usr/lib/x86_64-linux-gnu/libcoordgen.so' -- Found Python3: /usr/bin/python3 (found version "3.13.3") found components: Interpreter -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found Cairo: /usr/include/cairo -- Found Freetype: /usr/lib/x86_64-linux-gnu/libfreetype.so (found version "2.13.3") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server CMake Warning (dev) at Code/PgSQL/rdkit/CMakeLists.txt:303 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at Code/PgSQL/rdkit/CMakeLists.txt:303 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at Code/PgSQL/rdkit/CMakeLists.txt:303 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (2.5s) -- Generating done (1.2s) CMake Warning: Manually-specified variables were not used by the project: Boost_NO_BOOST_CMAKE CATCH_DIR CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED PYTHON_EXECUTABLE -- Build files have been written to: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu for v in $(pg_buildext supported-versions); do \ (mkdir -p Code/PgSQL/rdkit/build-$v && cd Code/PgSQL/rdkit/build-$v && cmake -DPostgreSQL_CONFIG=/usr/lib/postgresql/$v/bin/pg_config -DRDK_PGSQL_STATIC=OFF -DPostgreSQL_TYPE_INCLUDE_DIR="/usr/include/postgresql/$v/server" -DCMAKE_VERBOSE_MAKEFILE=1 -DRDKit_CodeDir=../../../Code ../); \ done -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PostgreSQL: /usr/lib/x86_64-linux-gnu/libpq.so (found version "17.4") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server CMake Warning (dev) at CMakeLists.txt:303 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:303 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:303 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (0.5s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17 make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' dh_auto_build cd obj-x86_64-linux-gnu && make -j6 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202503.1 -B/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o -MF CMakeFiles/RDGeneral.dir/Invariant.cpp.o.d -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Invariant.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o -MF CMakeFiles/hc.dir/hcdriver.c.o.d -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/Cluster/Murtagh/hcdriver.c [ 0%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,--dependency-file=CMakeFiles/hc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o -MF CMakeFiles/RDGeneral.dir/types.cpp.o.d -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/types.cpp [ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/ga/BinaryStringChromosomePolicy.cpp [ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/util/Util.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -MF CMakeFiles/RDGeneral.dir/utils.cpp.o.d -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/utils.cpp [ 1%] Linking CXX static library librdkitCatch.a cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 /usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o /usr/bin/ranlib librdkitCatch.a make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 1%] Built target rdkitCatch [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -MF CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDGeneralExceptions.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o -MF CMakeFiles/RDGeneral.dir/RDLog.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDLog.cpp [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -MF CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o.d -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/LocaleSwitcher.cpp [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -MF CMakeFiles/RDGeneral.dir/versions.cpp.o.d -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/versions.cpp [ 2%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDStreams.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2025.03.1 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 2%] Built target RDStreams [ 2%] Linking CXX shared library ../../lib/libRDKitga.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ga.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2025.03.1 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDGeneral.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2025.03.1 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o [ 2%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o [ 3%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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/build/reproducible-path/rdkit-202503.1/Code/RDGeneral/testDict.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -MF CMakeFiles/testRDValue.dir/testRDValue.cpp.o.d -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/testRDValue.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -MF CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o.d -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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/build/reproducible-path/rdkit-202503.1/Code/DataStructs/BitVect.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o -MF CMakeFiles/RDBoost.dir/Wrap.cpp.o.d -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDBoost/Wrap.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -MF CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o.d -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/testConcurrentQueue.cpp [ 3%] Linking CXX executable testConcurrentQueue cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -MF CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o.d -o CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/catch_dict.cpp [ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/SparseBitVect.cpp [ 4%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -MF CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o.d -o CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/catch_logs.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/ExplicitBitVect.cpp [ 5%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Utils.cpp [ 6%] Linking CXX executable testRDValue cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Catalogs/CatalogEntry.cpp make -f 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 8%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -MF CMakeFiles/rdBase.dir/RDBase.cpp.o.d -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDBoost/Wrap/RDBase.cpp [ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/MaxMinPicker.cpp [ 8%] Linking CXX executable testQuery cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testQuery.dir/link.d CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 8%] Built target testQuery [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/FPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/FPBReader.cpp [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/MultiFPBReader.cpp [ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/HierarchicalClusterPicker.cpp [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/RealValueVect.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/RealValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/RealValueVect.cpp [ 8%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/Clustering.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 8%] Built target Clustering [ 8%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SimDivPickers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2025.03.1 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2025.03.1 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 8%] Built target SimDivPickers make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -MF CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o.d -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/testPickers.cpp [ 9%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2025.03.1 CMakeFiles/DataStructs.dir/BitVect.cpp.o 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -MF CMakeFiles/RDGeometryLib.dir/point.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/point.cpp [ 10%] Linking CXX executable testSimDivPickers cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -MF CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o.d -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp [ 11%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -MF CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/GridUtils.cpp [ 12%] Linking CXX executable testDataStructs cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDataStructs.dir/link.d CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 12%] Built target testDataStructs make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap 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/build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap/MaxMinPicker.cpp [ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/DiscreteValueVect.cpp [ 12%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 12%] Built target rdMetricMatrixCalc make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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-g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/InfoBitRanker.cpp [ 12%] Linking CXX executable pickersTestsCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 [ 12%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script 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-I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -MF CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/SparseIntVect.cpp [ 12%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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-I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/RealValueVect.cpp [ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -MF CMakeFiles/GraphMol.dir/Atom.cpp.o.d -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Atom.cpp [ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp [ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/wrap_SparseBV.cpp [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -MF CMakeFiles/GraphMol.dir/QueryAtom.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryAtom.cpp [ 13%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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/build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/AlignPoints.cpp [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -MF CMakeFiles/GraphMol.dir/QueryBond.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryBond.cpp [ 13%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Bond.cpp make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 13%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -MF CMakeFiles/testTransforms.dir/testTransforms.cpp.o.d -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/testTransforms.cpp [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 15%] Built target geometryTestsCatch make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Numerics /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/testConrec.cpp [ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -MF CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o.d -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/Wrap/rdAlignment.cpp [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/atomic_data.cpp [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK 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object Code/Features/CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Features/CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Features/testFeatures.cpp [ 17%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap 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-Wl,--dependency-file=CMakeFiles/rdGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 17%] Built target rdGeometry make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -MF CMakeFiles/cQuantize.dir/cQuantize.cpp.o.d -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/Data/cQuantize.cpp [ 18%] Linking CXX executable testBaseFeatures cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBaseFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 18%] Built target rdAlignment [ 18%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -MF CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp [ 18%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 [ 18%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2025.03.1 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2025.03.1 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 18%] Built target ChemicalFeatures /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/cQuantize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Canon.cpp [ 18%] Built target cQuantize make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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-c /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/testChemicalFeatures.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -MF CMakeFiles/GraphMol.dir/AtomIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/AtomIterators.cpp [ 18%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp [ 18%] Linking CXX executable testChemicalFeatures cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testChemicalFeatures.dir/link.d CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures ../../lib/libRDKitChemicalFeatures.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 18%] Built target testChemicalFeatures [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/BondIterators.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Aromaticity.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -MF CMakeFiles/GraphMol.dir/Kekulize.cpp.o.d -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Kekulize.cpp [ 18%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 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Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o -MF CMakeFiles/GraphMol.dir/AddHs.cpp.o.d -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/AddHs.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o -MF CMakeFiles/GraphMol.dir/Chirality.cpp.o.d -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Chirality.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RingInfo.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Conformer.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o -MF CMakeFiles/GraphMol.dir/Renumber.cpp.o.d -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Renumber.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -MF CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o.d -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/AdjustQuery.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -MF CMakeFiles/GraphMol.dir/StereoGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StereoGroup.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/new_canon.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -MF CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstanceGroup.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o -MF CMakeFiles/GraphMol.dir/FindStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FindStereo.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -MF CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MonomerInfo.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o cd 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-fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -MF CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/NontetrahedralStereo.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atropisomers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Atropisomers.cpp.o -MF CMakeFiles/GraphMol.dir/Atropisomers.cpp.o.d -o CMakeFiles/GraphMol.dir/Atropisomers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Atropisomers.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -MF CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o.d -o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/WedgeBonds.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolProps.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolProps.cpp.o -MF CMakeFiles/GraphMol.dir/MolProps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolProps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProps.cpp [ 20%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GraphMol.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2025.03.1 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesParse.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/Subgraphs.cpp [ 20%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Trajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2025.03.1 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 20%] Built target Trajectory [ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesParseOps.cpp [ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesWrite.cpp [ 21%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 21%] Built target MolTransforms make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 22%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/GasteigerCharges.cpp [ 22%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GenericGroups.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 22%] Built target GenericGroups make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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-DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -MF CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o.d -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp [ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Mancude.cpp [ 22%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -MF CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o.d -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/SubgraphUtils.cpp [ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/CIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Digraph.cpp [ 22%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmartsWrite.cpp [ 22%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp [ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 23%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp [ 23%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 23%] Built target rdMolTransforms [ 23%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 23%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -MF CMakeFiles/MolInterchange.dir/Parser.cpp.o.d -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Parser.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/CIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Edge.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/CIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Sort.cpp [ 23%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/MolCatalogParams.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Configuration.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 23%] Built target MolCatalog [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 23%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -MF CMakeFiles/SLNParse.dir/SLNParse.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/SLNParse.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ShapeHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2025.03.1 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2025.03.1 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 23%] Built target ShapeHelpers [ 23%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -MF CMakeFiles/MolInterchange.dir/Writer.cpp.o.d -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Writer.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesJSONParsers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesJSONParsers.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesJSONParsers.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesJSONParsers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesJSONParsers.cpp [ 23%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/SLNAttribs.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o cd 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/smarts.tab.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInterchange.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 CMakeFiles/MolInterchange.dir/Parser.cpp.o 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-DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o -MF CMakeFiles/rdqueries.dir/rdqueries.cpp.o.d -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rdqueries.cpp [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/smiles.tab.cpp [ 23%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/lex.yysln.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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24%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp [ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/lex.yysmiles.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2025.03.1 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2025.03.1 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 24%] Built target SLNParse make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 24%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructMatch.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp [ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rdTrajectory.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule5.cpp [ 25%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SmilesParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o CMakeFiles/SmilesParse.dir/SmilesJSONParsers.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 25%] Built target SmilesParse [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule6.cpp [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp [ 26%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 26%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ 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Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -MF CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o.d -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/BFGSOpt.cpp [ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructUtils.cpp [ 26%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 26%] Built target rdqueries [ 26%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/LinearSearch.cpp make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 26%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o [ 27%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 27%] Built target rdtrajectory make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 27%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -MF CMakeFiles/graphmolIterTest.dir/itertest.cpp.o.d -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/itertest.cpp [ 27%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Optimizer.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2025.03.1 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 27%] Built target Optimizer make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol 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graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 27%] Built target graphmolMemTest1 make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/catch_tests.cpp [ 27%] Linking CXX executable smiTest2 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest2.dir/link.d CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 27%] Built target smiTest2 make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog 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CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp [ 28%] Linking CXX executable v2smiTestCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2smiTestCatch.dir/link.txt --verbose=1 [ 28%] Linking CXX executable molbundleTestsCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molbundleTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2smiTestCatch.dir/link.d 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/usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -MF CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o.d -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -MF CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o.d -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp [ 32%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FragCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 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Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 32%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -MF CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o.d -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp [ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdCIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 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-DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -MF CMakeFiles/testSLNParse.dir/test.cpp.o.d -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/test.cpp [ 33%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2025.03.1 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 33%] Built target MolChemicalFeatures make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 33%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -MF CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o.d -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp [ 33%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2025.03.1 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2025.03.1 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so [ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 [ 33%] Built target ReducedGraphs make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 33%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/testOptimizer.cpp [ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/ForceField.cpp [ 34%] Linking CXX executable testOptimizer cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testOptimizer.dir/link.d CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -MF CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o.d -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/querytest.cpp [ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so cd 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/usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 34%] Built target rdSLNParse make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraint.cpp [ 34%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -MF CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp [ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraints.cpp [ 34%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2025.03.1 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 34%] Built target MolAlign make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 34%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o -MF CMakeFiles/FilterCatalog.dir/Filters.cpp.o.d -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Filters.cpp [ 34%] Linking CXX executable moliteratorTestsCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraint.cpp make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Fingerprints.cpp [ 34%] Linking CXX executable testSLNParse cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSLNParse.dir/link.d CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 34%] Built target testSLNParse [ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 35%] Built target graphmolqueryTest [ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/PatternFingerprints.cpp [ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp [ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o cd 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/BondStretch.cpp [ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganFingerprints.cpp [ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && 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Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Nonbonded.cpp [ 35%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp [ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Inversion.cpp [ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp [ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/AtomPairs.cpp [ 35%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatchers.cpp [ 35%] Linking CXX executable smaTest1 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smaTest1.dir/link.d CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 35%] Built target smaTest1 [ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Inversions.cpp [ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp [ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o cd 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Params.cpp [ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp [ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o cd 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp [ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Utils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Utils.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Utils.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Utils.cpp [ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/BondStretch.cpp make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends 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-DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/test1.cpp [ 37%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FilterCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 37%] Built target FilterCatalog make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp [ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/OopBend.cpp make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 37%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK 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Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp [ 37%] Linking CXX executable testReducedGraphs cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReducedGraphs.dir/link.d CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 37%] Built target testReducedGraphs [ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganGenerator.cpp [ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/TorsionAngle.cpp [ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp [ 38%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so 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Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCoordGen_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -MF CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o.d -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/CoordGen/Wrap/rdCoordGen.cpp [ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp [ 38%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o cd 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-Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp [ 39%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/DepictUtils.cpp [ 39%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Fingerprints.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2025.03.1 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 39%] Built target Fingerprints [ 39%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp [ 39%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2025.03.1 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 39%] Built target ForceField [ 39%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o -MF CMakeFiles/Depictor.dir/Templates.cpp.o.d -o CMakeFiles/Depictor.dir/Templates.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Templates.cpp make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 39%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp [ 39%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdCoordGen.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 39%] Built target rdCoordGen make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp [ 40%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Depictor.dir/link.d -Wl,-z,relro -Wl,-z,now 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/INCHI-API /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o -MF CMakeFiles/RDInchiLib.dir/inchi.cpp.o.d -o CMakeFiles/RDInchiLib.dir/inchi.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/INCHI-API/inchi.cpp [ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o cd 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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-DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -MF CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o.d -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/ChemTransforms.cpp [ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMHFPFingerprint.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 42%] Built target RDInchiLib make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/hashfunctions.cpp [ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 42%] Built target rdFingerprintGenerator [ 42%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/MolFragmenter.cpp [ 42%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o cd 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.cpp [ 42%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/normalize.cpp [ 42%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 [ 42%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/MolFragmenterJSONParser.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 42%] Built target ForceFieldHelpers make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o -MF CMakeFiles/rdinchi.dir/pyInchi.cpp.o.d -o CMakeFiles/rdinchi.dir/pyInchi.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/INCHI-API/Wrap/pyInchi.cpp [ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDepictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 42%] Built target rdDepictor make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ForceField /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/catch_tests.cpp [ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 [ 42%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && 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../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2025.03.1 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 42%] Built target MolHash make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Entering directory 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/Wrap/ForceField.cpp [ 42%] Linking CXX executable ForceFieldsCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp [ 43%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so cd 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp [ 43%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E 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Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInteractionFields_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERACTIONFIELDS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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../../../lib/libRDKitChemTransforms.so.1.2025.03.1 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 43%] Built target ChemTransforms make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/TriangleSmooth.cpp [ 44%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/DistViolationContribs.cpp [ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 44%] Built target rdMolHash [ 44%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/ChiralViolationContribs.cpp [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -MF CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/Mol2FileParser.cpp [ 44%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInteractionFields.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInteractionFields.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInteractionFields.so.1 -o ../../../lib/libRDKitMolInteractionFields.so.1.2025.03.1 CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2025.03.1 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 44%] Built target MolInteractionFields make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 44%] Building CXX object Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMIF_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o -MF CMakeFiles/rdMIF.dir/rdMIF.cpp.o.d -o CMakeFiles/rdMIF.dir/rdMIF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/rdMIF.cpp [ 44%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 [ 44%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2025.03.1 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 44%] Built target DistGeometry /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolFileParser.cpp [ 44%] Built target rdForceField make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 44%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp [ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 44%] Built target rdForceFieldHelpers [ 44%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Embedder.cpp [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSGroupWriting.cpp [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolFileStereochem.cpp [ 44%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp [ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMIF.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMIF.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 44%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/testDistGeom.cpp [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SDMolSupplier.cpp [ 45%] Linking CXX executable testDistGeom cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDistGeom.dir/link.d CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/Wrap/DistGeom.cpp [ 45%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeomHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared 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../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 45%] Built target DistGeomHelpers [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SDWriter.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp [ 45%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 45%] Built target DistGeom [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SmilesWriter.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TDTWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/TDTWriter.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/TplFileWriter.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/XYZFileParser.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MaeWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MaeWriter.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SequenceWriters.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -MF CMakeFiles/FileParsers.dir/SVGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SVGParser.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o -MF CMakeFiles/FileParsers.dir/PNGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/PNGParser.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp [ 47%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 47%] Built target FileParsers make -f 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 48%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o [ 48%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o [ 48%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o [ 48%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -MF CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o.d -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/testUFFForceField.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/testChirality.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/molopstest.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -MF CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o.d -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/testPickler.cpp [ 48%] Linking CXX executable testUFFForceField cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testUFFForceField.dir/link.d CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 48%] Built target testUFFForceField make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/testPicklerGlobalSettings.cpp [ 48%] Linking CXX executable testCoordGen cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoordGen.dir/link.d CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 48%] Built target testCoordGen make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -MF CMakeFiles/hanoiTest.dir/hanoitest.cpp.o.d -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/hanoitest.cpp [ 48%] Linking CXX executable graphmoltestPicklerGlobalSetting cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.d CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 48%] Linking CXX executable testMMFFForceField cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 [ 48%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/resMolSupplierTest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceField.dir/link.d CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 48%] Built target testMMFFForceField make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -MF CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o.d -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/testMolBundle.cpp [ 48%] Linking CXX executable hanoiTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hanoiTest.dir/link.d CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 48%] Built target hanoiTest make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o -MF CMakeFiles/testSGroup.dir/testSGroup.cpp.o.d -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/testSGroup.cpp [ 49%] Linking CXX executable graphmoltestChirality cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestChirality.dir/link.d CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 49%] Built target graphmoltestChirality make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 49%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -MF CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o.d -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/test-valgrind.cpp [ 49%] Linking CXX executable graphmoltestPickler cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPickler.dir/link.d CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 49%] Built target graphmoltestPickler make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -MF CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o.d -o CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_organometallics.cpp [ 49%] Linking CXX executable molBundleTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molBundleTest.dir/link.d CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -MF CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o.d -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_sgroups.cpp [ 49%] Linking CXX executable resMolSupplierTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -MF CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o.d -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_adjustquery.cpp [ 50%] Linking CXX executable graphmolOrganometallicsCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolOrganometallicsCatch.dir/link.txt --verbose=1 [ 50%] Linking CXX executable testSGroup cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/canonTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -MF CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o.d -o CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_canon.cpp [ 51%] Linking CXX executable graphmolSGroupCatch cd 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -MF CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o.d -o 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object Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -MF CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o.d -o CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_molops.cpp [ 51%] Linking CXX executable canonTestsCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/canonTestsCatch.dir/link.d CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 51%] Built target canonTestsCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o -MF CMakeFiles/smiTest1.dir/test.cpp.o.d -o CMakeFiles/smiTest1.dir/test.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/test.cpp [ 51%] Linking CXX executable pickleTestsCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickleTestsCatch.dir/link.txt --verbose=1 [ 51%] Linking CXX executable molopsTestsCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Reaction.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 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/build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/catch_tests.cpp [ 51%] Linking CXX executable graphmolMolOpsTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so 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Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -MF CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o.d -o CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp [ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/test1.cpp [ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionWriter.cpp [ 52%] Linking CXX executable smiTest1 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest1.dir/link.d CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 52%] Built target smiTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make 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52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -MF CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o.d -o CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testAtropisomers.cpp [ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp [ 52%] Built target smiTestCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -MF CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o.d -o CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testSquiggleDoubleBonds.cpp [ 53%] Linking CXX executable depictorCatch cd 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cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionUtils.cpp [ 54%] Linking CXX executable testAtropisomers cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAtropisomers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAtropisomers.dir/link.d CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -o testAtropisomers ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Built target testAtropisomers make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -MF CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o.d -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testGeneralFileReader.cpp [ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/MoleculeParser.cpp [ 54%] Linking CXX executable testSquiggleDoubleBonds cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSquiggleDoubleBonds.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSquiggleDoubleBonds.dir/link.d CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -o testSquiggleDoubleBonds ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Built target testSquiggleDoubleBonds make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp [ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionRunner.cpp [ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/PreprocessRxn.cpp [ 54%] Linking CXX executable testGeneralFileReader cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGeneralFileReader.dir/link.d CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Built target testGeneralFileReader make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testMolWriter.cpp [ 54%] Linking CXX executable testMultithreadedMolSupplier cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMultithreadedMolSupplier.dir/link.d CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 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CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF CMakeFiles/testTplParser.dir/testTpls.cpp.o.d -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testTpls.cpp [ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testMol2ToMol.cpp [ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -fpermissive -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp [ 54%] Linking CXX executable testMol2ToMol cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMol2ToMol.dir/link.d CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testSequence.cpp [ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp [ 54%] Linking CXX executable testMolWriter cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolWriter.dir/link.d CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp [ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp [ 54%] Linking CXX executable testSequence cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake "--color=" make[4]: 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/file_parsers_catch.cpp make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -MF CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o.d -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testPropertyLists.cpp [ 54%] Linking CXX executable testExtendedStereoParsing cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testExtendedStereoParsing.dir/link.d 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/usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Built target testExtendedStereoParsing make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp [ 54%] Linking CXX executable fileParsersTest1 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersTest1.dir/link.d CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 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-DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -MF CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o.d -o CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp [ 56%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ChemReactions.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2025.03.1 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o 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../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Built target ChemReactions make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -MF CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o.d -o CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/connectTheDots_catch.cpp [ 56%] Linking CXX executable XYZFileParserCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/XYZFileParserCatchTest.dir/link.d CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Built target XYZFileParserCatchTest make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -MF CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o.d -o CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/v2_suppliers_catch.cpp [ 56%] Linking CXX executable connectTheDotsTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/connectTheDotsTest.dir/link.d CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Built target connectTheDotsTest make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -MF CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o.d -o CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/v2_file_parsers_catch.cpp [ 56%] Linking CXX executable cdxmlParserCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cdxmlParserCatchTest.dir/link.d CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Built target cdxmlParserCatchTest make -f Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -MF CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o.d -o CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/atropisomers_catch.cpp [ 56%] Linking CXX executable testPropertyLists cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testPropertyLists.dir/link.d CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Built target testPropertyLists make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -MF CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o.d -o CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp [ 56%] Linking CXX executable molfileStereoCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molfileStereoCatchTest.dir/link.d CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Built target molfileStereoCatchTest make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/test1.cpp [ 56%] Linking CXX executable v2FileParsersCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2FileParsersCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2FileParsersCatchTest.dir/link.d CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -o v2FileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Built target v2FileParsersCatchTest make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/catch_tests.cpp [ 56%] Linking CXX executable atropisomersCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/atropisomersCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/atropisomersCatch.dir/link.d CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -o atropisomersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Built target atropisomersCatch make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -MF CMakeFiles/testReaction.dir/testReaction.cpp.o.d -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testReaction.cpp [ 57%] Linking CXX executable v2MolSuppliers cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2MolSuppliers.dir/link.d CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -o v2MolSuppliers ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 57%] Built target v2MolSuppliers make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -MF CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o.d -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp [ 57%] Linking CXX executable multithreadedSupplierCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/multithreadedSupplierCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/multithreadedSupplierCatchTest.dir/link.d CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -o multithreadedSupplierCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 57%] Built target multithreadedSupplierCatchTest make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -MF CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o.d -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp [ 58%] Linking CXX executable testReactionFingerprints cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReactionFingerprints.dir/link.d 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/catch_tests.cpp [ 58%] Linking CXX executable testSubstructMatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubstructMatch.dir/link.d CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so 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Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -MF CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o.d -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/testChemTransforms.cpp [ 58%] Linking CXX executable substructTestCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructTestCatch.dir/link.d CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 58%] Built target substructTestCatch make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/catch_tests.cpp [ 58%] Linking CXX executable testEnumeration cd 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Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Pipeline.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -MF CMakeFiles/MolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Pipeline.cpp [ 58%] Linking CXX executable fileParsersCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 59%] Built target filterCatalogTest make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/test1.cpp [ 59%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/MolStandardize.cpp [ 59%] Linking CXX executable testChemTransforms cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testChemTransforms.dir/link.d CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 59%] Built target testChemTransforms make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp [ 59%] Linking CXX executable chemTransformsTestCatch cd 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../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 59%] Built target chemTransformsTestCatch make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make[4]: Entering directory 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-g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/test1.cpp [ 59%] Linking CXX executable rxnTestCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.cpp [ 59%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Metal.cpp [ 59%] Linking CXX executable testMHFPFingerprint cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMHFPFingerprint.dir/link.d CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint 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/usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp [ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 60%] Built target testReaction make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp [ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -MF CMakeFiles/Descriptors.dir/MolSurf.cpp.o.d -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MolSurf.cpp [ 61%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp [ 61%] Linking CXX executable testFingerprints cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFingerprints.dir/link.d CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints 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/usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 61%] Built target testFingerprints [ 61%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Charge.cpp [ 61%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Tautomer.cpp [ 61%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/MolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Fragment.cpp [ 61%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfragcatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 61%] Built target rdfragcatalog [ 62%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp [ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Lipinski.cpp [ 62%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp [ 62%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp [ 62%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/catch_tests.cpp [ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp [ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o cd 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -MF CMakeFiles/Descriptors.dir/Property.cpp.o.d -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Property.cpp [ 62%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp [ 62%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp [ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/catch_tests.cpp [ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -MF CMakeFiles/Descriptors.dir/AtomFeat.cpp.o.d -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/AtomFeat.cpp [ 64%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/catch_tests.cpp [ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o -MF CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o.d -o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/OxidationNumbers.cpp [ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DCLV.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DCLV.cpp.o -MF CMakeFiles/Descriptors.dir/DCLV.cpp.o.d -o CMakeFiles/Descriptors.dir/DCLV.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/DCLV.cpp [ 64%] Linking CXX executable testMolTransforms cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 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../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 64%] Built target testMolTransforms make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp [ 65%] Linking CXX executable molTransformsTestCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTransformsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molTransformsTestCatch.dir/link.d CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -o molTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 65%] Built target molTransformsTestCatch make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp [ 65%] Linking CXX executable fpGenTestCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fpGenTestCatch.dir/link.d CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 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fpGenTestCatch make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -MF CMakeFiles/Descriptors.dir/EEM.cpp.o.d -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/EEM.cpp [ 65%] Linking CXX executable forceFieldHelpersCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/forceFieldHelpersCatch.dir/link.txt --verbose=1 [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -MF CMakeFiles/Descriptors.dir/PBF.cpp.o.d -o CMakeFiles/Descriptors.dir/PBF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/PBF.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/forceFieldHelpersCatch.dir/link.d CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -o forceFieldHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 65%] Built target forceFieldHelpersCatch make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp [ 65%] Linking CXX executable testMMFFForceFieldHelpersMultiThread cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.d CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 65%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -MF CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o.d -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -MF CMakeFiles/Descriptors.dir/PMI.cpp.o.d -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/PMI.cpp [ 65%] Linking CXX executable testCrystalForceField cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCrystalForceField.dir/link.d CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 65%] Built target testCrystalForceField make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/catch_tests.cpp [ 65%] Linking CXX executable testMMFFForceFieldHelpers cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpers.dir/link.d CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 65%] Built target testMMFFForceFieldHelpers make -f 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o cd 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/AUTOCORR3D.cpp [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -MF CMakeFiles/Descriptors.dir/RDF.cpp.o.d -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/RDF.cpp [ 65%] Linking CXX executable testUFFForceFieldHelpers cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testUFFForceFieldHelpers.dir/link.d CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -MF CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o.d -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testMolAlign.cpp [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o -MF CMakeFiles/Descriptors.dir/MORSE.cpp.o.d -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MORSE.cpp [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o cd 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -MF CMakeFiles/Descriptors.dir/GETAWAY.cpp.o.d -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/GETAWAY.cpp [ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/WHIM.cpp [ 66%] Linking CXX executable testMolAlign cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script 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object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/catch_tests.cpp [ 66%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/test1.cpp [ 66%] Linking CXX executable molAlignCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 66%] Built target molAlignCatchTest [ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -MF CMakeFiles/Descriptors.dir/CoulombMat.cpp.o.d -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/CoulombMat.cpp [ 66%] Linking CXX executable testShapeHelpers cd 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp [ 67%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/SubstructMatchCustom.cpp [ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o cd 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-DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.cpp [ 67%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2025.03.1 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 67%] Built target MMPA [ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Deprotect.cpp [ 68%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory/trajectoryTest.cpp [ 68%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp [ 68%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/PositionVariation.cpp [ 68%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Deprotect.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDeprotect.so.1 -o ../../../lib/libRDKitDeprotect.so.1.2025.03.1 CMakeFiles/Deprotect.dir/Deprotect.cpp.o ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 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-DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -MF CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o.d -o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp [ 68%] Linking CXX executable trajectoryTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -MF CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o.d -o CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/molinterchange_catch.cpp [ 68%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/AtomSymbol.cpp [ 68%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/RepeatUnit.cpp [ 70%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalResult.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalResult.cpp [ 70%] Linking CXX executable molInterchangeTest1 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rdmolops.cpp [ 70%] Linking CXX executable molInterchangeCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molInterchangeCatchTest.dir/link.d CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MolOps.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -MF CMakeFiles/molStandardizeTest.dir/test1.cpp.o.d -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/test1.cpp [ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp [ 70%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o 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../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 70%] Built target MolEnumerator make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMol.cpp [ 71%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/ChiralityOps.cpp [ 71%] Linking CXX executable molStandardizeTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o -MF CMakeFiles/molChargeTest.dir/testCharge.cpp.o.d -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/testCharge.cpp make -f 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Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o [ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/testTautomer.cpp [ 72%] Linking CXX executable molChargeTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molChargeTest.dir/link.d CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 72%] Built target molChargeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -MF CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o.d -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/test2.cpp [ 72%] Linking CXX executable 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../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 72%] Built target molValidateTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -MF CMakeFiles/molFragmentTest.dir/testFragment.cpp.o.d -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/testFragment.cpp [ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp [ 72%] Linking CXX executable molStandardizeSmallTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeSmallTest.dir/link.d CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 72%] Built target molStandardizeSmallTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/catch_tests.cpp [ 72%] Linking CXX executable molFragmentTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molFragmentTest.dir/link.d CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 72%] Built target molFragmentTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -MF CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o.d -o CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/testPipeline.cpp make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 73%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp In file included from /usr/include/c++/14/vector:62, from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: In static member function ‘static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]’, inlined from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]’ at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from ‘_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]’ at /usr/include/c++/14/bits/stl_algobase.h:548:42, inlined from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]’ at /usr/include/c++/14/bits/stl_algobase.h:555:31, inlined from ‘_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]’ at /usr/include/c++/14/bits/stl_algobase.h:651:7, inlined from ‘static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:1022:38, inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1488:19, inlined from ‘void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const’ at /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: /usr/include/c++/14/bits/stl_algobase.h:452:30: warning: ‘void* __builtin_memmove(void*, const void*, long unsigned int)’ writing between 5 and 9223372036854775804 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63: In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]’, inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]’ at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:1013:40, inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:1488:19, inlined from ‘void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const’ at /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawShape.cpp [ 73%] Linking CXX executable molTautomerTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molTautomerTest.dir/link.d CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 73%] Built target molTautomerTest [ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawText.cpp [ 73%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdmolops.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 73%] Built target rdmolops [ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp [ 73%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Validate.cpp [ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp [ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp [ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextJS.cpp [ 74%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp [ 74%] Linking CXX executable molStandardizePipelineTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizePipelineTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 74%] Built target molStandardizePipelineTest make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 74%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Charge.cpp [ 75%] Linking CXX executable molStandardizeCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeCatchTest.dir/link.d CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 75%] Built target molStandardizeCatchTest make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/enumerator_catch.cpp [ 75%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp [ 75%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFT.cpp [ 75%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp [ 76%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2025.03.1 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2025.03.1 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so [ 76%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 76%] Built target ScaffoldNetwork make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Pipeline.cpp [ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so cd 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/usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 77%] Built target rdMolEnumerator make -f Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/MarvinParser.cpp [ 79%] Linking CXX executable testAbbreviations cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 [ 79%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolProcessing.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o -MF CMakeFiles/testDescriptors.dir/test.cpp.o.d -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/test.cpp make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd 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[ 80%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o -MF CMakeFiles/testBCUT.dir/testBCUT.cpp.o.d -o CMakeFiles/testBCUT.dir/testBCUT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/testBCUT.cpp [ 80%] Linking CXX executable testAUTOCORR2D cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o -MF CMakeFiles/testPBF.dir/testPBF.cpp.o.d -o CMakeFiles/testPBF.dir/testPBF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/testPBF.cpp [ 80%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -MF CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o.d -o CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/testRDFcustom.cpp [ 80%] Linking CXX executable testBCUT cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/catch_tests.cpp [ 83%] Linking CXX executable descriptorsTestCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 83%] Built target descriptorsTestCatch make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/rxn_test1.cpp [ 83%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 83%] Built target O3AAlign make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -MF CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o.d -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp [ 83%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MarvinParser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 83%] Built target MarvinParser make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/testFMCS_Unit.cpp [ 83%] Linking CXX executable moldraw2DRxnTest1 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DRxnTest1.dir/link.d CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 83%] Built target moldraw2DRxnTest1 make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 84%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp [ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolDescriptors.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 84%] Built target rdMolDescriptors make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 84%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -MF CMakeFiles/FMCStest.dir/testFMCS.cpp.o.d -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Test/testFMCS.cpp [ 84%] Linking CXX executable moldraw2DTest1 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTest1.dir/link.d CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 84%] Built target moldraw2DTest1 make -f 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object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/MMPA_UnitTest.cpp [ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdFMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 84%] Built target rdFMCS make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 84%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp [ 84%] Linking CXX executable testFMCS cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFMCS.dir/link.d CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 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Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -MF CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o.d -o CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/mces_catch.cpp [ 84%] Linking CXX executable testMMPA cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMPA.dir/link.d CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2025.03.1 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 84%] Built target testMMPA make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -MF CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o.d -o CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/mces_cluster_catch.cpp [ 84%] Linking CXX executable FMCStest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -MF CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o.d -o CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp [ 84%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 [ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 84%] Built target rdMolDraw2D make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make 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directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 84%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/catch_tests.cpp [ 84%] Linking CXX executable testRascalCluster cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalCluster.dir/link.d CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/CIPMol.cpp [ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRascalMCES.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/deprotectTest.cpp [ 85%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/CIPLabeler.cpp [ 85%] Linking CXX executable testRascalMCES cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalMCES.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalMCES.dir/link.d CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -o testRascalMCES ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/TextIO.cpp [ 85%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp [ 85%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp [ 85%] Linking CXX executable deprotectTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp [ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp [ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp [ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -MF CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o.d -o CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp [ 90%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 92%] Built target rdGeneralizedSubstruct make -f Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build.make Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap 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CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o.d -o CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap/rdMolProcessing.cpp [ 92%] Linking CXX executable testMolProcessing cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolProcessing.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolProcessing.dir/link.d CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -o testMolProcessing ../../RDGeneral/librdkitCatch.a 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 92%] Built target testMolProcessing make -f Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/build.make Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/adapter.cpp.o -MF CMakeFiles/rdkit.dir/adapter.cpp.o.d -o CMakeFiles/rdkit.dir/adapter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp [ 92%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 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CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecompJSONParsers.cpp [ 92%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/TDTMolSupplier.cpp /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp: In function ‘void* makeAvalonBFP(CROMol, bool, unsigned int)’: /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp:1636:38: warning: unused parameter ‘data’ [-Wunused-parameter] 1636 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, | ~~~~~~~^~~~ /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp:1636:49: warning: unused parameter ‘isQuery’ [-Wunused-parameter] 1636 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, | ~~~~~^~~~~~~ /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp:1637:44: warning: unused parameter ‘bitFlags’ [-Wunused-parameter] 1637 | unsigned int bitFlags) { | ~~~~~~~~~~~~~^~~~~~~~ [ 92%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -MF CMakeFiles/rdchem.dir/Chirality.cpp.o.d -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Chirality.cpp [ 92%] Linking CXX shared module ../../../../rdkit/Chem/rdMolProcessing.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolProcessing.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolProcessing.so CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o ../../../../lib/libRDKitMolProcessing.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDStreams.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 92%] Built target rdMolProcessing [ 92%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT 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-fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o -MF CMakeFiles/rdkit.dir/bfp_op.c.o.d -o CMakeFiles/rdkit.dir/bfp_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bfp_op.c [ 92%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o -MF CMakeFiles/rdkit.dir/cache.c.o.d -o CMakeFiles/rdkit.dir/cache.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/cache.c [ 92%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o cd 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/usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -MF CMakeFiles/rdkit.dir/guc.c.o.d -o CMakeFiles/rdkit.dir/guc.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/guc.c [ 92%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -MF CMakeFiles/rdkit.dir/mol_op.c.o.d -o CMakeFiles/rdkit.dir/mol_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/mol_op.c [ 92%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 [ 92%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 92%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o [ 92%] Built target 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/SmilesMolSupplier.cpp make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 92%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -MF CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o.d -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/cxsmiles_test.cpp [ 92%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o -MF CMakeFiles/rdkit.dir/bfp_gist.c.o.d -o CMakeFiles/rdkit.dir/bfp_gist.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bfp_gist.c [ 92%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o -MF CMakeFiles/rdkit.dir/bfp_gin.c.o.d -o CMakeFiles/rdkit.dir/bfp_gin.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bfp_gin.c [ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT 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Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o -MF CMakeFiles/rdkit.dir/bitstring.c.o.d -o CMakeFiles/rdkit.dir/bitstring.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bitstring.c [ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o -MF CMakeFiles/rdkit.dir/rdkit_io.c.o.d -o CMakeFiles/rdkit.dir/rdkit_io.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/rdkit_io.c [ 93%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/SmilesWriter.cpp make -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 93%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -MF CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o.d -o CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/testMrvToMol.cpp [ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o -MF CMakeFiles/rdkit.dir/rxn_op.c.o.d -o CMakeFiles/rdkit.dir/rxn_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/rxn_op.c [ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o -MF CMakeFiles/rdkit.dir/sfp_op.c.o.d -o CMakeFiles/rdkit.dir/sfp_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/sfp_op.c [ 93%] Linking CXX shared library librdkit.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/rdkit.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o CMakeFiles/rdkit.dir/sfp_op.c.o -L/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/lib /usr/lib/x86_64-linux-gnu/libpq.so ../../../lib/libRDKitRDInchiLib.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libinchi.so ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitMolHash.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/sql /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/sql cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/data /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/data cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/expected make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 93%] Built target rdkit make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/GenericGroups/generic_tests.cpp [ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/SDWriter.cpp make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -MF CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o.d -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp [ 94%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/catch_tests.cpp [ 94%] Linking CXX executable testMrvToMol cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMrvToMol.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMrvToMol.dir/link.d CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -o testMrvToMol ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 94%] Built target testMrvToMol make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -MF CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o.d -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp [ 94%] Linking CXX executable testGenericGroups cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGenericGroups.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGenericGroups.dir/link.d CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 94%] Built target testGenericGroups make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 94%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp [ 94%] Linking CXX executable cxsmilesTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 94%] Built target cxsmilesTest [ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/TDTWriter.cpp [ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/PDBWriter.cpp [ 94%] Linking CXX executable tautomerQueryTestCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tautomerQueryTestCatch.dir/link.d CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 94%] Built target tautomerQueryTestCatch make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 94%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp [ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp [ 94%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 In file included from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: In copy constructor ‘boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]’, inlined from ‘std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]’ at /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: ‘*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px’ may be used uninitialized [-Wmaybe-uninitialized] 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) | ~~^~ /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function ‘std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]’: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: ‘’ declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:18: In copy constructor ‘boost::detail::shared_count::shared_count(const boost::detail::shared_count&)’, inlined from ‘boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]’ at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, inlined from ‘std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]’ at /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: ‘((const boost::detail::shared_count*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)))[1].boost::detail::shared_count::pi_’ may be used uninitialized [-Wmaybe-uninitialized] 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) | ~~^~~ /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function ‘std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]’: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: ‘’ declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdTautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 94%] Built target rdTautomerQuery [ 94%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -MF CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o.d -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp In copy constructor ‘boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]’, inlined from ‘std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]’ at /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: ‘*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px’ may be used uninitialized [-Wmaybe-uninitialized] 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) | ~~^~ /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function ‘std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]’: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: ‘’ declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In copy constructor ‘boost::detail::shared_count::shared_count(const boost::detail::shared_count&)’, inlined from ‘boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]’ at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, inlined from ‘std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]’ at /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: ‘((const boost::detail::shared_count*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)))[1].boost::detail::shared_count::pi_’ may be used uninitialized [-Wmaybe-uninitialized] 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) | ~~^~~ /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function ‘std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]’: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: ‘’ declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp [ 94%] Linking CXX executable testO3AAlign cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testO3AAlign.dir/link.d CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 94%] Built target testO3AAlign make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 95%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.cpp make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd 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/usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 96%] Built target rdmolfiles make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.cpp [ 96%] Linking CXX executable testRGroupDecompInternals cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 96%] Built target gaExample [ 96%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSet.cpp [ 96%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ 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/usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 96%] Built target SubstructLibrary make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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-Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp [ 96%] Linking CXX executable testRGroupDecomp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 96%] Built target rdRGroupDecomposition [ 96%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.cpp [ 96%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp [ 97%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 97%] Built target substructLibraryTest [ 97%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.cpp [ 97%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceRascalSearcher.cpp [ 97%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 97%] Built target substructLibraryCatchTest [ 97%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceHitSet.cpp [ 97%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SearchResults.cpp [ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/MemoryMappedFileReader.cpp [ 98%] Linking CXX shared library ../../../lib/libRDKitSynthonSpaceSearch.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/SynthonSpaceSearch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSynthonSpaceSearch.so.1 -o ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1 ../../../lib/libRDKitSynthonSpaceSearch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 98%] Built target SynthonSpaceSearch make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/depend make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/depend make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o [ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/rascal_search_catch_tests.cpp [ 99%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -MF CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o.d -o CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Wrap/rdSynthonSpaceSearch.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp [ 99%] Linking CXX executable testSynthonSpaceRascalSearch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceRascalSearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSynthonSpaceRascalSearch.dir/link.d CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -o testSynthonSpaceRascalSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 99%] Built target testSynthonSpaceRascalSearch [ 99%] Linking CXX executable testSynthonSpaceSubstructureSearch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.txt --verbose=1 /usr/bin/ld: CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o: in function `CATCH2_INTERNAL_TEST_20()': ./obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/./Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp:334:(.text+0x1866): warning: the use of `tmpnam' is dangerous, better use `mkstemp' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.d CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -o testSynthonSpaceSubstructureSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 99%] Built target testSynthonSpaceSubstructureSearch [ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdSynthonSpaceSearch.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSynthonSpaceSearch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSynthonSpaceSearch.so CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o ../../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 99%] Built target rdSynthonSpaceSearch [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [100%] Built target rdSubstructLibrary make[3]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' for v in $(pg_buildext supported-versions); do \ (cd Code/PgSQL/rdkit/build-$v && make || $(cat ../../../../obj-*/Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/link.txt | sed -e 's#\.\./\.\./#../../../../obj-*/Code/#g')); \ done make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17' /usr/bin/cmake -S/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit -B/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17/CMakeFiles /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17' make -f CMakeFiles/rdkit.dir/build.make CMakeFiles/rdkit.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17' cd /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17 /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17 /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17/CMakeFiles/rdkit.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17' make -f CMakeFiles/rdkit.dir/build.make CMakeFiles/rdkit.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17' [ 7%] Building CXX object CMakeFiles/rdkit.dir/adapter.cpp.o /usr/bin/c++ -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/adapter.cpp.o -MF CMakeFiles/rdkit.dir/adapter.cpp.o.d -o CMakeFiles/rdkit.dir/adapter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp [ 14%] Building C object CMakeFiles/rdkit.dir/bfp_op.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/bfp_op.c.o -MF CMakeFiles/rdkit.dir/bfp_op.c.o.d -o CMakeFiles/rdkit.dir/bfp_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bfp_op.c [ 21%] Building C object CMakeFiles/rdkit.dir/cache.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/cache.c.o -MF CMakeFiles/rdkit.dir/cache.c.o.d -o CMakeFiles/rdkit.dir/cache.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/cache.c [ 28%] Building C object CMakeFiles/rdkit.dir/guc.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/guc.c.o -MF CMakeFiles/rdkit.dir/guc.c.o.d -o CMakeFiles/rdkit.dir/guc.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/guc.c [ 35%] Building C object CMakeFiles/rdkit.dir/low_gist.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/low_gist.c.o -MF CMakeFiles/rdkit.dir/low_gist.c.o.d -o CMakeFiles/rdkit.dir/low_gist.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/low_gist.c [ 42%] Building C object CMakeFiles/rdkit.dir/mol_op.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/mol_op.c.o -MF CMakeFiles/rdkit.dir/mol_op.c.o.d -o CMakeFiles/rdkit.dir/mol_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/mol_op.c [ 50%] Building C object CMakeFiles/rdkit.dir/rdkit_gist.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/rdkit_gist.c.o -MF CMakeFiles/rdkit.dir/rdkit_gist.c.o.d -o CMakeFiles/rdkit.dir/rdkit_gist.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/rdkit_gist.c [ 57%] Building C object CMakeFiles/rdkit.dir/bfp_gist.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/bfp_gist.c.o -MF CMakeFiles/rdkit.dir/bfp_gist.c.o.d -o CMakeFiles/rdkit.dir/bfp_gist.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bfp_gist.c [ 64%] Building C object CMakeFiles/rdkit.dir/bfp_gin.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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-DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/rdkit_io.c.o -MF CMakeFiles/rdkit.dir/rdkit_io.c.o.d -o CMakeFiles/rdkit.dir/rdkit_io.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/rdkit_io.c [ 85%] Building C object CMakeFiles/rdkit.dir/rxn_op.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/rxn_op.c.o -MF CMakeFiles/rdkit.dir/rxn_op.c.o.d -o CMakeFiles/rdkit.dir/rxn_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/rxn_op.c [ 92%] Building C object CMakeFiles/rdkit.dir/sfp_op.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/sfp_op.c.o -MF CMakeFiles/rdkit.dir/sfp_op.c.o.d -o CMakeFiles/rdkit.dir/sfp_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/sfp_op.c [100%] Linking CXX shared library librdkit.so /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 /usr/bin/ld: cannot find -lGeneralizedSubstruct: No such file or directory /usr/bin/ld: cannot find -lMolEnumerator: No such file or directory /usr/bin/ld: cannot find -lTautomerQuery: No such file or directory /usr/bin/ld: cannot find -lMolDraw2D: No such file or directory /usr/bin/ld: cannot find -lMolTransforms: No such file or directory /usr/bin/ld: cannot find -lMolHash: No such file or directory /usr/bin/ld: cannot find -lFMCS: No such file or directory /usr/bin/ld: cannot find -lChemReactions: No such file or directory /usr/bin/ld: cannot find -lChemTransforms: No such file or directory /usr/bin/ld: cannot find -lFileParsers: No such file or directory /usr/bin/ld: cannot find -lSmilesParse: No such file or directory /usr/bin/ld: cannot find -lFingerprints: No such file or directory /usr/bin/ld: cannot find -lSubgraphs: No such file or directory /usr/bin/ld: cannot find -lDescriptors: No such file or directory /usr/bin/ld: cannot find -lPartialCharges: No such file or directory /usr/bin/ld: cannot find -lSubstructMatch: No such file or directory /usr/bin/ld: cannot find -lGraphMol: No such file or directory /usr/bin/ld: cannot find -lEigenSolvers: No such file or directory /usr/bin/ld: cannot find -lDataStructs: No such file or directory /usr/bin/ld: cannot find -lDepictor: No such file or directory /usr/bin/ld: cannot find -lRDGeometryLib: No such file or directory /usr/bin/ld: cannot find -lRDGeneral: No such file or directory /usr/bin/ld: cannot find -lrdkit_base: No such file or directory collect2: error: ld returned 1 exit status /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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Leaving directory '/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17' make[3]: *** [CMakeFiles/Makefile2:90: CMakeFiles/rdkit.dir/all] Error 2 make[3]: Leaving directory '/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17' make[2]: *** [Makefile:139: all] Error 2 make[2]: Leaving directory '/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17' (cd /build/reproducible-path/rdkit-202503.1/Code; doxygen doxygen/doxygen.config) warning: Tag 'TCL_SUBST' at line 213 of file 'doxygen/doxygen.config' has become obsolete. 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To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: argument 'a4wide' for option PAPER_TYPE is not a valid enum value Using the default: a4! warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. Doxygen version used: 1.9.8 Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... 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Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Abbreviations.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Atom.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Atom.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/atomic_data.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/atomic_data.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/AtomIterators.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/AtomIterators.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Atropisomers.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Atropisomers.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Bond.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Bond.h... 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Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule4c.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule4c.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule5.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule5.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule5New.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule5New.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule6.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule6.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rules.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rules.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/SequenceRule.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/SequenceRule.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Sort.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Sort.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/TooManyNodesException.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/TooManyNodesException.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Conformer.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Conformer.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/DepictUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/DepictUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/EmbeddedFrag.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/EmbeddedFrag.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/RDDepictor.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/RDDepictor.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Templates.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Templates.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/TemplateSmiles.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/TemplateSmiles.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Deprotect.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Deprotect.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/AtomFeat.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/AtomFeat.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/AUTOCORR2D.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/AUTOCORR2D.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/AUTOCORR3D.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/AUTOCORR3D.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/CoulombMat.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/CoulombMat.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Crippen.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Crippen.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/DCLV.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/DCLV.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/EEM.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/EEM.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/GETAWAY.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/GETAWAY.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Lipinski.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Lipinski.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MolDescriptors.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MolDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MolDescriptors3D.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MolDescriptors3D.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MolSurf.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MolSurf.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MORSE.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MORSE.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MQN.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MQN.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/OxidationNumbers.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/OxidationNumbers.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/PBF.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/PBF.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/PMI.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/PMI.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Property.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Property.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/RDF.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/RDF.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/RegisterDescriptor.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/RegisterDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/USRDescriptor.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/USRDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/WHIM.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/WHIM.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/details.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/details.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds/DetermineBonds.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds/DetermineBonds.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Embedder.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Embedder.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/CDXMLParser.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/CDXMLParser.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileParsers.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileParsers.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileParserUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileParserUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/GeneralFileReader.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/GeneralFileReader.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MaestroProperties.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MaestroProperties.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolFileStereochem.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolFileStereochem.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSGroupParsing.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSGroupParsing.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSGroupWriting.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSGroupWriting.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.v1API.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.v1API.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolWriters.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolWriters.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/PNGParser.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/PNGParser.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/ProximityBonds.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/ProximityBonds.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SequenceParsers.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SequenceParsers.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SequenceWriters.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SequenceWriters.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterCatalog.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterCatalog.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatchers.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatchers.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Filters.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Filters.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/AtomPairs.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/AtomPairs.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Fingerprints.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Fingerprints.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintUtil.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintUtil.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MACCS.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MACCS.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MHFP.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MHFP.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganFingerprints.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganFingerprints.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganGenerator.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganGenerator.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Composition2N.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Composition2N.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/DebugTrace.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/DebugTrace.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/FMCS.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/FMCS.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Graph.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Graph.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/MatchTable.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/MatchTable.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Seed.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Seed.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/SeedSet.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/SeedSet.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/SubstructMatchCustom.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/SubstructMatchCustom.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/SubstructureCache.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/SubstructureCache.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Target.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Target.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/TargetMatch.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/TargetMatch.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragCatGenerator.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragCatGenerator.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragCatParams.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragCatParams.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/XQMol.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/XQMol.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GenericGroups/GenericGroups.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GenericGroups/GenericGroups.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GraphMol.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GraphMol.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/MarvinDefs.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/MarvinDefs.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/MarvinParser.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/MarvinParser.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/MMPA.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/MMPA.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/AlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/AlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolBundle.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolBundle.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/MolCatalog.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/MolCatalog.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/MolCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/MolCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/AtomSymbol.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/AtomSymbol.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawAnnotation.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawAnnotation.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMol.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMol.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCH.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCH.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawShape.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawShape.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawText.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawText.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFT.h... Parsing file /build/reproducible-path/rdkit-2025/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.h:233: warning: unbalanced grouping commands 03.1/Code/GraphMol/MolDraw2D/DrawTextFT.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextJS.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextJS.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextNotFT.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextNotFT.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Fonts/roboto_regular.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Fonts/roboto_regular.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/StringRect.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/StringRect.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/LinkNode.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerato/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolOps.h:522: warning: unbalanced grouping commands /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolOps.h:782: warning: unbalanced grouping commands r/LinkNode.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/mf.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/mf.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/MolHash.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/MolHash.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/nmmolhash.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/nmmolhash.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/MIFDescriptors.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/MIFDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/details.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/details.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/MolInterchange.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/MolInterchange.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolOps.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolOps.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolPickler.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolPickler.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/MolProcessing.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/MolProcessing.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Charge.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Charge.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Fragment.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Fragment.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Metal.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Metal.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/MolStandardize.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/MolStandardize.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Normalize.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Normalize.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Pipeline.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Pipeline.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Tautomer.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Tautomer.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Validate.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Validate.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/MolTransforms.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/MolTransforms.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MonomerInfo.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MonomerInfo.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/new_canon.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/new_canon.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/GasteigerCharges.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/GasteigerCharges.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/GasteigerParams.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/GasteigerParams.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PeriodicTable.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PeriodicTable.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryAtom.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryAtom.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryBond.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryBond.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/PartitionSet.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/PartitionSet.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalClusterOptions.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalClusterOptions.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalDetails.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalDetails.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalMCES.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalMCES.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalOptions.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalOptions.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalResult.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalResult.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RDKitBase.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RDKitBase.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RDKitQueries.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RDKitQueries.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Resonance.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Resonance.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupData.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupData.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecompJSONParsers.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecompJSONParsers.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupGa.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupGa.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupUtils.h/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ROMol.h:416: warning: unbalanced grouping commands ... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RingInfo.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RingInfo.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Rings.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Rings.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ROMol.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ROMol.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RWMol.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RWMol.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SanitException.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SanitException.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/detail.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/detail.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/SLNAttribs.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/SLNAttribs.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/SLNParse.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/SLNParse.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/SLNParseOps.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/SLNParseOps.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmartsWrite.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmartsWrite.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesJSONParsers.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesJSONParsers.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesParse.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesParse.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesParseOps.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesParseOps.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesWrite.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesWrite.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StereoGroup.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StereoGroup.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/Pattern.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/Pattern.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/ReCharge.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/ReCharge.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/Stereo.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/Stereo.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/StripSmallFragments.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/StripSmallFragments.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/StructChecker.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/StructChecker.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/StructCheckerOptions.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/StructCheckerOptions.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/Tautomer.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/Tautomer.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/Utilites.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker/Utilites.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/Subgraphs.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/Subgraphs.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/SubgraphUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/SubgraphUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstanceGroup.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstanceGroup.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructMatch.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructMatch.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/PatternFactory.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/PatternFactory.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/MemoryMappedFileReader.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/MemoryMappedFileReader.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SearchResults.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SearchResults.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Synthon.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Synthon.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSet.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSet.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceHitSet.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceHitSet.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceRascalSearcher.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceRascalSearcher.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/TautomerQuery.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/TautomerQuery.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory/Snapshot.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory/Snapshot.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory/Trajectory.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory/Trajectory.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Catalogs/Catalog.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Catalogs/Catalog.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Catalogs/CatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Catalogs/CatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Catalogs/CatalogParams.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Catalogs/CatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/base64.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/base64.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/BitOps.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/BitOps.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/BitVect.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/BitVect.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/BitVects.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/BitVects.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/BitVectUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/BitVectUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/DatastructsException.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/DatastructsException.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/DatastructsStreamOps.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/DatastructsStreamOps.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/DiscreteDistMat.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/DiscreteDistMat.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/DiscreteValueVect.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/DiscreteValueVect.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/ExplicitBitVect.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/ExplicitBitVect.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/FPBReader.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/FPBReader.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/MultiFPBReader.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/MultiFPBReader.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/RealValueVect.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/RealValueVect.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/SparseBitVect.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/SparseBitVect.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataStructs/SparseIntVect.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataStructs/SparseIntVect.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Query/AndQuery.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Query/AndQuery.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Query/EqualityQuery.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Query/EqualityQuery.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Query/GreaterEqualQuery.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Query/GreaterEqualQuery.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Query/GreaterQuery.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Query/GreaterQuery.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Query/LessEqualQuery.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Query/LessEqualQuery.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Query/LessQuery.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Query/LessQuery.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Query/NullQueryAlgebra.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Query/NullQueryAlgebra.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Query/OrQuery.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Query/OrQuery.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Query/Query.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Query/Query.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Query/QueryObjects.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Query/QueryObjects.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Query/RangeQuery.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Query/RangeQuery.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Query/SetQuery.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Query/SetQuery.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Query/XOrQuery.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Query/XOrQuery.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/CorrMatGenerator.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/CorrMatGenerator.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/InfoBitRanker.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/InfoBitRanker.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/InfoGainFuncs.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/InfoGainFuncs.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/DistPicker.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/DistPicker.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/HierarchicalClusterPicker.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/HierarchicalClusterPicker.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/LeaderPicker.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/LeaderPicker.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/MaxMinPicker.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/MaxMinPicker.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/BadFileException.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/BadFileException.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/BetterEnums.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/BetterEnums.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/BoostEndInclude.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/BoostEndInclude.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/BoostStartInclude.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/BoostStartInclude.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/ConcurrentQueue.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/ConcurrentQueue.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/ControlCHandler.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/ControlCHandler.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Dict.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Dict.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/enum.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/enum.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Exceptions.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Exceptions.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/export.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/export.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/FileParseException.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/FileParseException.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/hanoiSort.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/hanoiSort.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Invariant.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Invariant.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/LocaleSwitcher.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/LocaleSwitcher.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Ranking.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Ranking.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDAny.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDAny.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDConfig.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDConfig.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDExportMacros.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDExportMacros.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDLog.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDLog.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDProps.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDProps.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDThreads.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDThreads.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDValue-doublemagic.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDValue-doublemagic.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDValue-taggedunion.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDValue-taggedunion.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDValue.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDValue.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/StreamOps.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/StreamOps.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/types.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/types.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/utils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/utils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/versions.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/versions.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDBoost/boost_numpy.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDBoost/boost_numpy.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDBoost/import_array.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDBoost/import_array.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDBoost/pyint_api.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDBoost/pyint_api.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDBoost/PySequenceHolder.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDBoost/PySequenceHolder.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDBoost/python.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDBoost/python.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/RDBoost/python_streambuf.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/RDBoost/python_streambuf.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DistGeom/BoundsMatrix.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DistGeom/BoundsMatrix.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DistGeom/ChiralSet.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DistGeom/ChiralSet.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DistGeom/ChiralViolationContribs.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DistGeom/ChiralViolationContribs.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DistGeom/DistGeomUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DistGeom/DistGeomUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DistGeom/DistViolationContribs.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DistGeom/DistViolationContribs.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DistGeom/FourthDimContribs.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DistGeom/FourthDimContribs.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/DistGeom/TriangleSmooth.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/DistGeom/TriangleSmooth.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraints.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraints.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/Contrib.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/Contrib.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraints.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraints.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/ForceField.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/ForceField.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/AngleBend.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/AngleBend.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/BondStretch.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/BondStretch.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Contribs.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Contribs.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Nonbonded.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Nonbonded.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/OopBend.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/OopBend.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Params.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/StretchBend.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/StretchBend.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/AngleBend.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/AngleBend.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/BondStretch.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/BondStretch.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Contribs.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Contribs.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Inversion.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Inversion.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Inversions.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Inversions.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Nonbonded.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Nonbonded.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Params.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Utils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Utils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/AlignPoints.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/AlignPoints.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Numerics/Conrec.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Numerics/Conrec.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Numerics/Matrix.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Numerics/Matrix.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/BFGSOpt.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/BFGSOpt.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Numerics/SquareMatrix.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Numerics/SquareMatrix.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Numerics/SymmMatrix.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Numerics/SymmMatrix.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Numerics/Vector.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Numerics/Vector.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Geometry/Grid3D.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Geometry/Grid3D.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Geometry/GridUtils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Geometry/GridUtils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Geometry/point.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Geometry/point.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform2D.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform2D.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform3D.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform3D.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Geometry/UniformGrid3D.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Geometry/UniformGrid3D.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Geometry/UniformRealValueGrid3D.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Geometry/UniformRealValueGrid3D.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Geometry/Utils.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/Geometry/Utils.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/Features/Feature.h.../build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h:62: warning: documented symbol 'for experimental torsion angle RDKit::DGeomHelpers::preferences' was not declared or defined. /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolOps.h:1222: warning: documented symbol 'modifies molecule in RDKit::MolOps::place' was not declared or defined. /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolOps.h:1238: warning: documented symbol 'modifies molecule in RDKit::MolOps::place' was not declared or defined. /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Pipeline.h:90: warning: documented symbol 'enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::PipelineStatus' was not declared or defined. /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupUtils.h:94: warning: no matching file member found for RDKIT_RGROUPDECOMPOSITION_EXPORT std::string RDKit::toJSON(const std::map &rgr, const std::string &prefix="") Possible candidates: 'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupRow &rgr, const std::string &prefix="")' at line 82 of file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupUtils.h 'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupRows &rgr, const std::string &prefix="")' at line 86 of file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupUtils.h 'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupColumn &rgr, const std::string &prefix="")' at line 90 of file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupUtils.h /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' Parsing file /build/reproducible-path/rdkit-202503.1/Code/Features/Feature.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/ChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/ChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/FreeChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/FreeChemicalFeature.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Associating documentation with modules... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Computing module relations... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file Catalog.h... Generating code for file CatalogEntry.h... Generating code for file CatalogParams.h... Generating code for file ChemicalFeature.h... Generating code for file FreeChemicalFeature.h... Generating code for file MetricFuncs.h... Generating code for file MetricMatrixCalc.h... Generating code for file base64.h... Generating code for file BitOps.h... Generating code for file BitVect.h... Generating code for file BitVects.h... Generating code for file BitVectUtils.h... Generating code for file DatastructsException.h... Generating code for file DatastructsStreamOps.h... Generating code for file DiscreteDistMat.h... Generating code for file DiscreteValueVect.h... Generating code for file ExplicitBitVect.h... Generating code for file FPBReader.h... Generating code for file MultiFPBReader.h... Generating code for file RealValueVect.h... Generating code for file SparseBitVect.h... Generating code for file SparseIntVect.h... Generating code for file BoundsMatrix.h... Generating code for file ChiralSet.h... Generating code for file ChiralViolationContribs.h... Generating code for file DistGeomUtils.h... Generating code for file DistViolationContribs.h... Generating code for file FourthDimContribs.h... Generating code for file TriangleSmooth.h... Generating code for file Feature.h... Generating code for file AngleConstraints.h... Generating code for file Contrib.h... Generating code for file DistanceConstraints.h... Generating code for file ForceField.h... Generating code for file OopBend.h... Generating code for file StretchBend.h... Generating code for file AngleBend.h... Generating code for file AngleBend.h... Generating code for file AngleConstraint.h... Generating code for file AngleConstraint.h... Generating code for file AngleConstraint.h... Generating code for file BondStretch.h... Generating code for file BondStretch.h... Generating code for file Contribs.h... Generating code for file Contribs.h... Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... Generating code for file Inversion.h... Generating code for file Inversions.h... Generating code for file Nonbonded.h... Generating code for file Nonbonded.h... Generating code for file Params.h... Generating code for file Params.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngle.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionConstraint.h... Generating code for file Utils.h... Generating code for file Utils.h... Generating code for file Grid3D.h... Generating code for file GridUtils.h... Generating code for file point.h... Generating code for file Transform.h... Generating code for file Transform2D.h... Generating code for file Transform3D.h... Generating code for file UniformGrid3D.h... Generating code for file UniformRealValueGrid3D.h... Generating code for file Abbreviations.h... Generating code for file Atom.h... Generating code for file atomic_data.h... Generating code for file AtomIterators.h... Generating code for file Atropisomers.h... Generating code for file Bond.h... Generating code for file BondIterators.h... Generating code for file Canon.h... Generating code for file CartesianProduct.h... Generating code for file Enumerate.h... Generating code for file EnumerateBase.h... Generating code for file EnumerateTypes.h... Generating code for file EnumerationPickler.h... Generating code for file EnumerationStrategyBase.h... Generating code for file EvenSamplePairs.h... Generating code for file RandomSample.h... Generating code for file RandomSampleAllBBs.h... Generating code for file PreprocessRxn.h... Generating code for file Reaction.h... Generating code for file ReactionFingerprints.h... Generating code for file ReactionParser.h... Generating code for file ReactionPickler.h... Generating code for file ReactionRunner.h... Generating code for file ReactionUtils.h... Generating code for file SanitizeRxn.h... Generating code for file ChemTransforms.h... Generating code for file MolFragmenter.h... Generating code for file MolFragmenterJSONParser.h... Generating code for file Chirality.h... Generating code for file CIPLabeler.h... Generating code for file CIPMol.h... Generating code for file AtropisomerBond.h... Generating code for file Configuration.h... Generating code for file Sp2Bond.h... Generating code for file Tetrahedral.h... Generating code for file Descriptor.h... Generating code for file Digraph.h... Generating code for file Edge.h... Generating code for file Mancude.h... Generating code for file Node.h... Generating code for file Priority.h... Generating code for file Pairlist.h... Generating code for file Rule1a.h... Generating code for file Rule1b.h... Generating code for file Rule2.h... Generating code for file Rule3.h... Generating code for file Rule4a.h... Generating code for file Rule4b.h... Generating code for file Rule4c.h... Generating code for file Rule5.h... Generating code for file Rule5New.h... Generating code for file Rule6.h... Generating code for file Rules.h... Generating code for file SequenceRule.h... Generating code for file Sort.h... Generating code for file TooManyNodesException.h... Generating code for file Conformer.h... Generating code for file DepictUtils.h... Generating code for file EmbeddedFrag.h... Generating code for file RDDepictor.h... Generating code for file Templates.h... Generating code for file TemplateSmiles.h... Generating code for file Deprotect.h... Generating code for file AtomFeat.h... Generating code for file AUTOCORR2D.h... Generating code for file AUTOCORR3D.h... Generating code for file BCUT.h... Generating code for file ConnectivityDescriptors.h... Generating code for file CoulombMat.h... Generating code for file Crippen.h... Generating code for file Data3Ddescriptors.h... Generating code for file DCLV.h... Generating code for file EEM.h... Generating code for file GETAWAY.h... Generating code for file Lipinski.h... Generating code for file MolData3Ddescriptors.h... Generating code for file MolDescriptors.h... Generating code for file MolDescriptors3D.h... Generating code for file MolSurf.h... Generating code for file MORSE.h... Generating code for file MQN.h... Generating code for file OxidationNumbers.h... Generating code for file PBF.h... Generating code for file PMI.h... Generating code for file Property.h... Generating code for file RDF.h... Generating code for file RegisterDescriptor.h... Generating code for file USRDescriptor.h... Generating code for file WHIM.h... Generating code for file details.h... Generating code for file details.h... Generating code for file DetermineBonds.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Embedder.h... Generating code for file CDXMLParser.h... Generating code for file FileParsers.h... Generating code for file FileParserUtils.h... Generating code for file FileWriters.h... Generating code for file GeneralFileReader.h... Generating code for file MaestroProperties.h... Generating code for file MolFileStereochem.h... Generating code for file MolSGroupParsing.h... Generating code for file MolSGroupWriting.h... Generating code for file MolSupplier.h... Generating code for file MolSupplier.v1API.h... Generating code for file MolWriters.h... Generating code for file MultithreadedMolSupplier.h... Generating code for file MultithreadedSDMolSupplier.h... Generating code for file MultithreadedSmilesMolSupplier.h... Generating code for file PNGParser.h... Generating code for file ProximityBonds.h... Generating code for file SequenceParsers.h... Generating code for file SequenceWriters.h... Generating code for file FilterCatalog.h... Generating code for file FilterCatalogEntry.h... Generating code for file FilterMatcherBase.h... Generating code for file FilterMatchers.h... Generating code for file Filters.h... Generating code for file FunctionalGroupHierarchy.h... Generating code for file AtomPairGenerator.h... Generating code for file AtomPairs.h... Generating code for file FingerprintGenerator.h... Generating code for file Fingerprints.h... Generating code for file FingerprintUtil.h... Generating code for file MACCS.h... Generating code for file MHFP.h... Generating code for file MorganFingerprints.h... Generating code for file MorganGenerator.h... Generating code for file RDKitFPGenerator.h... Generating code for file TopologicalTorsionGenerator.h... Generating code for file Composition2N.h... Generating code for file DebugTrace.h... Generating code for file DuplicatedSeedCache.h... Generating code for file FMCS.h... Generating code for file Graph.h... Generating code for file MatchTable.h... Generating code for file MaximumCommonSubgraph.h... Generating code for file Seed.h... Generating code for file SeedSet.h... Generating code for file SubstructMatchCustom.h... Generating code for file SubstructureCache.h... Generating code for file Target.h... Generating code for file TargetMatch.h... Generating code for file TorsionAngleContribs.h... Generating code for file TorsionAngleM6.h... Generating code for file TorsionPreferences.h... Generating code for file FFConvenience.h... Generating code for file MMFF.h... Generating code for file AtomTyper.h... Generating code for file AtomTyper.h... Generating code for file Builder.h... Generating code for file Builder.h... Generating code for file UFF.h... Generating code for file FragCatalogEntry.h... Generating code for file FragCatalogUtils.h... Generating code for file FragCatGenerator.h... Generating code for file FragCatParams.h... Generating code for file FragFPGenerator.h... Generating code for file XQMol.h... Generating code for file GenericGroups.h... Generating code for file GraphMol.h... Generating code for file MarvinDefs.h... Generating code for file MarvinParser.h... Generating code for file MMPA.h... Generating code for file AlignMolecules.h... Generating code for file O3AAlignMolecules.h... Generating code for file MolBundle.h... Generating code for file MolCatalog.h... Generating code for file MolCatalogEntry.h... Generating code for file MolCatalogParams.h... Generating code for file FeatureParser.h... Generating code for file MolChemicalFeature.h... Generating code for file MolChemicalFeatureDef.h... Generating code for file MolChemicalFeatureFactory.h... Generating code for file AtomSymbol.h... Generating code for file DrawAnnotation.h... Generating code for file DrawMol.h... Generating code for file DrawMolMCH.h... Generating code for file DrawMolMCHCircleAndLine.h... Generating code for file DrawMolMCHLasso.h... Generating code for file DrawShape.h... Generating code for file DrawText.h... Generating code for file DrawTextCairo.h... Generating code for file DrawTextFT.h... Generating code for file DrawTextFTCairo.h... Generating code for file DrawTextFTJS.h... Generating code for file DrawTextFTSVG.h... Generating code for file DrawTextJS.h... Generating code for file DrawTextNotFT.h... Generating code for file DrawTextSVG.h... Generating code for file roboto_regular.h... Generating code for file telex_regular.h... Generating code for file MolDraw2D.h... Generating code for file MolDraw2DCairo.h... Generating code for file MolDraw2DDetails.h... Generating code for file MolDraw2DHelpers.h... Generating code for file MolDraw2DJS.h... Generating code for file MolDraw2DSVG.h... Generating code for file MolDraw2DUtils.h... Generating code for file MolDraw2Dwx.h... Generating code for file DrawTextFTQt.h... Generating code for file DrawTextQt.h... Generating code for file MolDraw2DQt.h... Generating code for file StringRect.h... Generating code for file LinkNode.h... Generating code for file MolEnumerator.h... Generating code for file mf.h... Generating code for file MolHash.h... Generating code for file nmmolhash.h... Generating code for file MIFDescriptors.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... Generating code for file MolProcessing.h... Generating code for file AcidBaseCatalogEntry.h... Generating code for file AcidBaseCatalogParams.h... Generating code for file AcidBaseCatalogUtils.h... Generating code for file Charge.h... Generating code for file Fragment.h... Generating code for file FragmentCatalogEntry.h... Generating code for file FragmentCatalogParams.h... Generating code for file FragmentCatalogUtils.h... Generating code for file Metal.h... Generating code for file MolStandardize.h... Generating code for file Normalize.h... Generating code for file Pipeline.h... Generating code for file Tautomer.h... Generating code for file Tautomer.h... Generating code for file TautomerCatalogEntry.h... Generating code for file TautomerCatalogParams.h... Generating code for file TautomerCatalogUtils.h... Generating code for file TransformCatalogEntry.h... Generating code for file TransformCatalogParams.h... Generating code for file TransformCatalogUtils.h... Generating code for file Validate.h... Generating code for file MolTransforms.h... Generating code for file MonomerInfo.h... Generating code for file new_canon.h... Generating code for file GasteigerCharges.h... Generating code for file GasteigerParams.h... Generating code for file PeriodicTable.h... Generating code for file QueryAtom.h... Generating code for file QueryBond.h... Generating code for file QueryOps.h... Generating code for file PartitionSet.h... Generating code for file RascalClusterOptions.h... Generating code for file RascalDetails.h... Generating code for file RascalMCES.h... Generating code for file RascalOptions.h... Generating code for file RascalResult.h... Generating code for file RDKitBase.h... Generating code for file RDKitQueries.h... Generating code for file ReducedGraphs.h... Generating code for file Resonance.h... Generating code for file RGroupCore.h... Generating code for file RGroupData.h... Generating code for file RGroupDecomp.h... Generating code for file RGroupDecompData.h... Generating code for file RGroupDecompJSONParsers.h... Generating code for file RGroupDecompParams.h... Generating code for file RGroupFingerprintScore.h... Generating code for file RGroupGa.h... Generating code for file RGroupMatch.h... Generating code for file RGroupScore.h... Generating code for file RGroupUtils.h... Generating code for file RingInfo.h... Generating code for file Rings.h... Generating code for file ROMol.h... Generating code for file RWMol.h... Generating code for file SanitException.h... Generating code for file detail.h... Generating code for file ScaffoldNetwork.h... Generating code for file ShapeEncoder.h... Generating code for file ShapeUtils.h... Generating code for file SLNAttribs.h... Generating code for file SLNParse.h... Generating code for file SLNParseOps.h... Generating code for file CanonicalizeStereoGroups.h... Generating code for file SmartsWrite.h... Generating code for file SmilesJSONParsers.h... Generating code for file SmilesParse.h... Generating code for file SmilesParseOps.h... Generating code for file SmilesWrite.h... Generating code for file StereoGroup.h... Generating code for file Pattern.h... Generating code for file ReCharge.h... Generating code for file Stereo.h... Generating code for file StripSmallFragments.h... Generating code for file StructChecker.h... Generating code for file StructCheckerOptions.h... Generating code for file Utilites.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... Generating code for file SubstanceGroup.h... Generating code for file SubstructMatch.h... Generating code for file SubstructUtils.h... Generating code for file PatternFactory.h... Generating code for file SubstructLibrary.h... Generating code for file SubstructLibrarySerialization.h... Generating code for file MemoryMappedFileReader.h... Generating code for file SearchResults.h... Generating code for file Synthon.h... Generating code for file SynthonSet.h... Generating code for file SynthonSpace.h... Generating code for file SynthonSpaceFingerprintSearcher.h... Generating code for file SynthonSpaceHitSet.h... Generating code for file SynthonSpaceRascalSearcher.h... Generating code for file SynthonSpaceSearch_details.h... Generating code for file SynthonSpaceSearcher.h... Generating code for file SynthonSpaceSubstructureSearcher.h... Generating code for file TautomerQuery.h... Generating code for file Snapshot.h... Generating code for file Trajectory.h... Generating code for file CorrMatGenerator.h... Generating code for file InfoBitRanker.h... Generating code for file InfoGainFuncs.h... Generating code for file AlignPoints.h... Generating code for file Conrec.h... Generating code for file PowerEigenSolver.h... Generating code for file Matrix.h... Generating code for file BFGSOpt.h... Generating code for file SquareMatrix.h... Generating code for file SymmMatrix.h... Generating code for file Vector.h... Generating code for file AndQuery.h... Generating code for file EqualityQuery.h... Generating code for file GreaterEqualQuery.h... Generating code for file GreaterQuery.h... Generating code for file LessEqualQuery.h... Generating code for file LessQuery.h... Generating code for file NullQueryAlgebra.h... Generating code for file OrQuery.h... Generating code for file Query.h... Generating code for file QueryObjects.h... Generating code for file RangeQuery.h... Generating code for file SetQuery.h... Generating code for file XOrQuery.h... Generating code for file boost_numpy.h... Generating code for file import_array.h... Generating code for file pyint_api.h... Generating code for file PySequenceHolder.h... Generating code for file python.h... Generating code for file python_streambuf.h... Generating code for file BadFileException.h... Generating code for file BetterEnums.h/build/reproducible-path/rdkit-202503.1/Code/DataStructs/BitOps.h:188: warning: found at different nesting level (7) than expected (4) /build/reproducible-path/rdkit-202503.1/Code/DataStructs/BitOps.h:189: warning: end of comment block while expecting command ... Generating code for file BoostEndInclude.h... Generating code for file BoostStartInclude.h... Generating code for file ConcurrentQueue.h... Generating code for file ControlCHandler.h... Generating code for file Dict.h... Generating code for file enum.h... Generating code for file Exceptions.h... Generating code for file export.h... Generating code for file FileParseException.h... Generating code for file hanoiSort.h... Generating code for file Invariant.h... Generating code for file LocaleSwitcher.h... Generating code for file Ranking.h... Generating code for file RDAny.h... Generating code for file RDConfig.h... Generating code for file RDExportMacros.h... Generating code for file RDLog.h... Generating code for file RDProps.h... Generating code for file RDThreads.h... Generating code for file RDValue-doublemagic.h... Generating code for file RDValue-taggedunion.h... Generating code for file RDValue.h... Generating code for file StreamOps.h... Generating code for file types.h... Generating code for file utils.h... Generating code for file versions.h... Generating code for file DistPicker.h... Generating code for file HierarchicalClusterPicker.h... Generating code for file LeaderPicker.h... Generating code for file MaxMinPicker.h... Generating file documentation... Generating docs for file Catalog.h... Generating docs for file CatalogEntry.h... Generating docs for file CatalogParams.h... Generating docs for file ChemicalFeature.h... Generating docs for file FreeChemicalFeature.h... Generating docs for file MetricFuncs.h... Generating docs for file MetricMatrixCalc.h... Generating docs for file base64.h... Generating docs for file BitOps.h... Generating docs for file BitVect.h... Generating docs for file BitVects.h... Generating docs for file BitVectUtils.h... Generating docs for file DatastructsException.h... Generating docs for file DatastructsStreamOps.h... Generating docs for file DiscreteDistMat.h... Generating docs for file DiscreteValueVect.h... Generating docs for file ExplicitBitVect.h... Generating docs for file FPBReader.h... Generating docs for file MultiFPBReader.h... Generating docs for file RealValueVect.h... Generating docs for file SparseBitVect.h... Generating docs for file SparseIntVect.h... Generating docs for file BoundsMatrix.h... Generating docs for file ChiralSet.h... Generating docs for file ChiralViolationContribs.h... Generating docs for file DistGeomUtils.h... Generating docs for file DistViolationContribs.h... Generating docs for file FourthDimContribs.h... Generating docs for file TriangleSmooth.h... Generating docs for file Feature.h... Generating docs for file AngleConstraints.h... Generating docs for file Contrib.h... Generating docs for file DistanceConstraints.h... Generating docs for file ForceField.h... Generating docs for file OopBend.h... Generating docs for file StretchBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleConstraint.h... Generating docs for file AngleConstraint.h... Generating docs for file AngleConstraint.h... Generating docs for file BondStretch.h... Generating docs for file BondStretch.h... Generating docs for file Contribs.h... Generating docs for file Contribs.h... Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... Generating docs for file Inversion.h... Generating docs for file Inversions.h... Generating docs for file Nonbonded.h... Generating docs for file Nonbonded.h... Generating docs for file Params.h... 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Generating docs for file DrawTextFT./build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' h... Generating docs for file DrawTextFTCairo.h... Generating docs for file DrawTextFTJS.h... Generating docs for file DrawTextFTSVG.h... Generating docs for file DrawTextJS.h... Generating docs for file DrawTextNotFT.h... Generating docs for file DrawTextSVG.h... Generating docs for file roboto_regular.h... Generating docs for file telex_regular.h... Generating docs for file MolDraw2D.h... Generating docs for file MolDraw2DCairo.h... Generating docs for file MolDraw2DDetails.h... Generating docs for file MolDraw2DHelpers.h... Generating docs for file MolDraw2DJS.h... Generating docs for file MolDraw2DSVG.h... Generating docs for file MolDraw2DUtils.h... Generating docs for file MolDraw2Dwx.h... 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Generating docs for file Hierarc/build/reproducible-path/rdkit-202503.1/Code/DistGeom/DistGeomUtils.h:93: warning: The following parameter of DistGeom::constructForceField(const BoundsMatrix &mmat, RDGeom::PointPtrVect &positions, const VECT_CHIRALSET &csets, double weightChiral=1.0, double weightFourthDim=0.1, std::map< std::pair< int, int >, double > *extraWeights=nullptr, double basinSizeTol=5.0, boost::dynamic_bitset<> *fixedPts=nullptr) is not documented: parameter 'fixedPts' /build/reproducible-path/rdkit-202503.1/Code/DistGeom/ChiralViolationContribs.h:53: warning: argument 'cset' of command @param is not found in the argument list of DistGeom::ChiralViolationContribs::ChiralViolationContribs(ForceFields::ForceField *owner) /build/reproducible-path/rdkit-202503.1/Code/DistGeom/ChiralViolationContribs.h:53: warning: argument 'weight' of command @param is not found in the argument list of DistGeom::ChiralViolationContribs::ChiralViolationContribs(ForceFields::ForceField *owner) /build/reproducible-path/rdkit-202503.1/Code/DistGeom/FourthDimContribs.h:36: warning: argument 'idx' of command @param is not found in the argument list of DistGeom::FourthDimContribs::FourthDimContribs(ForceFields::ForceField *owner) /build/reproducible-path/rdkit-202503.1/Code/DistGeom/FourthDimContribs.h:36: warning: argument 'weight' of command @param is not found in the argument list of DistGeom::FourthDimContribs::FourthDimContribs(ForceFields::ForceField *owner) /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraint.h:24: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraint.h:24: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraint.h:24: warning: The following parameters of ForceFields::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraints.h:65: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraints.h:65: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraints.h:65: warning: The following parameters of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraints.h:53: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraints.h:53: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraints.h:53: warning: The following parameters of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraints.h:61: warning: argument 'forceConst' of command @param is not found in the argument list of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, bool relative, double minLen, double maxLen, double forceConstant) /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraints.h:61: warning: The following parameter of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, bool relative, double minLen, double maxLen, double forceConstant) is not documented: parameter 'forceConstant' /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraints.h:50: warning: argument 'forceConst' of command @param is not found in the argument list of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, double minLen, double maxLen, double forceConstant) /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraints.h:50: warning: The following parameter of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, double minLen, double maxLen, double forceConstant) is not documented: parameter 'forceConstant' /build/reproducible-path/rdkit-202503.1/Code/ForceField/ForceField.h:159: warning: argument 'snapshotFreq' of command @param is not found in the argument list of ForceFields::ForceField::minimize(unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) /build/reproducible-path/rdkit-202503.1/Code/ForceField/ForceField.h:159: warning: argument 'snapshotVect' of command @param is not found in the argument list of ForceFields::ForceField::minimize(unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) /build/reproducible-path/rdkit-202503.1/Code/ForceField/ForceField.h:144: warning: The following parameters of ForceFields::ForceField::minimize(unsigned int snapshotFreq, RDKit::SnapshotVect *snapshotVect, unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) are not documented: parameter 'snapshotFreq' parameter 'snapshotVect' /build/reproducible-path/rdkit-202503.1/Code/ForceField/PositionConstraint.h:25: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst) hicalClusterPicker.h... Generating docs for file LeaderPicker.h... Generating docs for file MaxMinPicker.h... Generating page documentation... Generating docs for page deprecated... Generating group documentation... Generating class documentation... Generating docs for compound BitVect... Generating docs for compound Data3Ddescriptors... Generating docs for compound DatastructsException... Generating docs for compound ExplicitBitVect... Generating docs for compound IndexErrorException... Generating docs for compound KeyErrorException... Generating docs for compound MolData3Ddescriptors... Generating docs for compound PySequenceHolder... Generating docs for compound SparseBitVect... Generating docs for compound ValueErrorException... Generating concept documentation... Generating module documentation... Generating namespace documentation... Generating docs for namespace better_enums Generating docs for compound better_enums::_eat_assign... 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Generating docs for compound DistGeom::FourthDimContribsParams... Generating docs for namespace ForceFields Generating docs for compound ForceFields::AngleConstraintContrib... Generating docs for compound ForceFields::AngleConstraintContribs... Generating docs for compound ForceFields::AngleConstraintContribsParams... Generating docs for compound ForceFields::DistanceConstraintContrib... Generating docs for compound ForceFields::DistanceConstraintContribs... Generating docs for compound ForceFields::DistanceConstraintContribsParams... Generating docs for compound ForceFields::ForceField... Generating docs for compound ForceFields::ForceFieldContrib... Generating docs for compound ForceFields::PositionConstraintContrib... Generating docs for compound ForceFields::TorsionConstraintContrib... Generating docs for namespace ForceFields::CrystalFF Generating docs for compound ForceFields::CrystalFF::CrystalFFDetails... Generating docs for compound ForceFields::CrystalFF::ExpTorsionAngle... Generating docs for compound ForceFields::CrystalFF::TorsionAngleContribM6... Generating docs for compound ForceFields::CrystalFF::TorsionAngleContribs... Generating docs for compound ForceFields::CrystalFF::TorsionAngleContribsParams... Generating docs for namesp/build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/AngleBend.h:28: warning: argument 'angleType' of command @param is not found in the argument list of ForceFields::MMFF::AngleBendContrib::addTerm(unsigned int idx1, unsigned int idx2, unsigned int idx3, const MMFFAngle *mmffAngleParams, const MMFFProp *mmffPropParamsCentralAtom) /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/AngleBend.h:28: warning: The following parameters of ForceFields::MMFF::AngleBendContrib::addTerm(unsigned int idx1, unsigned int idx2, unsigned int idx3, const MMFFAngle *mmffAngleParams, const MMFFProp *mmffPropParamsCentralAtom) are not documented: parameter 'mmffAngleParams' parameter 'mmffPropParamsCentralAtom' /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/BondStretch.h:27: warning: argument 'bondType' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::addTerm(const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/BondStretch.h:27: warning: argument 'end1Params' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::addTerm(const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/BondStretch.h:27: warning: argument 'end2Params' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::addTerm(const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/BondStretch.h:27: warning: The following parameter of ForceFields::MMFF::BondStretchContrib::addTerm(const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) is not documented: parameter 'mmffBondParams' /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Nonbonded.h:45: warning: argument 'idx1' of command @param is not found in the argument list of ForceFields::MMFF::EleContrib::EleContrib(ForceField *owner) /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Nonbonded.h:45: warning: argument 'idx2' of command @param is not found in the argument list of ForceFields::MMFF::EleContrib::EleContrib(ForceField *owner) /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/OopBend.h:26: warning: The following parameter of ForceFields::MMFF::OopBendContrib::addTerm(unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const MMFFOop *mmffOopParams) is not documented: parameter 'mmffOopParams' /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/StretchBend.h:32: warning: argument 'angleType' of command @param is not found in the argument list of ForceFields::MMFF::StretchBendContrib::addTerm(const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2) /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/StretchBend.h:32: warning: The following parameters of ForceFields::MMFF::StretchBendContrib::addTerm(const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2) are not documented: parameter 'mmffStbnParams' parameter 'mmffAngleParams' parameter 'mmffBondParams1' parameter 'mmffBondParams2' /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/TorsionAngle.h:33: warning: argument 'torsionType' of command @param is not found in the argument list of ForceFields::MMFF::TorsionAngleContrib::addTerm(unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const MMFFTor *mmffTorParams) /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/TorsionAngle.h:33: warning: The following parameter of ForceFields::MMFF::TorsionAngleContrib::addTerm(unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const MMFFTor *mmffTorParams) is not documented: parameter 'mmffTorParams' /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Inversion.h:27: warning: The following parameter of ForceFields::UFF::InversionContrib::InversionContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, int at2AtomicNum, bool isCBoundToO, double oobForceScalingFactor=1.0) is not documented: parameter 'oobForceScalingFactor' ace ForceFields::MMFF Generating docs for compound ForceFields::MMFF::AngleBendContrib... Generating docs for compound ForceFields::MMFF::BondStretchContrib... Generating docs for compound ForceFields::MMFF::EleContrib... Generating docs for compound ForceFields::MMFF::MMFFAngle... Generating docs for compound ForceFields::MMFF::MMFFAngleCollection... Generating docs for compound ForceFields::MMFF::MMFFAromCollection... Generating docs for compound ForceFields::MMFF::MMFFBndkCollection... Generating docs for compound ForceFields::MMFF::MMFFBond... Generating docs for compound ForceFields::MMFF::MMFFBondCollection... Generating docs for compound ForceFields::MMFF::MMFFChg... Generating docs for compound ForceFields::MMFF::MMFFChgCollection... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEle... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEleCollection... Generating docs for compound ForceFields::MMFF::MMFFDef... Generating docs for compound ForceFields::MMFF::MMFFDefCollection... Generating docs for compound ForceFields::MMFF::MMFFDfsbCollection... Generating docs for compound ForceFields::MMFF::MMFFHerschbachLaurie... Generating docs for compound ForceFields::MMFF::MMFFHerschbachLaurieCollection... Generating docs for compound ForceFields::MMFF::MMFFOop... Generating docs for compound ForceFields::MMFF::MMFFOopCollection... Generating docs for compound ForceFields::MMFF::MMFFPBCI... Generating docs for compound ForceFields::MMFF::MMFFPBCICollection... Generating docs for compound ForceFields::MMFF::MMFFProp... Generating docs for compound ForceFields::MMFF::MMFFPropCollection... Generating docs for compound ForceFields::MMFF::MMFFStbn... Generating docs for compound ForceFields::MMFF::MMFFStbnCollection... Generating docs for compound ForceFields::MMFF::MMFFTor... Generating docs for compound ForceFields::MMFF::MMFFTorCollection... Generating docs for compound ForceFields::MMFF::MMFFVdW... Generating docs for compound ForceFields::MMFF::MMFFVdWCollection... Generating docs for compound ForceFields::MMFF::MMFFVdWRijstarEps... Generating docs for compound ForceFields::MMFF::OopBendContrib... Generating docs for compound ForceFields::MMFF::StretchBendContrib... Generating docs for compound ForceFields::MMFF::TorsionAngleContrib... Generating docs for compound ForceFields::MMFF::VdWContrib... Generating docs for namespace ForceFields::MMFF::Utils Generating docs for namespace ForceFields::UFF Generating docs for compound ForceFields::UFF::AngleBendContrib... Generating docs for compound ForceFields::UFF::AtomicParams... Generating docs for compound ForceFields::UFF::BondStretchContrib... Generating docs for compound ForceFields::UFF::InversionContrib... Generating docs for compound ForceFields::UFF::InversionContribs... Generating docs for compound ForceFields::UFF::InversionContribsParams... Generating docs for compound ForceFields::UFF::ParamCollection... Generating docs for compound ForceFields::UFF::TorsionAngleContrib... Generating docs for compound ForceFields::UFF::UFFAngle... Generating docs for compound ForceFields::UFF::UFFBond... Generating docs for compound ForceFields::UFF::UFFInv... Generating docs for compound ForceFields::UFF::UFFTor... Generating docs for compound ForceFields::UFF::UFFVdW... Generating docs for compound ForceFields::UFF::vdWContrib... Generating docs for namespace ForceFields::UFF::Params Generating docs for namespace ForceFields::UFF::Utils Generating docs for namespace Invar Generating docs for compound Invar::Invariant... Generating docs for namespace MolTransforms Generating docs for namespace Queries Generating docs for compound Queries::AndQuery... Generating docs for compound Queries::EqualityQuery... Generating docs for compound Queries::GreaterEqualQuery... Generating docs for compound Queries::GreaterQuery... Generating docs for compound Queries::Int2Type... Generating docs for compound Queries::LessEqualQuery... Generating docs for compound Queries::LessQuery... Generating docs for compound Queries::OrQuery... Generating docs for compound Queries::Q/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/RDDepictor.h:392: warning: argument 'refPattern' of command @param is not found in the argument list of RDDepict::generateDepictionMatching3DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=nullptr, bool acceptFailure=false, bool forceRDKit=false) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/RDDepictor.h:392: warning: The following parameter of RDDepict::generateDepictionMatching3DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=nullptr, bool acceptFailure=false, bool forceRDKit=false) is not documented: parameter 'referencePattern' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstanceGroup.h:276: warning: The following parameter of RDKit::addSubstanceGroup(ROMol &mol, SubstanceGroup sgroup) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SequenceParsers.h:105: warning: argument 'seq' of command @param is not found in the argument list of RDKit::HELMToMol(const char *helm, bool sanitize=true) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SequenceParsers.h:105: warning: The following parameter of RDKit::HELMToMol(const char *helm, bool sanitize=true) is not documented: parameter 'helm' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Fingerprints.h:69: warning: The following parameter of RDKit::LayeredFingerprintMol(const ROMol &mol, unsigned int layerFlags=0xFFFFFFFF, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool branchedPaths=true, const std::vector< std::uint32_t > *fromAtoms=nullptr) is not documented: parameter 'fromAtoms' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesWrite.h:224: warning: argument 'doRandom' of command @param is not found in the argument list of RDKit::MolFragmentToSmiles(const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h:35: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h:35: warning: The following parameter of RDKit::MolToMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h:110: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h:110: warning: The following parameter of RDKit::MolToMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/MarvinParser.h:180: warning: The following parameters of RDKit::MolToMrvBlock(const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool prettyPrint=false) are not documented: parameter 'mol' parameter 'includeStereo' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/MarvinParser.h:155: warning: The following parameters of RDKit::MolToMrvFile(const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool prettyPrint=false) are not documented: parameter 'mol' parameter 'fName' parameter 'includeStereo' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h:226: warning: argument 'fName' of command @param is not found in the argument list of RDKit::MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h:226: warning: The following parameter of RDKit::MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) is not documented: parameter 'fname' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h:96: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToV2KMolBlock(const ROMol &mol, const MolWriterParams ¶ms=MolWriterParams(), int confId=-1) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h:96: warning: The following parameter of RDKit::MolToV2KMolBlock(const ROMol &mol, const MolWriterParams ¶ms=MolWriterParams(), int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h:65: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToV3KMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h:65: warning: The following parameter of RDKit::MolToV3KMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h:141: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToV3KMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileWriters.h:141: warning: The following parameter of RDKit::MolToV3KMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Fingerprints.h:120: warning: The following parameter of RDKit::PatternFingerprintMol(const ROMol &mol, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool tautomericFingerprint=false) is not documented: parameter 'tautomericFingerprint' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Fingerprints.h:27: warning: argument 'useBondOrders' of command @param is not found in the argument list of RDKit::RDKFingerprintMol(const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t > > *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int > > > *bitInfo=nullptr) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Fingerprints.h:27: warning: The following parameters of RDKit::RDKFingerprintMol(const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t > > *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int > > > *bitInfo=nullptr) are not documented: parameter 'useBondOrder' parameter 'bitInfo' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionRunner.h:94: warning: The following parameter of RDKit::reduceProductToSideChains(const ROMOL_SPTR &product, bool addDummyAtoms=true) is not documented: parameter 'product' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/ChemTransforms.h:114: warning: argument 'useChirality' of command @param is not found in the argument list of RDKit::replaceCore(const ROMol &mol, const ROMol &core, const MatchVectType &matchVect, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionRunner.h:66: warning: argument 'reactantTemplateIdx' of command @param is not found in the argument list of RDKit::run_Reactant(const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionRunner.h:66: warning: The following parameters of RDKit::run_Reactant(const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx) are not documented: parameter 'rxn' parameter 'reactantIdx' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructMatch.h:84: warning: argument 'matchParams' of command @param is not found in the argument list of RDKit::SubstructMatch(const ROMol &mol, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructMatch.h:84: warning: The following parameter of RDKit::SubstructMatch(const ROMol &mol, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructMatch.h:97: warning: argument 'matchParams' of command @param is not found in the argument list of RDKit::SubstructMatch(ResonanceMolSupplier &resMolSuppl, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructMatch.h:97: warning: The following parameter of RDKit::SubstructMatch(ResonanceMolSupplier &resMolSuppl, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructMatch.h:152: warning: The following parameter of RDKit::SubstructMatch(T1 &mol, const T2 &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000, int numThreads=1) is not documented: parameter 'numThreads' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::AtomEnvironment::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const=0 are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Reaction.h:219: warning: argument 'maxProducts' of command @param is not found in the argument list of RDKit::ChemicalReaction::runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Reaction.h:219: warning: The following parameter of RDKit::ChemicalReaction::runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const is not documented: parameter 'numProducts' uery... Generating docs for compound Queries::RangeQuery... Generating docs for compound Queries::SetQuery... Generating docs for compound Queries::XOrQuery... Generating docs for namespace Rankers Generating docs for namespace RDCatalog Generating docs for compound RDCatalog::Catalog... Generating docs for compound RDCatalog::CatalogEntry... Generating docs for compound RDCatalog::CatalogParams... Generating docs for compound RDCatalog::HierarchCatalog... Generating docs for nested compound RDCatalog::HierarchCatalog::vertex_entry_t... Generating docs for namespace RDDataManip Generating docs for compound RDDataManip::MetricMatrixCalc... Generating docs for namespace RDDepict Generating docs for compound RDDepict::Compute2DCoordParameters... Generating docs for compound RDDepict::ConstrainedDepictionParams... Generating docs for compound RDDepict::CoordinateTemplates... Generating docs for compound RDDepict::DepictException... Generating docs for compound RDDepict::EmbeddedAtom... Generating docs for compound RDDepict::EmbeddedFrag... Generating docs for compound RDDepict::gtIIPair... Generating docs for namespace RDFeatures Generating docs for compound RDFeatures::ExplicitFeature... Generating docs for compound RDFeatures::ImplicitFeature... Generating docs for namespace RDGeom Generating docs for compound RDGeom::Grid3D... Generating docs for compound RDGeom::GridException... Generating docs for compound RDGeom::Point... Generating docs for compound RDGeom::Point2D... Generating docs for compound RDGeom::Point3D... Generating docs for compound RDGeom::PointND... Generating docs for compound RDGeom::Transform2D... Generating docs for compound RDGeom::Transform3D... Generating docs for compound RDGeom::UniformGrid3D... Generating docs for compound RDGeom::UniformRealValueGrid3D... Generating docs for namespace RDInfoTheory Generating docs for compound RDInfoTheory::BitCorrMatGenerator... Generating docs for compound RDInfoTheory::InfoBitRanker... Generating docs for namespace RDKit Generating docs for compound RDKit::AdditionalOutput... Generating docs for compound RDKit::AromaticAtomIterator_... Generating docs for compound RDKit::Atom... Generating docs for compound RDKit::AtomEnvironment... Generating docs for compound RDKit::AtomEnvironmentGenerator... Generating docs for compound RDKit::atomicData... Generating docs for compound RDKit::AtomInvariantsGenerator... Generating docs for compound RDKit::AtomIterator_... Generating docs for compound RDKit::AtomKekulizeException... Generating docs for compound RDKit::AtomMonomerInfo... Generating docs for compound RDKit::AtomPDBResidueInfo... Generating docs for compound RDKit::AtomRingQuery... Generating docs for compound RDKit::AtomSanitizeException... Generating docs for compound RDKit::AtomValenceException... Generating docs for compound RDKit::BadFileException... Generating docs for compound RDKit::Bond... Generating docs for compound RDKit::BondInvariantsGenerator... Generating docs for compound RDKit::BondIterator_... Generating docs for compound RDKit::CachedMolHolder... Generating docs for compound RDKit::CachedSmilesMolHolder... Generating docs for compound RDKit::CachedTrustedSmilesMolHolder... Generating docs for compound RDKit::CartesianProduct... Generating docs for compound RDKit::CartesianProductStrategy... Generating docs for compound RDKit::charptr_functor... Generating docs for compound RDKit::ChemicalReaction... Generating docs for compound RDKit::ChemicalReactionException... Generating docs for compound RDKit::ChemicalReactionParserException... Generating docs for compound RDKit::Conformer... Generating docs for compound RDKit::ConformerException... Generating docs for compound RDKit::ConstBondIterator_... Generating docs for compound RDKit::ControlCHandler... Generating docs for compound RDKit::CustomPropHandler... Generating docs for compound RDKit::CXXAtomIterator... Generating docs for nested compound RDKit::CXXAtomIterator::CXXAtomIter... Generating docs for compound RDKit::CXXBondIterator... Generating docs for nested compound RDKit::CXXBondItera/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatchers.h:430: warning: argument 'matches' of command @param is not found in the argument list of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 is not documented: parameter 'matchVect' tor::CXXBondIter... Generating docs for compound RDKit::DataStructsExplicitBitVecPropHandler... Generating docs for compound RDKit::Dict... Generating docs for nested compound RDKit::Dict::Pair... Generating docs for compound RDKit::DiscreteDistMat... Generating docs for compound RDKit::DiscreteValueVect... Generating docs for compound RDKit::DrawColour... Generating docs for compound RDKit::EnumerateLibrary... Generating docs for compound RDKit::EnumerateLibraryBase... Generating docs for compound RDKit::EnumerationParams... Generating docs for compound RDKit::EnumerationStrategyBase... Generating docs for compound RDKit::EnumerationStrategyException... Generating docs for compound RDKit::EvenSamplePairsStrategy... Generating docs for compound RDKit::ExclusionList... Generating docs for compound RDKit::FeatureFileParseException... Generating docs for compound RDKit::FileParseException... Generating docs for compound RDKit::FilterCatalog... Generating docs for compound RDKit::FilterCatalogEntry... Generating docs for compound RDKit::FilterCatalogParams... Generating docs for compound RDKit::FilterData_t... Generating docs for compound RDKit::FilterHierarchyMatcher... Generating docs for compound RDKit::FilterMatch... Generating docs for compound RDKit::FilterMatcherBase... Generating docs for compound RDKit::FilterProperty_t... Generating docs for compound RDKit::FingerprintArguments... Generating docs for compound RDKit::FingerprintFuncArguments... Generating docs for compound RDKit::FingerprintGenerator... Generating docs for compound RDKit::FingerprintVarianceScoreData... Generating docs for compound RDKit::FixedMolSizeMolBundle... Generating docs for compound RDKit::FPBReader... Generating docs for compound RDKit::FPHolderBase... Generating docs for compound RDKit::FragCatalogEntry... Generating docs for compound RDKit::FragCatGenerator... Generating docs for compound RDKit::FragCatParams... Generating docs for compound RDKit::FragFPGenerator... Generating docs for compound RDKit::GaResult... Generating docs for compound RDKit::GasteigerParams... Generating docs for compound RDKit::HasPropQuery... Generating docs for compound RDKit::HasPropWithValueQuery... Generating docs for compound RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >... Generating docs for compound RDKit::HasPropWithValueQuery< TargetPtr, std::string >... Generating docs for compound RDKit::HasPropWithValueQueryBase... Generating docs for compound RDKit::HeteroatomIterator_... Generating docs for compound RDKit::KekulizeException... Generating docs for compound RDKit::KeyFromPropHolder... Generating docs for compound RDKit::KeyHolderBase... Generating docs for compound RDKit::larger_of... Generating docs for compound RDKit::ltDouble... Generating docs for compound RDKit::MarvinArrow... Generating docs for compound RDKit::MarvinAtom... Generating docs for compound RDKit::MarvinAttachmentPoint... Generating docs for compound RDKit::MarvinBond... Generating docs for compound RDKit::MarvinBondStereo... Generating docs for compound RDKit::MarvinCondition... Generating docs for compound RDKit::MarvinDataSgroup... Generating docs for compound RDKit::MarvinGenericSgroup... Generating docs for compound RDKit::MarvinMol... Generating docs for compound RDKit::MarvinMolBase... Generating docs for compound RDKit::MarvinMonomerSgroup... Generating docs for compound RDKit::MarvinMulticenterSgroup... Generating docs for compound RDKit::MarvinMultipleSgroup... Generating docs for compound RDKit::MarvinPlus... Generating docs for compound RDKit::MarvinReaction... Generating docs for compound RDKit::MarvinRectangle... Generating docs for compound RDKit::MarvinSruCoModSgroup... Generating docs for compound RDKit::MarvinStereoGroup... Generating docs for compound RDKit::MarvinSuperatomSgroup... Generating docs for compound RDKit::MarvinSuperatomSgroupExpanded... Generating docs for compound RDKit::MarvinWriterException... Generating docs for compound RDKit::MatchingAtomIterator_... Generating docs for compound RDKit::MCSAtomCompareParameters... Generating docs /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.h:71: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecule has multiple @param documentation sections /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.h:71: warning: The following parameter of RDKit::MolDraw2D::drawMolecule(const ROMol &mol, const std::string &legend, const std::vector< int > *highlight_atoms, const std::vector< int > *highlight_bonds, const std::map< int, DrawColour > *highlight_atom_map=nullptr, const std::map< int, DrawColour > *highlight_bond_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1) is not documented: parameter 'highlight_bonds' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: argument 'highlight_atom_map' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: argument 'highlight_bond_map' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: argument 'confId' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecules has multiple @param documentation sections /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: The following parameters of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) are not documented: parameter 'highlight_bonds' parameter 'highlight_atom_maps' parameter 'highlight_bond_maps' parameter 'confIds' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Resonance.h:114: warning: argument 'numThreads' of command @param is not found in the argument list of RDKit::ResonanceMolSupplier::ResonanceMolSupplier(ROMol &mol, unsigned int flags=0, unsigned int maxStructs=1000) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatchers.h:336: warning: argument 'matches' of command @param is not found in the argument list of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' for compound RDKit::MCSBondCompareParameters... Generating docs for compound RDKit::MCSParameters... Generating docs for compound RDKit::MCSProgressData... Generating docs for compound RDKit::MCSResult... Generating docs for compound RDKit::MolBundle... Generating docs for compound RDKit::MolCatalogEntry... Generating docs for compound RDKit::MolCatalogParams... Generating docs for compound RDKit::MolChemicalFeature... Generating docs for compound RDKit::MolChemicalFeatureDef... Generating docs for compound RDKit::MolChemicalFeatureFactory... Generating docs for compound RDKit::MolDraw2D... Generating docs for compound RDKit::MolDraw2DCairo... Generating docs for compound RDKit::MolDraw2DJS... Generating docs for compound RDKit::MolDraw2DQt... Generating docs for compound RDKit::MolDraw2DSVG... Generating docs for compound RDKit::MolDraw2Dwx... Generating docs for compound RDKit::MolDrawOptions... Generating docs for compound RDKit::MolHolder... Generating docs for compound RDKit::MolHolderBase... Generating docs for compound RDKit::MolMatchFinalCheckFunctor... Generating docs for compound RDKit::MolPickler... Generating docs for compound RDKit::MolPicklerException... Generating docs for compound RDKit::MolSanitizeException... Generating docs for compound RDKit::MolWriter... Generating docs for compound RDKit::MolWriterParams... Generating docs for compound RDKit::MolzipParams... Generating docs for compound RDKit::MrvWriterParams... Generating docs for compound RDKit::MultiFPBReader... Generating docs for compound RDKit::PairHolder... Generating docs for compound RDKit::PatternHolder... Generating docs for compound RDKit::PDBWriter... Generating docs for compound RDKit::PeriodicTable... Generating docs for compound RDKit::QueryAtom... Generating docs for compound RDKit::QueryAtomIterator_... Generating docs for compound RDKit::QueryBond... Generating docs for compound RDKit::RandomSampleAllBBsStrategy... Generating docs for compound RDKit::RandomSampleStrategy... Generating docs for compound RDKit::RCore... Generating docs for compound RDKit::RDAny... Generating docs for compound RDKit::RDProps... Generating docs for compound RDKit::RDValue... Generating docs for compound RDKit::ReactionFingerprintParams... Generating docs for compound RDKit::ReactionPickler... Generating docs for compound RDKit::ReactionPicklerException... Generating docs for compound RDKit::RealValueVect... Generating docs for compound RDKit::RecursiveStructureQuery... Generating docs for compound RDKit::ResonanceMolSupplier... Generating docs for compound RDKit::ResonanceMolSupplierCallback... Generating docs for compound RDKit::RGroupData... Generating docs for compound RDKit::RGroupDecompData... Generating docs for nested compound RDKit::RGroupDecompData::UsedLabels... Generating docs for compound RDKit::RGroupDecomposition... Generating docs for compound RDKit::RGroupDecompositionChromosome... Generating docs for compound RDKit::RGroupDecompositionParameters... Generating docs for compound RDKit::RGroupDecompositionProcessResult... Generating docs for compound RDKit::RGroupGa... Generating docs for compound RDKit::RGroupMatch... Generating docs for compound RDKit::RGroupScorer... Generating docs for compound RDKit::RigorousEnhancedStereoException... Generating docs for compound RDKit::RingInfo... Generating docs for compound RDKit::ROMol... Generating docs for compound RDKit::RWMol... Generating docs for compound RDKit::RxnSanitizeException... Generating docs for compound RDKit::SDWriter... Generating docs for compound RDKit::SLNParseException... Generating docs for compound RDKit::SmartsMatcher... Generating docs for compound RDKit::SmilesWriteParams... Generating docs for compound RDKit::SmilesWriter... Generating docs for compound RDKit::Snapshot... Generating docs for compound RDKit::SparseIntVect... Generating docs for compound RDKit::StereoBondThresholds... Generating docs for compound RDKit::StereoGroup... Generating docs for compound RDKit::SubstanceGroup... Generating docs for nested compound RDKit::SubstanceGroup::AttachPoint... Generati/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Abbreviations.h:104: warning: The following parameter of RDKit::Abbreviations::findApplicableAbbreviationMatches(const ROMol &mol, const std::vector< AbbreviationDefinition > &abbrevs, double maxCoverage=0.4) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::AtomPair::AtomPairAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/AtomPairs.h:97: warning: The following parameter of RDKit::AtomPairs::getHashedAtomPairFingerprint(const ROMol &mol, unsigned int nBits=2048, unsigned int minLength=1, unsigned int maxLength=maxPathLen - 1, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const std::vector< std::uint32_t > *atomInvariants=nullptr, bool includeChirality=false, bool use2D=true, int confId=-1) is not documented: parameter 'confId' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintUtil.h:75: warning: The following parameter of RDKit::AtomPairs::getTopologicalTorsionCode(const std::vector< std::uint32_t > &atomCodes, bool includeChirality=false) is not documented: parameter 'includeChirality' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Canon.h:98: warning: The following parameters of RDKit::Canon::canonicalizeFragment(ROMol &mol, int atomIdx, std::vector< AtomColors > &colors, const std::vector< unsigned int > &ranks, MolStack &molStack, const boost::dynamic_bitset<> *bondsInPlay=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=false, bool doRandom=false, bool doChiralInversions=true) are not documented: parameter 'bondsInPlay' parameter 'bondSymbols' parameter 'doIsomericSmiles' parameter 'doRandom' parameter 'doChiralInversions' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Chirality.h:420: warning: The following parameters of RDKit::Chirality::findMesoCenters(const ROMol &mol, bool includeIsotopes=true, bool includeAtomMaps=false) are not documented: parameter 'includeIsotopes' parameter 'includeAtomMaps' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Chirality.h:143: warning: The following parameter of RDKit::Chirality::findPotentialStereo(ROMol &mol, bool cleanIt, bool flagPossible=true) is not documented: parameter 'flagPossible' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Chirality.h:195: warning: The following parameter of RDKit::Chirality::getTrigonalBipyramidalAxialBond(const Atom *center, int which=0) is not documented: parameter 'center' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/CIPLabeler.h:46: warning: The following parameter of RDKit::CIPLabeler::assignCIPLabels(ROMol &mol, unsigned int maxRecursiveIterations=0) is not documented: parameter 'maxRecursiveIterations' ng docs for nested compound RDKit::SubstanceGroup::CState... Generating docs for compound RDKit::SubstanceGroupException... Generating docs for compound RDKit::SubstructLibrary... Generating docs for compound RDKit::SubstructMatchParameters... Generating docs for compound RDKit::TautomerPatternHolder... Generating docs for compound RDKit::TautomerQuery... Generating docs for compound RDKit::TDTWriter... Generating docs for compound RDKit::Trajectory... Generating docs for compound RDKit::UnimplementedFPException... Generating docs for compound RDKit::UsedLabelMap... Generating docs for compound RDKit::VarianceDataForLabel... Generating docs for namespace RDKit::Abbreviations Generating docs for compound RDKit::Abbreviations::AbbreviationDefinition... Generating docs for compound RDKit::Abbreviations::AbbreviationMatch... Generating docs for namespace RDKit::Abbreviations::common_properties Generating docs for namespace RDKit::Abbreviations::Utils Generating docs for namespace RDKit::AtomPair Generating docs for compound RDKit::AtomPair::AtomPairArguments... Generating docs for compound RDKit::AtomPair::AtomPairAtomEnv... Generating docs for compound RDKit::AtomPair::AtomPairAtomInvGenerator... Generating docs for compound RDKit::AtomPair::AtomPairEnvGenerator... Generating docs for namespace RDKit::AtomPairs Generating docs for namespace RDKit::Atropisomers Generating docs for namespace RDKit::Canon Generating docs for compound RDKit::Canon::AtomCompareFunctor... Generating docs for compound RDKit::Canon::bondholder... Generating docs for compound RDKit::Canon::canon_atom... Generating docs for compound RDKit::Canon::ChiralAtomCompareFunctor... Generating docs for compound RDKit::Canon::MolStackElem... Generating docs for compound RDKit::Canon::MolStackUnion... Generating docs for compound RDKit::Canon::SpecialChiralityAtomCompareFunctor... Generating docs for compound RDKit::Canon::SpecialSymmetryAtomCompareFunctor... Generating docs for namespace RDKit::Canon::detail Generating docs for namespace RDKit::Chirality Generating docs for compound RDKit::Chirality::BondWedgingParameters... Generating docs for compound RDKit::Chirality::StereoInfo... Generating docs for compound RDKit::Chirality::WedgeInfoAtropisomer... Generating docs for compound RDKit::Chirality::WedgeInfoBase... Generating docs for compound RDKit::Chirality::WedgeInfoChiral... Generating docs for namespace RDKit::Chirality::detail Generating docs for namespace RDKit::CIPLabeler Generating docs for compound RDKit::CIPLabeler::AtropisomerBond... Generating docs for compound RDKit::CIPLabeler::CIPMol... Generating docs for compound RDKit::CIPLabeler::CIPMolSpan... Generating docs for nested compound RDKit::CIPLabeler::CIPMolSpan::CIPMolIter... Generating docs for compound RDKit::CIPLabeler::Configuration... Generating docs for compound RDKit::CIPLabeler::Digraph... Generating docs for compound RDKit::CIPLabeler::Edge... Generating docs for compound RDKit::CIPLabeler::MaxIterationsExceeded... Generating docs for compound RDKit::CIPLabeler::Node... Generating docs for compound RDKit::CIPLabeler::PairList... Generating docs for compound RDKit::CIPLabeler::Priority... Generating docs for compound RDKit::CIPLabeler::Rule1a... Generating docs for compound RDKit::CIPLabeler::Rule1b... Generating docs for compound RDKit::CIPLabeler::Rule2... Generating docs for compound RDKit::CIPLabeler::Rule3... Generating docs for compound RDKit::CIPLabeler::Rule4a... Generating docs for compound RDKit::CIPLabeler::Rule4b... Generating docs for compound RDKit::CIPLabeler::Rule4c... Generating docs for compound RDKit::CIPLabeler::Rule5... Generating docs for compound RDKit::CIPLabeler::Rule5New... Generating docs for compound RDKit::CIPLabeler::Rule6... Generating docs for compound RDKit::CIPLabeler::Rules... Generating docs for compound RDKit::CIPLabeler::SequenceRule... Generating docs for compound RDKit::CIPLabeler::Sort... Generating docs for compound RDKit::CIPLabeler::Sp2Bond... Generating docs for compound RDKit::CIPLabeler::Tetrahedral... Generating docs for compound RDKit/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Lipinski.h:45: warning: argument 'strict' of command @param is not found in the argument list of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Lipinski.h:45: warning: The following parameter of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) is not documented: parameter 'useStrictDefinition' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/USRDescriptor.h:68: warning: The following parameter of RDKit::Descriptors::USRCAT(const ROMol &mol, std::vector< double > &descriptor, std::vector< std::vector< unsigned int > > &atomIds, int confId=-1) is not documented: parameter 'atomIds' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Embedder.h:328: warning: The following parameter of RDKit::DGeomHelpers::EmbedMultipleConfs(ROMol &mol, INT_VECT &res, unsigned int numConfs=10, int numThreads=1, unsigned int maxIterations=30, int seed=-1, bool clearConfs=true, bool useRandomCoords=false, double boxSizeMult=2.0, bool randNegEig=true, unsigned int numZeroFail=1, double pruneRmsThresh=-1.0, const std::map< int, RDGeom::Point3D > *coordMap=nullptr, double optimizerForceTol=1e-3, bool ignoreSmoothingFailures=false, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0, bool onlyHeavyAtomsForRMS=false, unsigned int ETversion=2, bool useSmallRingTorsions=false, bool useMacrocycleTorsions=true, bool useMacrocycle14config=true, unsigned int timeout=0) is not documented: parameter 'timeout' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h:37: warning: The following parameter of RDKit::DGeomHelpers::setTopolBounds(const ROMol &mol, DistGeom::BoundsMatPtr mmat, bool set15bounds=true, bool scaleVDW=false, bool useMacrocycle14config=false, bool forceTransAmides=true) is not documented: parameter 'forceTransAmides' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatchers.h:98: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatchers.h:218: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatchers.h:161: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MHFP.h:93: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::CreateShingling(const ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MHFP.h:132: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::Encode(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MHFP.h:183: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::EncodeSECFP(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1, size_t length=2048) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/MMPA.h:28: warning: The following parameter of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > &result, unsigned int maxCuts=3, unsigned int maxCutBonds=20, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") is not documented: parameter 'pattern' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/MMPA.h:49: warning: The following parameter of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > &result, unsigned int minCuts, unsigned int maxCuts, unsigned int maxCutBonds, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") is not documented: parameter 'pattern' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/AlignMolecules.h:149: warning: argument 'trans' of command @param is not found in the argument list of RDKit::MolAlign::getBestRMS(ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, bool symmetrizeConjugatedTerminalGroups=true, const RDNumeric::DoubleVector *weights=nullptr, int numThreads=1) ::CIPLabeler::TooManyNodesException... Generating docs for namespace RDKit::CIPLabeler_detail Generating docs for namespace RDKit::common_properties Generating docs for namespace RDKit::constants Generating docs for namespace RDKit::Deprotect Generating docs for compound RDKit::Deprotect::DeprotectData... Generating docs for namespace RDKit::Descriptors Generating docs for compound RDKit::Descriptors::CrippenParamCollection... Generating docs for compound RDKit::Descriptors::CrippenParams... Generating docs for compound RDKit::Descriptors::DoubleCubicLatticeVolume... Generating docs for compound RDKit::Descriptors::Properties... Generating docs for compound RDKit::Descriptors::PropertyFunctor... Generating docs for namespace RDKit::Descriptors::detail Generating docs for namespace RDKit::detail Generating docs for compound RDKit::detail::MCSParametersInternal... Generating docs for namespace RDKit::details Generating docs for namespace RDKit::DGeomHelpers Generating docs for compound RDKit::DGeomHelpers::EmbedParameters... Generating docs for namespace RDKit::DTags Generating docs for namespace RDKit::EnumerationStrategyPickler Generating docs for namespace RDKit::EnumerationTypes Generating docs for namespace RDKit::FileParsers Generating docs for namespace RDKit::FileParsers::schrodinger Generating docs for namespace RDKit::FileParserUtils Generating docs for namespace RDKit::FilterMatchOps Generating docs for compound RDKit::FilterMatchOps::And... Generating docs for compound RDKit::FilterMatchOps::Not... Generating docs for compound RDKit::FilterMatchOps::Or... Generating docs for namespace RDKit::FMCS Generating docs for compound RDKit::FMCS::Composition2N... Generating docs for compound RDKit::FMCS::DuplicatedSeedCache... Generating docs for nested compound RDKit::FMCS::DuplicatedSeedCache::TKey... Generating docs for compound RDKit::FMCS::ExecStatistics... Generating docs for compound RDKit::FMCS::Graph... Generating docs for compound RDKit::FMCS::MaximumCommonSubgraph... Generating docs for compound RDKit::FMCS::MolFragment... Generating docs for compound RDKit::FMCS::NewBond... Generating docs for compound RDKit::FMCS::Seed... Generating docs for compound RDKit::FMCS::SeedSet... Generating docs for compound RDKit::FMCS::SubstructureCache... Generating docs for nested compound RDKit::FMCS::SubstructureCache::HashKey... Generating docs for nested compound RDKit::FMCS::SubstructureCache::KeyNumericMetrics... Generating docs for compound RDKit::FMCS::Target... Generating docs for compound RDKit::FMCS::TargetMatch... Generating docs for compound RDKit::FMCS::TArray2D... Generating docs for namespace RDKit::ForceFieldsHelper Generating docs for namespace RDKit::ForceFieldsHelper::detail Generating docs for namespace RDKit::GeneralizedSubstruct Generating docs for compound RDKit::GeneralizedSubstruct::ExtendedQueryMol... Generating docs for namespace RDKit::GeneralMolSupplier Generating docs for compound RDKit::GeneralMolSupplier::SupplierOptions... Generating docs for namespace RDKit::GenericGroups Generating docs for namespace RDKit::GenericGroups::Matchers Generating docs for namespace RDKit::Local Generating docs for namespace RDKit::MACCSFingerprints Generating docs for namespace RDKit::MHFPFingerprints Generating docs for compound RDKit::MHFPFingerprints::MHFPEncoder... Generating docs for namespace RDKit::MHFPFingerprints::FNV Generating docs for namespace RDKit::MMFF Generating docs for compound RDKit::MMFF::MMFFAtomProperties... Generating docs for compound RDKit::MMFF::MMFFMolProperties... Generating docs for namespace RDKit::MMFF::DefaultParameters Generating docs for namespace RDKit::MMFF::Tools Generating docs for compound RDKit::MMFF::Tools::DefaultTorsionBondSmarts... Generating docs for namespace RDKit::MMPA Generating docs for namespace RDKit::MMPA::detail Generating docs for namespace RDKit::MolAlign Generating docs for compound RDKit::MolAlign::LAP... Generating docs for compound RDKit::MolAlign::MolAlignException... Generating docs for compound RDKit::MolAlign::MolHistogram... Generating docs for co/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMol.h:45: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMol::DrawMol(const ROMol &mol, const std::string &legend, int width, int height, const MolDrawOptions &drawOptions, DrawText &textDrawer, const std::vector< int > *highlightAtoms=nullptr, const std::vector< int > *highlightBonds=nullptr, const std::map< int, DrawColour > *highlightAtomMap=nullptr, const std::map< int, DrawColour > *highlightBondMap=nullptr, const std::vector< std::pair< DrawColour, DrawColour > > *bondColours=nullptr, const std::map< int, double > *highlight_radii=nullptr, bool includeAnnotations=true, int confId=-1, bool isReactionMol=false) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMol.h:45: warning: The following parameters of RDKit::MolDraw2D_detail::DrawMol::DrawMol(const ROMol &mol, const std::string &legend, int width, int height, const MolDrawOptions &drawOptions, DrawText &textDrawer, const std::vector< int > *highlightAtoms=nullptr, const std::vector< int > *highlightBonds=nullptr, const std::map< int, DrawColour > *highlightAtomMap=nullptr, const std::map< int, DrawColour > *highlightBondMap=nullptr, const std::vector< std::pair< DrawColour, DrawColour > > *bondColours=nullptr, const std::map< int, double > *highlight_radii=nullptr, bool includeAnnotations=true, int confId=-1, bool isReactionMol=false) are not documented: parameter 'bondColours' parameter 'highlight_radii' parameter 'includeAnnotations' parameter 'isReactionMol' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCH.h:28: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMolMCH::DrawMolMCH(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCH.h:28: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCH::DrawMolMCH(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented: parameter 'highlight_radii' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h:24: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::DrawMolMCHCircleAndLine(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h:24: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::DrawMolMCHCircleAndLine(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented: parameter 'highlight_radii' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h:36: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMolMCHLasso::DrawMolMCHLasso(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h:36: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCHLasso::DrawMolMCHLasso(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented: parameter 'highlight_radii' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:263: warning: The following parameter of RDKit::MolEnumerator::enumerate(const ROMol &mol, size_t maxPerOperation=0) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/MolInterchange.h:81: warning: The following parameter of RDKit::MolInterchange::MolsToJSONData(const std::vector< T > &mols, const JSONWriteParameters ¶ms=defaultJSONWriteParameters) is not documented: parameter 'params' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/MolInterchange.h:90: warning: The following parameter of RDKit::MolInterchange::MolToJSONData(const T &mol, const JSONWriteParameters ¶ms=defaultJSONWriteParameters) is not documented: parameter 'params' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolOps.h:362: warning: The following parameters of RDKit::MolOps::mergeQueryHs(const ROMol &mol, bool mergeUnmappedOnly=false, bool mergeIsotopes=false) are not documented: parameter 'mergeUnmappedOnly' parameter 'mergeIsotopes' mpound RDKit::MolAlign::O3A... Generating docs for compound RDKit::MolAlign::O3AConstraint... Generating docs for compound RDKit::MolAlign::O3AConstraintVect... Generating docs for compound RDKit::MolAlign::O3AFuncData... Generating docs for compound RDKit::MolAlign::SDM... Generating docs for namespace RDKit::MolAlign::details Generating docs for namespace RDKit::MolDraw2D_detail Generating docs for compound RDKit::MolDraw2D_detail::AtomSymbol... Generating docs for compound RDKit::MolDraw2D_detail::DrawAnnotation... Generating docs for compound RDKit::MolDraw2D_detail::DrawMol... Generating docs for compound RDKit::MolDraw2D_detail::DrawMolMCH... Generating docs for compound RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawMolMCHLasso... Generating docs for compound RDKit::MolDraw2D_detail::DrawShape... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeArc... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeArrow... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeDashedWedge... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeEllipse... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapePolyLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeSimpleLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeSolidWedge... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeWavyLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawText... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextCairo... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFT... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTCairo... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTJS... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTQt... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTSVG... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextJS... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextNotFT... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextQt... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextSVG... Generating docs for compound RDKit::MolDraw2D_detail::LinePair... Generating docs for compound RDKit::MolDraw2D_detail::StringRect... Generating docs for namespace RDKit::MolDraw2DUtils Generating docs for compound RDKit::MolDraw2DUtils::ContourParams... Generating docs for namespace RDKit::MolEnumerator Generating docs for compound RDKit::MolEnumerator::LinkNode... Generating docs for compound RDKit::MolEnumerator::LinkNodeOp... Generating docs for compound RDKit::MolEnumerator::MolEnumeratorOp... Generating docs for compound RDKit::MolEnumerator::MolEnumeratorParams... Generating docs for compound RDKit::MolEnumerator::PositionVariationOp... Generating docs for compound RDKit::MolEnumerator::RepeatUnitOp... Generating docs for namespace RDKit::MolEnumerator::detail Generating docs for namespace RDKit::MolEnumerator::utils Generating docs for namespace RDKit::MolFragmenter Generating docs for compound RDKit::MolFragmenter::FragmenterBondType... Generating docs for namespace RDKit::MolHash Generating docs for namespace RDKit::MolInterchange Generating docs for compound RDKit::MolInterchange::JSONParseParameters... Generating docs for compound RDKit::MolInterchange::JSONWriteParameters... Generating docs for namespace RDKit::MolOps Generating docs for compound RDKit::MolOps::AddHsParameters... Generating docs for compound RDKit::MolOps::AdjustQueryParameters... Generating docs for compound RDKit::MolOps::Hybridizations... Generating docs for compound RDKit::MolOps::RemoveHsParameters... Generating docs for namespace RDKit::MolOps::details Generating docs for namespace RDKit::MolProcessing Generating docs for namespace RDKit::MolProcessing::details Generating docs for namespace RDKit::MolShapes Generating docs for namespace RDKit::MolStandardize Generating docs for compound RDKit::MolStandardize::AcidBaseCatalogEntry... Gener/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganGenerator.h:208: warning: argument 'countSimulation' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganGenerator.h:208: warning: argument 'includeChirality' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganGenerator.h:208: warning: argument 'onlyNonzeroInvariants' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganGenerator.h:273: warning: argument 'countSimulation' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganGenerator.h:273: warning: argument 'includeChirality' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganGenerator.h:273: warning: argument 'onlyNonzeroInvariants' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::MorganFingerprint::MorganAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganFingerprints.h:117: warning: The following parameter of RDKit::MorganFingerprints::getHashedFingerprint(const ROMol &mol, unsigned int radius, unsigned int nBits=2048, std::vector< boost::uint32_t > *invariants=nullptr, const std::vector< boost::uint32_t > *fromAtoms=nullptr, bool useChirality=false, bool useBondTypes=true, bool onlyNonzeroInvariants=false, BitInfoMap *atomsSettingBits=nullptr, bool includeRedundantEnvironments=false) is not documented: parameter 'nBits' ating docs for compound RDKit::MolStandardize::AcidBaseCatalogParams... Generating docs for compound RDKit::MolStandardize::AllowedAtomsValidation... Generating docs for compound RDKit::MolStandardize::ChargeCorrection... Generating docs for compound RDKit::MolStandardize::CleanupParameters... Generating docs for compound RDKit::MolStandardize::CompositeValidation... Generating docs for compound RDKit::MolStandardize::DisallowedAtomsValidation... Generating docs for compound RDKit::MolStandardize::DisallowedRadicalValidation... Generating docs for compound RDKit::MolStandardize::FeaturesValidation... Generating docs for compound RDKit::MolStandardize::FragmentCatalogEntry... Generating docs for compound RDKit::MolStandardize::FragmentCatalogParams... Generating docs for compound RDKit::MolStandardize::FragmentRemover... Generating docs for compound RDKit::MolStandardize::FragmentValidation... Generating docs for compound RDKit::MolStandardize::Is2DValidation... Generating docs for compound RDKit::MolStandardize::IsotopeValidation... Generating docs for compound RDKit::MolStandardize::LargestFragmentChooser... Generating docs for nested compound RDKit::MolStandardize::LargestFragmentChooser::Largest... Generating docs for compound RDKit::MolStandardize::Layout2DValidation... Generating docs for compound RDKit::MolStandardize::MetalDisconnector... Generating docs for compound RDKit::MolStandardize::MetalDisconnectorOptions... Generating docs for compound RDKit::MolStandardize::MolVSValidation... Generating docs for compound RDKit::MolStandardize::NeutralValidation... Generating docs for compound RDKit::MolStandardize::NoAtomValidation... Generating docs for compound RDKit::MolStandardize::Normalizer... Generating docs for compound RDKit::MolStandardize::Pipeline... Generating docs for compound RDKit::MolStandardize::PipelineLogEntry... Generating docs for compound RDKit::MolStandardize::PipelineOptions... Generating docs for compound RDKit::MolStandardize::PipelineResult... Generating docs for compound RDKit::MolStandardize::RDKitValidation... Generating docs for compound RDKit::MolStandardize::Reionizer... Generating docs for compound RDKit::MolStandardize::StereoValidation... Generating docs for compound RDKit::MolStandardize::Tautomer... Generating docs for compound RDKit::MolStandardize::TautomerCatalogEntry... Generating docs for compound RDKit::MolStandardize::TautomerCatalogParams... Generating docs for compound RDKit::MolStandardize::TautomerEnumerator... Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorCallback... Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorResult... Generating docs for nested compound RDKit::MolStandardize::TautomerEnumeratorResult::const_iterator... Generating docs for compound RDKit::MolStandardize::TautomerTransform... Generating docs for compound RDKit::MolStandardize::TransformCatalogEntry... Generating docs for compound RDKit::MolStandardize::TransformCatalogParams... Generating docs for compound RDKit::MolStandardize::Uncharger... Generating docs for compound RDKit::MolStandardize::ValidationMethod... Generating docs for namespace RDKit::MolStandardize::defaults Generating docs for namespace RDKit::MolStandardize::Operations Generating docs for namespace RDKit::MolStandardize::TautomerScoringFunctions Generating docs for compound RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm... Generating docs for namespace RDKit::MorganFingerprint Generating docs for compound RDKit::MorganFingerprint::MorganArguments... Generating docs for compound RDKit::MorganFingerprint::MorganAtomEnv... Generating docs for compound RDKit::MorganFingerprint::MorganAtomInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganBondInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganEnvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganFeatureAtomInvGenerator... Generating docs for namespace RDKit::MorganFingerprints Generating docs for compound RDKit::MorganFingerprints::ss_matcher... Generat/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/ReducedGraphs.h:26: warning: The following parameter of RDKit::ReducedGraphs::generateMolExtendedReducedGraph(const ROMol &mol, std::vector< boost::dynamic_bitset<> > *atomTypes=nullptr) is not documented: parameter 'atomTypes' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesWrite.h:96: warning: argument 'bondIn' of command @param is not found in the argument list of RDKit::SmilesWrite::GetAtomSmiles(const Atom *atom, bool doKekule=false, const Bond *=nullptr, bool allHsExplicit=false, bool isomericSmiles=true) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.h:235: warning: The following parameter of RDKit::SynthonSpaceSearch::SynthonSpace::readTextFile(const std::string &inFilename, bool &cancelled) is not documented: parameter 'cancelled' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.h:187: warning: The following parameter of RDKit::SynthonSpaceSearch::SynthonSpace::substructureSearch(const GeneralizedSubstruct::ExtendedQueryMol &query, const SubstructMatchParameters &matchParams=SubstructMatchParameters(), const SynthonSpaceSearchParams ¶ms=SynthonSpaceSearchParams()) is not documented: parameter 'matchParams' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.h:173: warning: The following parameter of RDKit::SynthonSpaceSearch::SynthonSpace::substructureSearch(const ROMol &query, const SubstructMatchParameters &matchParams=SubstructMatchParameters(), const SynthonSpaceSearchParams ¶ms=SynthonSpaceSearchParams()) is not documented: parameter 'matchParams' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:94: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(bool includeChirality=false, uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, bool countSimulation=true, std::uint32_t fpSize=2048, std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, bool ownsAtomInvGen=false) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:94: warning: The following parameter of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(bool includeChirality=false, uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, bool countSimulation=true, std::uint32_t fpSize=2048, std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, bool ownsAtomInvGen=false) is not documented: parameter 'countSimulation' ing docs for namespace RDKit::PicklerOps Generating docs for namespace RDKit::PNGData Generating docs for namespace RDKit::QueryOps Generating docs for namespace RDKit::RascalMCES Generating docs for compound RDKit::RascalMCES::PartitionSet... Generating docs for compound RDKit::RascalMCES::RascalClusterOptions... Generating docs for compound RDKit::RascalMCES::RascalOptions... Generating docs for compound RDKit::RascalMCES::RascalResult... Generating docs for namespace RDKit::RascalMCES::details Generating docs for compound RDKit::RascalMCES::details::ClusNode... Generating docs for namespace RDKit::RDKitFP Generating docs for compound RDKit::RDKitFP::RDKitFPArguments... Generating docs for compound RDKit::RDKitFP::RDKitFPAtomEnv... Generating docs for compound RDKit::RDKitFP::RDKitFPAtomInvGenerator... Generating docs for compound RDKit::RDKitFP::RDKitFPEnvGenerator... Generating docs for namespace RDKit::RDKitFPUtils Generating docs for namespace RDKit::RDTypeTag Generating docs for namespace RDKit::RDTypeTag::detail Generating docs for compound RDKit::RDTypeTag::detail::Value... Generating docs for namespace RDKit::ReactionRunnerUtils Generating docs for namespace RDKit::ReducedGraphs Generating docs for namespace RDKit::RxnOps Generating docs for namespace RDKit::ScaffoldNetwork Generating docs for compound RDKit::ScaffoldNetwork::NetworkEdge... Generating docs for compound RDKit::ScaffoldNetwork::ScaffoldNetwork... Generating docs for compound RDKit::ScaffoldNetwork::ScaffoldNetworkParams... Generating docs for namespace RDKit::ScaffoldNetwork::detail Generating docs for namespace RDKit::SGroupParsing Generating docs for namespace RDKit::SGroupWriting Generating docs for namespace RDKit::SLNParse Generating docs for compound RDKit::SLNParse::AttribType... Generating docs for namespace RDKit::SmartsWrite Generating docs for namespace RDKit::SmilesParse Generating docs for compound RDKit::SmilesParse::SmilesParseException... Generating docs for namespace RDKit::SmilesWrite Generating docs for namespace RDKit::SmilesWrite::detail Generating docs for namespace RDKit::StructureCheck Generating docs for compound RDKit::StructureCheck::AugmentedAtom... Generating docs for compound RDKit::StructureCheck::ChargeFix... Generating docs for compound RDKit::StructureCheck::IncEntry... Generating docs for compound RDKit::StructureCheck::Ligand... Generating docs for compound RDKit::StructureCheck::Neighbourhood... Generating docs for compound RDKit::StructureCheck::PathEntry... Generating docs for compound RDKit::StructureCheck::StructChecker... Generating docs for compound RDKit::StructureCheck::StructCheckerOptions... Generating docs for compound RDKit::StructureCheck::StructCheckTautomer... Generating docs for namespace RDKit::Subgraphs Generating docs for namespace RDKit::SubstanceGroupChecks Generating docs for namespace RDKit::SynthonSpaceSearch Generating docs for compound RDKit::SynthonSpaceSearch::SearchResults... Generating docs for compound RDKit::SynthonSpaceSearch::Synthon... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSet... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpace... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpaceFingerprintSearcher... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpaceFPHitSet... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpaceHitSet... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpaceRascalSearcher... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpaceSearcher... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpaceSearchParams... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpaceSubstructureSearcher... Generating docs for namespace RDKit::SynthonSpaceSearch::details Generating docs for compound RDKit::SynthonSpaceSearch::details::MemoryMappedFileReader... Generating docs for compound RDKit::SynthonSpaceSearch::details::Stepper... Generating docs for namespace RDKit::TopologicalTorsion Generating docs for compound RDKit::Top/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:32: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::TopologicalTorsion::TopologicalTorsionArguments::TopologicalTorsionArguments(const bool includeChirality=false, const uint32_t torsionAtomCount=4, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:32: warning: The following parameter of RDKit::TopologicalTorsion::TopologicalTorsionArguments::TopologicalTorsionArguments(const bool includeChirality=false, const uint32_t torsionAtomCount=4, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048) is not documented: parameter 'countSimulation' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:68: warning: The following parameter of RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::TopologicalTorsionAtomEnv(OutputType bitId, INT_VECT atomPath) is not documented: parameter 'atomPath' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/CDXMLParser.h:95: warning: argument 'fileName' of command @param is not found in the argument list of RDKit::v1::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/CDXMLParser.h:95: warning: The following parameter of RDKit::v1::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true) is not documented: parameter 'filename' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/FileParsers.h:76: warning: argument 'line' from the argument list of RDKit::v1::MolDataStreamToMol has multiple @param documentation sections /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/CDXMLParser.h:46: warning: argument 'fileName' of command @param is not found in the argument list of RDKit::v2::CDXMLParser::MolsFromCDXMLFile(const std::string &filename, const CDXMLParserParams ¶ms=CDXMLParserParams()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/CDXMLParser.h:46: warning: The following parameter of RDKit::v2::CDXMLParser::MolsFromCDXMLFile(const std::string &filename, const CDXMLParserParams ¶ms=CDXMLParserParams()) is not documented: parameter 'filename' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: argument 'removeHs' of command @param is not found in the argument list of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: argument 'strictParsing' of command @param is not found in the argument list of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: The following parameter of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'delimiter' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'smilesColumn' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'nameColumn' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'titleLine' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: The following parameter of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'nameRecord' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'confId2D' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'confId3D' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: The following parameter of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/MIFDescriptors.h:117: warning: argument 'pos' of command @param is not found in the argument list of RDMIF::Coulomb::Coulomb(const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/MIFDescriptors.h:117: warning: The following parameter of RDMIF::Coulomb::Coulomb(const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0) is not documented: parameter 'positions' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/MIFDescriptors.h:220: warning: argument 'pos' of command @param is not found in the argument list of RDMIF::CoulombDielectric::CoulombDielectric(const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0, double epsilon=80.0, double xi=4.0) /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/MIFDescriptors.h:220: warning: The following parameter of RDMIF::CoulombDielectric::CoulombDielectric(const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0, double epsilon=80.0, double xi=4.0) is not documented: parameter 'positions' /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/HierarchicalClusterPicker.h:48: warning: The following parameter of RDPickers::HierarchicalClusterPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize) const is not documented: parameter 'distMat' /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/LeaderPicker.h:48: warning: argument 'firstPicks' of command @param is not found in the argument list of RDPickers::LeaderPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/LeaderPicker.h:48: warning: argument 'seed' of command @param is not found in the argument list of RDPickers::LeaderPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/LeaderPicker.h:87: warning: The following parameters of RDPickers::LeaderPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize, const RDKit::INT_VECT &firstPicks, double threshold, int nthreads) const are not documented: parameter 'threshold' parameter 'nthreads' /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/MaxMinPicker.h:44: warning: argument 'firstPicks' of command @param is not found in the argument list of RDPickers::MaxMinPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/MaxMinPicker.h:44: warning: argument 'seed' of command @param is not found in the argument list of RDPickers::MaxMinPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const ologicalTorsion::TopologicalTorsionArguments... Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv... Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionEnvGenerator... Generating docs for namespace RDKit::UFF Generating docs for namespace RDKit::UFF::Tools Generating docs for compound RDKit::UFF::Tools::DefaultTorsionBondSmarts... Generating docs for namespace RDKit::Utils Generating docs for compound RDKit::Utils::LocaleSwitcher... Generating docs for namespace RDKit::Utils::detail Generating docs for namespace RDKit::v1 Generating docs for compound RDKit::v1::ForwardSDMolSupplier... Generating docs for compound RDKit::v1::MolSupplier... Generating docs for compound RDKit::v1::SDMolSupplier... Generating docs for compound RDKit::v1::SmartsParserParams... Generating docs for compound RDKit::v1::SmilesMolSupplier... Generating docs for compound RDKit::v1::SmilesParserParams... Generating docs for compound RDKit::v1::TDTMolSupplier... Generating docs for namespace RDKit::v2 Generating docs for namespace RDKit::v2::CDXMLParser Generating docs for compound RDKit::v2::CDXMLParser::CDXMLParserParams... Generating docs for namespace RDKit::v2::FileParsers Generating docs for compound RDKit::v2::FileParsers::ForwardSDMolSupplier... Generating docs for compound RDKit::v2::FileParsers::Mol2ParserParams... Generating docs for compound RDKit::v2::FileParsers::MolFileParserParams... Generating docs for compound RDKit::v2::FileParsers::MolFileUnhandledFeatureException... Generating docs for compound RDKit::v2::FileParsers::MolSupplier... Generating docs for compound RDKit::v2::FileParsers::PDBParserParams... Generating docs for compound RDKit::v2::FileParsers::SDMolSupplier... Generating docs for compound RDKit::v2::FileParsers::SmilesMolSupplier... Generating docs for compound RDKit::v2::FileParsers::SmilesMolSupplierParams... Generating docs for compound RDKit::v2::FileParsers::TDTMolSupplier... Generating docs for compound RDKit::v2::FileParsers::TDTMolSupplierParams... Generating docs for compound RDKit::v2::FileParsers::TPLParserParams... Generating docs for namespace RDKit::v2::MarvinParser Generating docs for compound RDKit::v2::MarvinParser::MrvParserParams... Generating docs for namespace RDKit::v2::ReactionParser Generating docs for namespace RDKit::v2::SmilesParse Generating docs for namespace RDLog Generating docs for namespace RDMIF Generating docs for compound RDMIF::Coulomb... Generating docs for compound RDMIF::CoulombDielectric... Generating docs for compound RDMIF::HBond... Generating docs for compound RDMIF::Hydrophilic... Generating docs for compound RDMIF::MMFFVdWaals... Generating docs for compound RDMIF::UFFVdWaals... Generating docs for compound RDMIF::VdWaals... Generating docs for namespace RDNumeric Generating docs for compound RDNumeric::Matrix... Generating docs for compound RDNumeric::SquareMatrix... Generating docs for compound RDNumeric::SymmMatrix... Generating docs for compound RDNumeric::Vector... Generating docs for namespace RDNumeric::Alignments Generating docs for namespace RDNumeric::EigenSolvers Generating docs for namespace RDPickers Generating docs for compound RDPickers::DistPicker... Generating docs for compound RDPickers::HierarchicalClusterPicker... Generating docs for compound RDPickers::LeaderPicker... Generating docs for compound RDPickers::LeaderPickerState... Generating docs for compound RDPickers::MaxMinPicker... Generating docs for compound RDPickers::MaxMinPickInfo... Generating docs for namespace RingUtils Generating docs for namespace SmilesParseOps Generating docs for namespace SmilesParseOps::detail Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating topic index... Generating module index... Generating module member index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... type lookup cache used 37742/65536 hits=222630 misses=41986 symbol lookup cache used 33412/65536 hits=297604 misses=33412 finished... (cd /build/reproducible-path/rdkit-202503.1/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202503.1 /usr/bin/make html) make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/reproducible-path/rdkit-202503.1/Code/docs/* _build/html/cppapi cp -r C++Examples _build/html/ sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v8.1.3 loading translations [en]... done WARNING: html_static_path entry '_static' does not exist myst v4.0.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 262 source files that are out of date updating environment: [new config] 262 added, 0 changed, 0 removed reading sources... 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[autosectionlabel.GettingStartedWithContributing] /build/reproducible-path/rdkit-202503.1/Docs/Book/Install.md:430: WARNING: duplicate label recommended extras, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/Install.md [autosectionlabel.Install] /build/reproducible-path/rdkit-202503.1/Docs/Book/Install.md:474: WARNING: duplicate label testing the build (optional, but recommended), other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/Install.md [autosectionlabel.Install] /build/reproducible-path/rdkit-202503.1/Docs/Book/Install.md:479: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/GettingStartedInPython.rst [autosectionlabel.Install] /build/reproducible-path/rdkit-202503.1/Docs/Book/Overview.md:107: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/Install.md [autosectionlabel.Overview] /build/reproducible-path/rdkit-202503.1/Docs/Book/RDKit_Book.rst:179: WARNING: duplicate label aromaticity, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/RDKit_Book.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202503.1/Docs/Book/RDKit_Book.rst:385: WARNING: duplicate label dative bonds, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/RDKit_Book.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202503.1/Docs/Book/RDKit_Book.rst:575: WARNING: duplicate label stereochemistry, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/Cookbook.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202503.1/Docs/Book/RDKit_Book.rst:1304: WARNING: duplicate label chemical features, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/GettingStartedInPython.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202503.1/Docs/Book/RDKit_Book.rst:2504: WARNING: duplicate label introduction, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/Cookbook.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202503.1/Docs/Book/RDKit_Book.rst:2602: WARNING: duplicate label rdkit fingerprints, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/GettingStartedInPython.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202503.1/Docs/Book/RDKit_Book.rst:2768: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/Overview.md [autosectionlabel.RDKit_Book] WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Avalon.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Avalon.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon] WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Chem] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.rst:28: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.rst:115: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem] WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.AtomPairs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.AtomPairs.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.ChemUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.ChemUtils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils] WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Draw.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Draw.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw] WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2DQt' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.EState.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.EState.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState] WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.FeatMaps.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.FeatMaps.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Features.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Features.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features] WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fingerprints.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fingerprints.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints] WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fraggle.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fraggle.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle] WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolDb.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolDb.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb] WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolKey.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolKey.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey] WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolStandardize.rst:6: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.MolStandardize] WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm2D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolStandardize.rst [autosectionlabel.source/rdkit.Chem.Pharm2D] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm2D.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.Pharm2D] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm3D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm3D.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D] WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.RegistrationHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Scaffolds.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Scaffolds.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds] WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum] WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SpacialScore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Subshape.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Subshape.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape] WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Suppliers.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Suppliers.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers] WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.fmcs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.fmcs.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs] WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdCIPLabeler' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDetermineBonds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdEHTTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolEnumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdShapeAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSynthonSpaceSearch' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdTautomerQuery' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.DataManip] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip] WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.Metric.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip.Metric] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.Metric.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.DataManip.Metric] WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataStructs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataStructs.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs] WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Dbase.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Dbase.rst:17: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase] WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DistanceGeometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DistanceGeometry.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry] WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ForceField.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.ForceField] WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Geometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.Geometry] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Geometry.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ForceField.rst [autosectionlabel.source/rdkit.Geometry] WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.ML] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.rst:18: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.rst:26: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML] WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Cluster.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Cluster.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster] WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Data.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Data.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data] WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.cQuantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Descriptors.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Descriptors.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors] WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.InfoTheory.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.InfoTheory.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory] WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.MLUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.MLUtils.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils] WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.SLT.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.SLT.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT] WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Scoring.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Scoring.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring] WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Numerics.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Numerics.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics] WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.SimDivFilters.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.SimDivFilters.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters] WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.VLib] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.rst:12: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib] WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.NodeLib.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.NodeLib.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib] WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.utils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.utils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils] WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/rdkit-202503.1/Docs/Book/data/README.md: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying downloadable files... [ 5%] C++Examples/example1.cpp copying downloadable files... [ 11%] C++Examples/example2.cpp copying downloadable files... [ 16%] C++Examples/example3.cpp copying downloadable files... [ 21%] C++Examples/example4.cpp copying downloadable files... [ 26%] C++Examples/example5.cpp copying downloadable files... [ 32%] C++Examples/example6.cpp copying downloadable files... [ 37%] C++Examples/example7.cpp copying downloadable files... [ 42%] C++Examples/example8.cpp copying downloadable files... [ 47%] C++Examples/example9.cpp copying downloadable files... [ 53%] ../Code/GraphMol/Bond.h copying downloadable files... [ 58%] C++Examples/example10.cpp copying downloadable files... [ 63%] C++Examples/CMakeLists.txt copying downloadable files... [ 68%] C++Examples/example11.cpp copying downloadable files... [ 74%] C++Examples/example12.cpp copying downloadable files... [ 79%] C++Examples/example13.cpp copying downloadable files... [ 84%] C++Examples/example17.cpp copying downloadable files... [ 89%] C++Examples/example14.cpp copying downloadable files... [ 95%] C++Examples/example15.cpp copying downloadable files... [100%] C++Examples/example16.cpp copying static files... Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/sphinxdoc.css copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 0%] BackwardsIncompatibleChanges writing output... [ 1%] Cartridge writing output... [ 1%] Cookbook writing output... [ 2%] GettingStartedInC++ writing output... [ 2%] GettingStartedInPython writing output... [ 2%] GettingStartedWithContributing writing output... [ 3%] Install writing output... [ 3%] Overview writing output... [ 3%] RDKit_Book writing output... [ 4%] api-docs writing output... [ 4%] data/README writing output... [ 5%] index writing output... [ 5%] source/rdkit writing output... [ 5%] source/rdkit.Avalon writing output... [ 6%] source/rdkit.Avalon.pyAvalonTools writing output... [ 6%] source/rdkit.Chem writing output... [ 6%] source/rdkit.Chem.AllChem writing output... [ 7%] source/rdkit.Chem.AtomPairs writing output... [ 7%] source/rdkit.Chem.AtomPairs.Pairs writing output... [ 8%] source/rdkit.Chem.AtomPairs.Sheridan writing output... [ 8%] source/rdkit.Chem.AtomPairs.Torsions writing output... [ 8%] source/rdkit.Chem.AtomPairs.Utils writing output... [ 9%] source/rdkit.Chem.BRICS writing output... [ 9%] source/rdkit.Chem.BuildFragmentCatalog writing output... [ 10%] source/rdkit.Chem.ChemUtils writing output... [ 10%] source/rdkit.Chem.ChemUtils.AlignDepict writing output... [ 10%] source/rdkit.Chem.ChemUtils.BulkTester writing output... [ 11%] source/rdkit.Chem.ChemUtils.DescriptorUtilities writing output... [ 11%] source/rdkit.Chem.ChemUtils.SDFToCSV writing output... [ 11%] source/rdkit.Chem.ChemUtils.TemplateExpand writing output... [ 12%] source/rdkit.Chem.ChemicalFeatures writing output... [ 12%] source/rdkit.Chem.ChemicalForceFields writing output... [ 13%] source/rdkit.Chem.Crippen writing output... [ 13%] source/rdkit.Chem.Descriptors writing output... [ 13%] source/rdkit.Chem.Descriptors3D writing output... [ 14%] source/rdkit.Chem.Draw writing output... [ 14%] source/rdkit.Chem.Draw.IPythonConsole writing output... [ 15%] source/rdkit.Chem.Draw.MolDrawing writing output... [ 15%] source/rdkit.Chem.Draw.SimilarityMaps writing output... [ 15%] source/rdkit.Chem.Draw.rdMolDraw2D writing output... [ 16%] source/rdkit.Chem.Draw.rdMolDraw2DQt writing output... [ 16%] source/rdkit.Chem.EState writing output... [ 16%] source/rdkit.Chem.EState.AtomTypes writing output... [ 17%] source/rdkit.Chem.EState.EState writing output... [ 17%] source/rdkit.Chem.EState.EState_VSA writing output... [ 18%] source/rdkit.Chem.EState.Fingerprinter writing output... [ 18%] source/rdkit.Chem.EnumerateHeterocycles writing output... [ 18%] source/rdkit.Chem.EnumerateStereoisomers writing output... [ 19%] source/rdkit.Chem.FastSDMolSupplier writing output... [ 19%] source/rdkit.Chem.FeatFinderCLI writing output... [ 19%] source/rdkit.Chem.FeatMaps writing output... [ 20%] source/rdkit.Chem.FeatMaps.FeatMapParser writing output... [ 20%] source/rdkit.Chem.FeatMaps.FeatMapPoint writing output... [ 21%] source/rdkit.Chem.FeatMaps.FeatMapUtils writing output... [ 21%] source/rdkit.Chem.FeatMaps.FeatMaps writing output... [ 21%] source/rdkit.Chem.Features writing output... [ 22%] source/rdkit.Chem.Features.FeatDirUtilsRD writing output... 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The HTML pages are in _build/html. make[2]: Leaving directory '/build/reproducible-path/rdkit-202503.1/Docs/Book' (cd /build/reproducible-path/rdkit-202503.1/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202503.1 /usr/bin/make latexpdf) make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/reproducible-path/rdkit-202503.1/Code/docs/* _build/html/cppapi sphinx-build -b latex -d _build/doctrees . _build/latex Running Sphinx v8.1.3 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist loading pickled environment... done myst v4.0.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [latex]: all documents updating environment: 0 added, 249 changed, 0 removed reading sources... 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[100%] source/rdkit.utils.spiral WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.rst:24: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.utils.rst [autosectionlabel.source/rdkit] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.rst:36: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.utils.rst [autosectionlabel.source/rdkit] WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Avalon.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Avalon.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon] WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Chem] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.rst:28: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.rst:115: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem] WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.AtomPairs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.AtomPairs.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.ChemUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.ChemUtils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils] WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Draw.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Draw.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw] WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2DQt' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.EState.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.EState.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState] WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.FeatMaps.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.FeatMaps.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Features.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Features.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features] WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fingerprints.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fingerprints.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints] WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fraggle.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fraggle.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle] WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolDb.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolDb.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb] WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolKey.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolKey.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey] WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm2D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.Pharm2D] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm2D.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.Pharm2D] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm3D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm3D.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D] WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.RegistrationHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Scaffolds.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Scaffolds.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds] WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum] WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SpacialScore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Subshape.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Subshape.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape] WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Suppliers.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Suppliers.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers] WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.fmcs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.fmcs.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs] WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdCIPLabeler' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDetermineBonds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdEHTTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolEnumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdShapeAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSynthonSpaceSearch' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdTautomerQuery' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.DataManip] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip] WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.Metric.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip.Metric] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.Metric.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.DataManip.Metric] WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataStructs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataStructs.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs] WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Dbase.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Dbase.rst:17: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase] WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DistanceGeometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DistanceGeometry.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry] WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ForceField.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.ForceField] WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Geometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.Geometry] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Geometry.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ForceField.rst [autosectionlabel.source/rdkit.Geometry] WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.ML] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.rst:18: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.rst:26: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML] WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Cluster.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Cluster.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster] WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Data.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Data.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data] WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.cQuantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Descriptors.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Descriptors.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors] WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.InfoTheory.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.InfoTheory.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory] WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.MLUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.MLUtils.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils] WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.SLT.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.SLT.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT] WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Scoring.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Scoring.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring] WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Numerics.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Numerics.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics] WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.SimDivFilters.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.SimDivFilters.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters] WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.VLib] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.rst:12: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib] WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.NodeLib.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.NodeLib.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib] WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.utils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils] /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.utils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202503.1/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils] WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/rdkit-202503.1/Docs/Book/data/README.md: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying TeX support files... Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/latexmkrc Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/Makefile Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/latexmkjarc Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/make.bat done copying assets: done processing RDKit.tex... index Overview Install GettingStartedInPython RDKit_Book GettingStartedWithContributing Cookbook Cartridge BackwardsIncompatibleChanges api-docs source/rdkit source/rdkit.Avalon source/rdkit.Avalon.pyAvalonTools source/rdkit.Chem source/rdkit.Chem.AtomPairs source/rdkit.Chem.AtomPairs.Pairs source/rdkit.Chem.AtomPairs.Sheridan source/rdkit.Chem.AtomPairs.Torsions source/rdkit.Chem.AtomPairs.Utils source/rdkit.Chem.ChemUtils source/rdkit.Chem.ChemUtils.AlignDepict source/rdkit.Chem.ChemUtils.BulkTester source/rdkit.Chem.ChemUtils.DescriptorUtilities source/rdkit.Chem.ChemUtils.SDFToCSV source/rdkit.Chem.ChemUtils.TemplateExpand source/rdkit.Chem.Draw source/rdkit.Chem.Draw.IPythonConsole source/rdkit.Chem.Draw.MolDrawing source/rdkit.Chem.Draw.SimilarityMaps source/rdkit.Chem.Draw.rdMolDraw2D source/rdkit.Chem.Draw.rdMolDraw2DQt source/rdkit.Chem.EState source/rdkit.Chem.EState.AtomTypes source/rdkit.Chem.EState.EState source/rdkit.Chem.EState.EState_VSA source/rdkit.Chem.EState.Fingerprinter source/rdkit.Chem.FeatMaps source/rdkit.Chem.FeatMaps.FeatMapParser source/rdkit.Chem.FeatMaps.FeatMapPoint source/rdkit.Chem.FeatMaps.FeatMapUtils source/rdkit.Chem.FeatMaps.FeatMaps source/rdkit.Chem.Features source/rdkit.Chem.Features.FeatDirUtilsRD source/rdkit.Chem.Features.ShowFeats source/rdkit.Chem.Fingerprints source/rdkit.Chem.Fingerprints.ClusterMols source/rdkit.Chem.Fingerprints.DbFpSupplier source/rdkit.Chem.Fingerprints.FingerprintMols source/rdkit.Chem.Fingerprints.MolSimilarity source/rdkit.Chem.Fingerprints.SimilarityScreener source/rdkit.Chem.Fraggle source/rdkit.Chem.Fraggle.FraggleSim source/rdkit.Chem.MolDb source/rdkit.Chem.MolDb.FingerprintUtils source/rdkit.Chem.MolDb.Loader source/rdkit.Chem.MolDb.Loader_orig source/rdkit.Chem.MolDb.Loader_sa source/rdkit.Chem.MolKey source/rdkit.Chem.MolKey.InchiInfo source/rdkit.Chem.MolKey.MolKey source/rdkit.Chem.Pharm2D source/rdkit.Chem.Pharm2D.Generate source/rdkit.Chem.Pharm2D.Gobbi_Pharm2D source/rdkit.Chem.Pharm2D.Matcher source/rdkit.Chem.Pharm2D.SigFactory source/rdkit.Chem.Pharm2D.Utils source/rdkit.Chem.Pharm3D source/rdkit.Chem.Pharm3D.EmbedLib source/rdkit.Chem.Pharm3D.ExcludedVolume source/rdkit.Chem.Pharm3D.Pharmacophore source/rdkit.Chem.Scaffolds source/rdkit.Chem.Scaffolds.MurckoScaffold source/rdkit.Chem.Scaffolds.rdScaffoldNetwork source/rdkit.Chem.SimpleEnum source/rdkit.Chem.SimpleEnum.Enumerator source/rdkit.Chem.Subshape source/rdkit.Chem.Subshape.BuilderUtils source/rdkit.Chem.Subshape.SubshapeAligner source/rdkit.Chem.Subshape.SubshapeBuilder source/rdkit.Chem.Subshape.SubshapeObjects source/rdkit.Chem.Suppliers source/rdkit.Chem.Suppliers.DbMolSupplier source/rdkit.Chem.Suppliers.MolSupplier source/rdkit.Chem.fmcs source/rdkit.Chem.fmcs.fmcs source/rdkit.Chem.AllChem source/rdkit.Chem.BRICS source/rdkit.Chem.BuildFragmentCatalog source/rdkit.Chem.ChemicalFeatures source/rdkit.Chem.ChemicalForceFields source/rdkit.Chem.Crippen source/rdkit.Chem.Descriptors source/rdkit.Chem.Descriptors3D source/rdkit.Chem.EnumerateHeterocycles source/rdkit.Chem.EnumerateStereoisomers source/rdkit.Chem.FastSDMolSupplier source/rdkit.Chem.FeatFinderCLI source/rdkit.Chem.FilterCatalog source/rdkit.Chem.FragmentCatalog source/rdkit.Chem.FragmentMatcher source/rdkit.Chem.Fragments source/rdkit.Chem.FunctionalGroups source/rdkit.Chem.GraphDescriptors source/rdkit.Chem.Graphs source/rdkit.Chem.Lipinski source/rdkit.Chem.MACCSkeys source/rdkit.Chem.MolCatalog source/rdkit.Chem.MolStandardize source/rdkit.Chem.MolStandardize.rdMolStandardize source/rdkit.Chem.MolSurf source/rdkit.Chem.PandasTools source/rdkit.Chem.PeriodicTable source/rdkit.Chem.PropertyMol source/rdkit.Chem.PyMol source/rdkit.Chem.QED source/rdkit.Chem.Randomize source/rdkit.Chem.Recap source/rdkit.Chem.ReducedGraphs source/rdkit.Chem.RegistrationHash source/rdkit.Chem.SATIS source/rdkit.Chem.SaltRemover source/rdkit.Chem.ShowMols source/rdkit.Chem.SpacialScore source/rdkit.Chem.TemplateAlign source/rdkit.Chem.TorsionFingerprints source/rdkit.Chem.inchi source/rdkit.Chem.rdchem source/rdkit.Chem.rdDistGeom source/rdkit.Chem.rdqueries source/rdkit.Chem.rdFMCS source/rdkit.Chem.rdMolAlign source/rdkit.Chem.rdMolHash source/rdkit.Chem.rdReducedGraphs source/rdkit.Chem.rdtrajectory source/rdkit.Chem.rdMolTransforms source/rdkit.Chem.rdmolfiles source/rdkit.Chem.rdPartialCharges source/rdkit.Chem.rdMolCatalog source/rdkit.Chem.rdCoordGen source/rdkit.Chem.rdMolChemicalFeatures source/rdkit.Chem.rdMMPA source/rdkit.Chem.rdRGroupDecomposition source/rdkit.Chem.rdForceFieldHelpers source/rdkit.Chem.rdDepictor source/rdkit.Chem.rdChemicalFeatures source/rdkit.Chem.rdmolops source/rdkit.Chem.rdFreeSASA source/rdkit.Chem.rdMolInterchange source/rdkit.Chem.rdShapeHelpers source/rdkit.Chem.rdinchi source/rdkit.Chem.rdChemReactions source/rdkit.Chem.rdSubstructLibrary source/rdkit.Chem.rdfiltercatalog source/rdkit.Chem.rdfragcatalog source/rdkit.Chem.rdMolDescriptors source/rdkit.Chem.rdFingerprintGenerator source/rdkit.Chem.rdMHFPFingerprint source/rdkit.Chem.rdSLNParse source/rdkit.Chem.rdAbbreviations source/rdkit.Chem.rdDeprotect source/rdkit.Chem.rdMolEnumerator source/rdkit.Chem.rdCIPLabeler source/rdkit.Chem.rdTautomerQuery source/rdkit.Chem.rdEHTTools source/rdkit.Chem.rdDetermineBonds source/rdkit.Chem.rdShapeAlign source/rdkit.Chem.rdSynthonSpaceSearch source/rdkit.DataManip source/rdkit.DataManip.Metric source/rdkit.DataManip.Metric.rdMetricMatrixCalc source/rdkit.DataStructs source/rdkit.DataStructs.BitEnsemble source/rdkit.DataStructs.BitEnsembleDb source/rdkit.DataStructs.BitUtils source/rdkit.DataStructs.LazySignature source/rdkit.DataStructs.TopNContainer source/rdkit.DataStructs.VectCollection source/rdkit.DataStructs.cDataStructs source/rdkit.Dbase source/rdkit.Dbase.DbConnection source/rdkit.Dbase.DbInfo source/rdkit.Dbase.DbModule source/rdkit.Dbase.DbResultSet source/rdkit.Dbase.DbUtils source/rdkit.Dbase.StorageUtils source/rdkit.DistanceGeometry source/rdkit.DistanceGeometry.DistGeom source/rdkit.ForceField source/rdkit.ForceField.rdForceField source/rdkit.Geometry source/rdkit.Geometry.rdGeometry source/rdkit.ML source/rdkit.ML.Cluster source/rdkit.ML.Cluster.Butina source/rdkit.ML.Cluster.ClusterUtils source/rdkit.ML.Cluster.ClusterVis source/rdkit.ML.Cluster.Clusters source/rdkit.ML.Cluster.Murtagh source/rdkit.ML.Cluster.Resemblance source/rdkit.ML.Cluster.Standardize source/rdkit.ML.Cluster.Clustering source/rdkit.ML.Data source/rdkit.ML.Data.DataUtils source/rdkit.ML.Data.FindQuantBounds source/rdkit.ML.Data.MLData source/rdkit.ML.Data.Quantize source/rdkit.ML.Data.cQuantize source/rdkit.ML.Data.SplitData source/rdkit.ML.Data.Stats source/rdkit.ML.Data.Transforms source/rdkit.ML.Descriptors source/rdkit.ML.Descriptors.CompoundDescriptors source/rdkit.ML.Descriptors.Descriptors source/rdkit.ML.Descriptors.MoleculeDescriptors source/rdkit.ML.Descriptors.Parser source/rdkit.ML.InfoTheory source/rdkit.ML.InfoTheory.BitClusterer source/rdkit.ML.InfoTheory.BitRank source/rdkit.ML.InfoTheory.entropy source/rdkit.ML.InfoTheory.rdInfoTheory source/rdkit.ML.MLUtils source/rdkit.ML.MLUtils.VoteImg source/rdkit.ML.SLT source/rdkit.ML.SLT.Risk source/rdkit.ML.Scoring source/rdkit.ML.Scoring.Scoring source/rdkit.ML.MatOps source/rdkit.ML.files source/rdkit.Numerics source/rdkit.Numerics.rdAlignment source/rdkit.SimDivFilters source/rdkit.SimDivFilters.SimilarityPickers source/rdkit.SimDivFilters.rdSimDivPickers source/rdkit.VLib source/rdkit.VLib.NodeLib source/rdkit.VLib.NodeLib.DbMolSupply source/rdkit.VLib.NodeLib.DbPickleSupplier source/rdkit.VLib.NodeLib.SDSupply source/rdkit.VLib.NodeLib.SmartsMolFilter source/rdkit.VLib.NodeLib.SmartsRemover source/rdkit.VLib.NodeLib.SmilesDupeFilter source/rdkit.VLib.NodeLib.SmilesOutput source/rdkit.VLib.NodeLib.SmilesSupply source/rdkit.VLib.Filter source/rdkit.VLib.Node source/rdkit.VLib.Output source/rdkit.VLib.Supply source/rdkit.VLib.Transform source/rdkit.utils source/rdkit.utils.cactvs source/rdkit.utils.chemutils source/rdkit.utils.fileutils source/rdkit.utils.listutils source/rdkit.utils.spiral source/rdkit.rdBase source/rdkit.RDConfig source/rdkit.RDLogger source/rdkit.RDPaths source/rdkit.RDRandom source/rdkit.TestRunner GettingStartedInC++ resolving references... /build/reproducible-path/rdkit-202503.1/Docs/Book/GettingStartedWithContributing.md:273: WARNING: 'myst' cross-reference target not found: 'building-rdkit-for-development' [myst.xref_missing] WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError(": Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))] processing RDKit.tex: done writing... done copying images... 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[1] [2] Chapter 1. (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Underfull \hbox (badness 10000) in paragraph at lines 131--133 []\T1/qtm/m/n/10 Chem-in-for-mat-ics nodes for KN-IME (dis-tributed from the KN -IME com-mu-nity site: [1{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [2] Chapter 2. [3] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 636--638 []\T1/qtm/m/n/10 If you want to use the python wrap-pers: \T1/txtt/m/n/10 ./boo tstrap.sh [][]with[]libraries=python, [7] [8] Underfull \hbox (badness 10000) in paragraph at lines 803--805 []\T1/qtm/m/n/10 You can en-able sup-port for gen-er-at-ing InChI strings and I nChI keys by adding the ar-gu-ment [9] [10] Underfull \hbox (badness 5490) in paragraph at lines 1028--1030 \T1/qtm/m/n/10 This sec-tion as-sumes that python is in-stalled in \T1/txtt/m/n /10 C:[]Python36 that the boost libraries have been [11] Underfull \hbox (badness 10000) in paragraph at lines 1079--1082 []\T1/txtt/m/n/10 DBOOST_ROOT=C:/boost []DRDK_BUILD_INCHI_SUPPORT=ON []DRDK_BUI LD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 1079--1082 []\T1/txtt/m/n/10 DRDK_BUILD_PGSQL=ON []DPostgreSQL_ROOT="C:[]Program Files[]Po stgreSQL[]9.5" []G"Visual Underfull \hbox (badness 10000) in paragraph at lines 1093--1095 []\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po stgresql[]9.5" []D "C:[] Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po stgresql[]9.5" []D "C:[] [12] Chapter 3. [13] [14 <./Cc1ccccc1.png>] [15] [16] LaTeX Warning: Hyper reference `GettingStartedInPython:chem-vs-allchem' on page 17 undefined on input line 1446. [17] [18] [19] [20] LaTeX Warning: Hyper reference `GettingStartedInPython:the-sssr-problem' on pag e 21 undefined on input line 1686. [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1836--1839 []\T1/qtm/m/n/10 An-other op-tion for Com-pute2DCoords al-lows you to gen-er-at e 2D de-pic-tions for molecules that Underfull \hbox (badness 10000) in paragraph at lines 1836--1839 \T1/qtm/m/n/10 closely mimic 3D con-form-ers. This is avail-able us-ing the fun c-tion \T1/txtt/m/n/10 rdkit.Chem.AllChem. Underfull \hbox (badness 10000) in paragraph at lines 1861--1867 []\T1/qtm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/txtt/m/n/10 rdkit.Chem.rdDepictor. 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[96] [97 <./parastereo_2.png> <./parastereo_1.png> <./potential_stereo_double_bond1. png> <./potential_stereo_double_bond2.png>] [98 <./potential_stereo_double_bond3.png>] [99] [100 <./nontetstereo_sp1.png> <./nontetstereo_sp2.png> <./nontetstereo_sp3.png> <./nontetstereo_sp4.png>] [101 <./nontetstereo_tb2.png> <./nontetstereo_tb1.png>] Package longtable Warning: Column widths have changed (longtable) in table 1 on input line 9400. [102 <./nontetstereo_oh2.png> <./nontetstereo_oh1.png>] Underfull \hbox (badness 10000) in paragraph at lines 9413--9415 []\T1/qtm/m/n/10 The clas-sic ex-am-ple of this is cis-platin - \T1/txtt/m/n/10 Cl[Pt@SP1](Cl)(<[][NH3])<[][NH3] \T1/qtm/m/n/10 - vs trans-platin - [103 <./nontetstereo_ex1.png> <./nontetstereo_ex2.png> <./nontetstereo_missing1 .png>] [104] [105] [106] [107] [108] [109] LaTeX Warning: Hyper reference `RDKit_Book:ph4-figure' on page 110 undefined on input line 9970. 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[113 <./ary_group.png>] [114] [115] Underfull \hbox (badness 10000) in paragraph at lines 10871--10873 \T1/qtm/m/n/10 Here's the rd-kitj-son rep-re-sen-ta-tion of the stereo groups f rom the molecule [116] Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 mol-Rxn-Com-po- [117] [118] Underfull \hbox (badness 10000) in paragraph at lines 11271--11276 []\T1/qtm/m/n/10 By de-fault the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.SDMolSup plier \T1/qtm/m/n/10 and \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. 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[151] [152 <./RDKitCB_0_im0.png> <./RDKitCB_0_im1.png>] [153 <./RDKitCB_0_im2.png> <./RDKitCB_40_im0.png>] [154 <./RDKitCB_40_im1.png> <./RDKitCB_23_im0.png>] [155 <./RDKitCB_23_im1.png> <./RDKitCB_32_im0.png>] [156 <./RDKitCB_32_im1.png> <./RDKitCB_1_im0.png (PNG copy)>] [157 <./RDKitCB_1_im1.png (PNG copy)> <./RDKitCB_1_im2.png (PNG copy)>] [158 <./RDKitCB_1_im3.png (PNG copy)> <./RDKitCB_2_im0.png>] [159 <./RDKitCB_2_im1.png> <./RDKitCB_36_im0.png>] [160 <./RDKitCB_36_im1.png>] [161 <./RDKitCB_38_im0.png>] [162 <./RDKitCB_39_im0.png (PNG copy)>] [163 <./RDKitCB_17_im0.png> <./RDKitCB_17_im1.png>] [164 <./RDKitCB_34_im0.png> <./RDKitCB_34_im1.png> <./RDKitCB_34_im2.png>] [165] Overfull \hbox (396.49246pt too wide) in paragraph at lines 14208--14208 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [166 <./RDKitCB_37_im0.png>] Overfull \hbox (396.49246pt too wide) in paragraph at lines 14237--14237 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [167 <./RDKitCB_37_im1.png>] [168 <./RDKitCB_37_im2.png>] [169 <./RDKitCB_35_im0.png>] [170] [171 <./RDKitCB_3_im0.png> <./RDKitCB_8_im0.png>] [172] [173 <./RDKitCB_30_im0.png>] [174 <./RDKitCB_30_im1.png>] [175 <./RDKitCB_7_im0.png> <./RDKitCB_7_im1.png>] [176 <./RDKitCB_7_im2.png (PNG copy)> <./RDKitCB_7_im3.png> <./RDKitCB_7_im4.pn g>] [177 <./RDKitCB_7_im5.png> <./RDKitCB_7_im6.png (PNG copy)>] [178] [179] [180 <./RDKitCB_29_im0.png (PNG copy)>] Underfull \vbox (badness 1043) detected at line 14891 [181 <./RDKitCB_33_im0.png (PNG copy)>] Overfull \vbox (0.99814pt too high) detected at line 14926 [182 <./RDKitCB_33_im1.png (PNG copy)>] [183 <./RDKitCB_33_im2.png (PNG copy)>] Overfull \hbox (490.99219pt too wide) in paragraph at lines 14992--14992 []\T1/txtt/m/n/10 "[][]CC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[C@@H](C[C@@]([C@@H]([C @H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2C[C@@]([C@H]([C@@H](O2)C)O)(C)OC)C)O[C@H]3[C@ @H]([C@H](C[C@H](O3)C)N(C)C)O)(C)O)C)C)O)(C)O[][] [184 <./RDKitCB_13_im0.png>] [185 <./RDKitCB_13_im1.png>] [186] [187 <./RDKitCB_20_im0.png>] [188 <./RDKitCB_21_im0.png>] [189 <./RDKitCB_21_im1.png>] [190 <./RDKitCB_21_im2.png (PNG copy)> <./RDKitCB_21_im3.png>] [191 <./RDKitCB_21_im4.png>] [192 <./RDKitCB_21_im5.png (PNG copy)>] [193 <./RDKitCB_22_im0.png>] [194 <./RDKitCB_22_im1.png>] [195 <./RDKitCB_6_im0.png (PNG copy)>] [196 <./RDKitCB_6_im1.png (PNG copy)> <./RDKitCB_6_im2.png (PNG copy)>] [197] [198 <./RDKitCB_15_im0.png> <./RDKitCB_15_im1.png>] [199] [200] [201] [202 <./RDKitCB_19_im0.png>] [203] [204] [205 <./RDKitCB_28_im0.png (PNG copy)> <./RDKitCB_28_im1.png (PNG copy)>] [206] [207] [208] Chapter 7. 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[229] [230] [231] Underfull \hbox (badness 10000) in paragraph at lines 17791--17795 \T1/qtm/m/n/10 Un-charger::uncharge() will now neu-tral-ize \T1/txtt/m/n/10 [Cl ,Br,I][O[]], [Cl,Br,I](=O)[O[]], [Cl, Underfull \hbox (badness 10000) in paragraph at lines 17791--17795 \T1/txtt/m/n/10 Br,I](=O)(=O)[O[]], [Cl,Br,I](=O)(=O)(=O)[O[]], [O[]]N=N[O[]], [N,P](=O)[O[]], Underfull \hbox (badness 10000) in paragraph at lines 17791--17795 \T1/txtt/m/n/10 [N+](=O)([O[]])[O[]], P(=O)([O[]])[O[]], P(=O)([O[]])([O[]])[O[ ]], S([O[]])[O[]], S(=O)([O[]])[O[]], [232] [233] [234] Chapter 9. [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] Chapter 10. [247] [248] [249] Underfull \hbox (badness 10000) in paragraph at lines 19693--19697 \T1/qtm/m/n/10 Groups of molecules are read us-ing a Sup-plier (for ex-am-ple, an \T1/txtt/m/n/10 RDKit::SDMolSupplier \T1/qtm/m/n/10 or an [250] [251] [252] [253] [254] Overfull \vbox (0.8796pt too high) detected at line 20130 [255] [256] Underfull \hbox (badness 6691) in paragraph at lines 20233--20235 []\T1/qtm/m/n/10 The \T1/txtt/m/n/10 auto\TS1/txtt/m/n/10 ' \T1/txtt/m/n/10 key word here is hiding the fact that \T1/qtm/m/n/10 get-Bond-Be-tweenAtoms\T1/txtt /m/n/10 returns the index of the [257] [258] LaTeX Warning: Hyper reference `GettingStartedInC++:the-sssr-problem' on page 2 59 undefined on input line 20361. LaTeX Warning: Hyper reference `GettingStartedInC++:two-add-hs' on page 259 und efined on input line 20391. [259] [260] [261] [262] [263] [264] [265] [266] [267] [268] Overfull \vbox (1.8739pt too high) detected at line 21250 [269] [270] [271] [272] Chapter 11. [273] [274] Chapter 12. No file RDKit.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. [275] (./RDKit.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `RDKit.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) Output written on RDKit.pdf (279 pages, 2913715 bytes). Transcript written on RDKit.log. Latexmk: Getting log file 'RDKit.log' Latexmk: Examining 'RDKit.fls' Latexmk: Examining 'RDKit.log' Latexmk: Index file 'RDKit.idx' was written Latexmk: Missing input file 'RDKit.toc' (or dependence on it) from following: No file RDKit.toc. Latexmk: Missing input file 'RDKit.ind' (or dependence on it) from following: No file RDKit.ind. Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'RDKit.pdf' Have index file 'RDKit.idx', RDKit.ind RDKit Latexmk: applying rule 'makeindex RDKit.idx'... Rule 'makeindex RDKit.idx': Reasons for rerun Category 'other': Rerun of 'makeindex RDKit.idx' forced or previously required: Reason or flag: 'Initial set up of rule' ------------ Run number 1 of rule 'makeindex RDKit.idx' ------------ ------------ Running 'makeindex -s python.ist -o "RDKit.ind" "RDKit.idx"' ------------ This is makeindex, version 2.17 [TeX Live 2025/dev] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file RDKit.idx...done (0 entries accepted, 0 rejected). Nothing written in RDKit.ind. Transcript written in RDKit.ilg. Latexmk: applying rule 'pdflatex'... 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(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Underfull \hbox (badness 10000) in paragraph at lines 131--133 []\T1/qtm/m/n/10 Chem-in-for-mat-ics nodes for KN-IME (dis-tributed from the KN -IME com-mu-nity site: [1{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [2] Chapter 2. [3] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 636--638 []\T1/qtm/m/n/10 If you want to use the python wrap-pers: \T1/txtt/m/n/10 ./boo tstrap.sh [][]with[]libraries=python, [7] [8] Underfull \hbox (badness 10000) in paragraph at lines 803--805 []\T1/qtm/m/n/10 You can en-able sup-port for gen-er-at-ing InChI strings and I nChI keys by adding the ar-gu-ment [9] [10] Underfull \hbox (badness 5490) in paragraph at lines 1028--1030 \T1/qtm/m/n/10 This sec-tion as-sumes that python is in-stalled in \T1/txtt/m/n /10 C:[]Python36 that the boost libraries have been [11] Underfull \hbox (badness 10000) in paragraph at lines 1079--1082 []\T1/txtt/m/n/10 DBOOST_ROOT=C:/boost []DRDK_BUILD_INCHI_SUPPORT=ON []DRDK_BUI LD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 1079--1082 []\T1/txtt/m/n/10 DRDK_BUILD_PGSQL=ON []DPostgreSQL_ROOT="C:[]Program Files[]Po stgreSQL[]9.5" []G"Visual Underfull \hbox (badness 10000) in paragraph at lines 1093--1095 []\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po stgresql[]9.5" []D "C:[] Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po stgresql[]9.5" []D "C:[] [12] Chapter 3. [13] [14 <./Cc1ccccc1.png>] [15] [16] [17] [18] [19] [20] [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1836--1839 []\T1/qtm/m/n/10 An-other op-tion for Com-pute2DCoords al-lows you to gen-er-at e 2D de-pic-tions for molecules that Underfull \hbox (badness 10000) in paragraph at lines 1836--1839 \T1/qtm/m/n/10 closely mimic 3D con-form-ers. This is avail-able us-ing the fun c-tion \T1/txtt/m/n/10 rdkit.Chem.AllChem. Underfull \hbox (badness 10000) in paragraph at lines 1861--1867 []\T1/qtm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/txtt/m/n/10 rdkit.Chem.rdDepictor. 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[85 <./picture_9.png (PNG copy)>] [86 <./picture_8.png> <./picture_7.png (PNG copy)>] [87 <./picture_10.png> <./picture_12.png>] [88 <./picture_11.png>] [89] [90] [91] [92] [93] [94] Underfull \hbox (badness 10000) in paragraph at lines 7298--7303 []\T1/qtm/m/n/10 Hence, a sin-gle change to SMARTS in-ter-pre-ta-tion, for ex-p res-sions of the form: [95] [96] [97 <./parastereo_2.png> <./parastereo_1.png> <./potential_stereo_double_bond1. png> <./potential_stereo_double_bond2.png>] [98 <./potential_stereo_double_bond3.png>] [99] [100 <./nontetstereo_sp1.png> <./nontetstereo_sp2.png> <./nontetstereo_sp3.png> <./nontetstereo_sp4.png>] [101 <./nontetstereo_tb2.png> <./nontetstereo_tb1.png>] [102 <./nontetstereo_oh 2.png> <./nontetstereo_oh1.png>] Underfull \hbox (badness 10000) in paragraph at lines 9413--9415 []\T1/qtm/m/n/10 The clas-sic ex-am-ple of this is cis-platin - \T1/txtt/m/n/10 Cl[Pt@SP1](Cl)(<[][NH3])<[][NH3] \T1/qtm/m/n/10 - vs trans-platin - [103 <./nontetstereo_ex1.png> <./nontetstereo_ex2.png> <./nontetstereo_missing1 .png>] [104] [105] [106] [107] [108] [109] [110] [111 <./picture_10.jpg>] Overfull \vbox (2.86082pt too high) detected at line 10236 [112] [113 <./ary_group.png>] [114] [115] Underfull \hbox (badness 10000) in paragraph at lines 10871--10873 \T1/qtm/m/n/10 Here's the rd-kitj-son rep-re-sen-ta-tion of the stereo groups f rom the molecule [116] Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 mol-Rxn-Com-po- [117] [118] Underfull \hbox (badness 10000) in paragraph at lines 11271--11276 []\T1/qtm/m/n/10 By de-fault the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.SDMolSup plier \T1/qtm/m/n/10 and \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. 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[123] [124 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./EnhancedS tereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_molE.png > <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [125] [126 <./atrop_example1.png> <./atrop_example2.png> <./atrop_example3.png>] [127 <./atrop_representation1.png>] [128 <./atrop_example4.png>] [129 <./atrop_example5.png> <./atrop_representation2.png>] [130 <./query_bonds.png>] [131 <./query_bonds.2.png> <./query_atoms.png>] [132] [133] Underfull \hbox (badness 10000) in paragraph at lines 12578--12588 []\T1/txtt/m/n/10 allowNontetrahedralChirality\T1/qtm/m/n/10 : when this is \T1 /txtt/m/n/10 true \T1/qtm/m/n/10 non-tetrahedral chi-ral-ity will be per- Underfull \hbox (badness 10000) in paragraph at lines 12578--12588 \T1/qtm/m/n/10 ceived from 3D co-or-di-nates. The de-fault value is \T1/txtt/m/ n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron-ment vari- Underfull \hbox (badness 10000) in paragraph at lines 12578--12588 \T1/qtm/m/n/10 able \T1/txtt/m/n/10 RDK_ENABLE_NONTETRAHEDRAL_STEREO \T1/qtm/m/ n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked from Underfull \hbox (badness 10000) in paragraph at lines 12578--12588 \T1/qtm/m/n/10 C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality::setA llowNontetrahedralChirality() \T1/qtm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 12578--12588 \T1/txtt/m/n/10 RDKit::Chirality::getAllowNontetrahedralChirality() \T1/qtm/m/n /10 or from Python us-ing the func-tions Underfull \hbox (badness 10000) in paragraph at lines 12590--12600 []\T1/txtt/m/n/10 useLegacyStereoPerception\T1/qtm/m/n/10 : when this is \T1/tx tt/m/n/10 true \T1/qtm/m/n/10 the legacy im-ple-men-ta-tion for per- Underfull \hbox (badness 10000) in paragraph at lines 12590--12600 \T1/qtm/m/n/10 ceiv-ing stere-o-chem-istry will be used. The de-fault value is \T1/txtt/m/n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 12590--12600 \T1/qtm/m/n/10 ment vari-able \T1/txtt/m/n/10 RDK_USE_LEGACY_STEREO_PERCEPTION \T1/qtm/m/n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked Underfull \hbox (badness 10000) in paragraph at lines 12590--12600 \T1/qtm/m/n/10 from C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality: :setUseLegacyStereoPerception() \T1/qtm/m/n/10 / [134] [135] [136] Chapter 5. [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \vbox (badness 1226) detected at line 13540 [148] [149] [150] Chapter 6. [151] [152 <./RDKitCB_0_im0.png> <./RDKitCB_0_im1.png>] [153 <./RDKitCB_0_im2.png> <./RDKitCB_40_im0.png>] [154 <./RDKitCB_40_im1.png> <./RDKitCB_23_im0.png>] [155 <./RDKitCB_23_im1.png> <./RDKitCB_32_im0.png>] [156 <./RDKitCB_32_im1.png> <./RDKitCB_1_im0.png (PNG copy)>] [157 <./RDKitCB_1_im1.png (PNG copy)> <./RDKitCB_1_im2.png (PNG copy)>] [158 <./RDKitCB_1_im3.png (PNG copy)> <./RDKitCB_2_im0.png>] [159 <./RDKitCB_2_im1.png> <./RDKitCB_36_im0.png>] [160 <./RDKitCB_36_im1.png>] [161 <./RDKitCB_38_im0.png>] [162 <./RDKitCB_39_im0.png (PNG copy)>] [163 <./RDKitCB_17_im0.png> <./RDKitCB_17_im1.png>] [164 <./RDKitCB_34_im0.png> <./RDKitCB_34_im1.png> <./RDKitCB_34_im2.png>] [165] Overfull \hbox (396.49246pt too wide) in paragraph at lines 14208--14208 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [166 <./RDKitCB_37_im0.png>] Overfull \hbox (396.49246pt too wide) in paragraph at lines 14237--14237 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [167 <./RDKitCB_37_im1.png>] [168 <./RDKitCB_37_im2.png>] [169 <./RDKitCB_35_im0.png>] [170] [171 <./RDKitCB_3_im0.png> <./RDKitCB_8_im0.png>] [172] [173 <./RDKitCB_30_im0.png>] [174 <./RDKitCB_30_im1.png>] [175 <./RDKitCB_7_im0.png> <./RDKitCB_7_im1.png>] [176 <./RDKitCB_7_im2.png (PNG copy)> <./RDKitCB_7_im3.png> <./RDKitCB_7_im4.pn g>] [177 <./RDKitCB_7_im5.png> <./RDKitCB_7_im6.png (PNG copy)>] [178] [179] [180 <./RDKitCB_29_im0.png (PNG copy)>] Underfull \vbox (badness 1043) detected at line 14891 [181 <./RDKitCB_33_im0.png (PNG copy)>] Overfull \vbox (0.99814pt too high) detected at line 14926 [182 <./RDKitCB_33_im1.png (PNG copy)>] [183 <./RDKitCB_33_im2.png (PNG copy)>] Overfull \hbox (490.99219pt too wide) in paragraph at lines 14992--14992 []\T1/txtt/m/n/10 "[][]CC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[C@@H](C[C@@]([C@@H]([C @H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2C[C@@]([C@H]([C@@H](O2)C)O)(C)OC)C)O[C@H]3[C@ @H]([C@H](C[C@H](O3)C)N(C)C)O)(C)O)C)C)O)(C)O[][] [184 <./RDKitCB_13_im0.png>] [185 <./RDKitCB_13_im1.png>] [186] [187 <./RDKitCB_20_im0.png>] [188 <./RDKitCB_21_im0.png>] [189 <./RDKitCB_21_im1.png>] [190 <./RDKitCB_21_im2.png (PNG copy)> <./RDKitCB_21_im3.png>] [191 <./RDKitCB_21_im4.png>] [192 <./RDKitCB_21_im5.png (PNG copy)>] [193 <./RDKitCB_22_im0.png>] [194 <./RDKitCB_22_im1.png>] [195 <./RDKitCB_6_im0.png (PNG copy)>] [196 <./RDKitCB_6_im1.png (PNG copy)> <./RDKitCB_6_im2.png (PNG copy)>] [197] [198 <./RDKitCB_15_im0.png> <./RDKitCB_15_im1.png>] [199] [200] [201] [202 <./RDKitCB_19_im0.png>] [203] [204] [205 <./RDKitCB_28_im0.png (PNG copy)> <./RDKitCB_28_im1.png (PNG copy)>] [206] [207] [208] Chapter 7. [209] [210] [211] [212] Overfull \hbox (1052.74055pt too wide) in paragraph at lines 16538--16538 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@H ]([C@@H](C)CC)NC(=O)[C@H](CO)NC(=O)[C@H](C)NC(=O)[C@H]([C@H](C)O)NC(=O)[C@@H]2C SSC[C@H](NC1=O)C(=O)N[C@@H](Cc1cnc[nH]1)C(=O)N[C@H](Cc1ccccc1)C(=O)N[C@@H](CCCN C(=N)N)C(=O)N[C@@H](Cc1c[nH]c3ccccc13)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 16540--16540 []\T1/txtt/m/n/10 CN1C(=O)[C@H](CCCNC(=N)N)NC(=O)[C@@H](Cc2ccc(O)cc2)NC(=O)[C@@ H]2CCCN2C(=O)[C@H](Cc2ccc3ccccc3c2)NC(=O)[C@@H]1CC(=O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 16541--16541 []\T1/txtt/m/n/10 NCCCC[C@H](NC(=O)[C@H](Cc1ccc(OP(=O)(O)O)cc1)NC(=O)Cc1ccccc1) C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc1ccccc1)C(N)=O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 16542--16542 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC(=O)CN(CC(=O)NC(C)(C)C(=O)N[C@@H](Cc1ccccc1 )C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N1CCC[ C@H]1C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CC(N)=O)C(N)=O)C(=O)c1cccnc1| Overfull \hbox (464.74226pt too wide) in paragraph at lines 16543--16543 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCN(CCCCCCCCCCCCCCCC)CCCCCC(=O)NC(C)(C)C(=O)NC( Cc1ccccc1)C(=O)NC(CC(C)C)C(=O)NC(Cc1ccccc1)C(=O)NC(CCCNC(=N)N)C(=O)N1CCCC1C(=O) NC(CCCNC(=N)N)C(=O)NC(CC(N)=O)C(N)=O| Overfull \hbox (359.74257pt too wide) in paragraph at lines 16544--16544 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CCSC)NC1=O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 16545--16545 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CC[S+](C)[O- Overfull \hbox (422.74239pt too wide) in paragraph at lines 16546--16546 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H](Cc 2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CCSC)NC(=O)[C@H](CC( C)C)NC(=O)[C@H](CC[S+](C)[O- Overfull \hbox (249.49289pt too wide) in paragraph at lines 16547--16547 []\T1/txtt/m/n/10 ])NC(=O)[C@H](C(C)C)NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H] (Cc2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CC[S+](C)[O- Overfull \vbox (2.3893pt too high) detected at line 16549 [213] Overfull \hbox (1052.74055pt too wide) in paragraph at lines 16561--16561 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@H ]([C@@H](C)CC)NC(=O)[C@H](CO)NC(=O)[C@H](C)NC(=O)[C@H]([C@H](C)O)NC(=O)[C@@H]2C SSC[C@H](NC1=O)C(=O)N[C@@H](Cc1cnc[nH]1)C(=O)N[C@H](Cc1ccccc1)C(=O)N[C@@H](CCCN C(=N)N)C(=O)N[C@@H](Cc1c[nH]c3ccccc13)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 16563--16563 []\T1/txtt/m/n/10 CN1C(=O)[C@H](CCCNC(=N)N)NC(=O)[C@@H](Cc2ccc(O)cc2)NC(=O)[C@@ H]2CCCN2C(=O)[C@H](Cc2ccc3ccccc3c2)NC(=O)[C@@H]1CC(=O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 16564--16564 []\T1/txtt/m/n/10 NCCCC[C@H](NC(=O)[C@H](Cc1ccc(OP(=O)(O)O)cc1)NC(=O)Cc1ccccc1) C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc1ccccc1)C(N)=O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 16565--16565 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC(=O)CN(CC(=O)NC(C)(C)C(=O)N[C@@H](Cc1ccccc1 )C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N1CCC[ C@H]1C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CC(N)=O)C(N)=O)C(=O)c1cccnc1| Overfull \hbox (359.74257pt too wide) in paragraph at lines 16566--16566 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CCSC)NC1=O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 16567--16567 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CC[S+](C)[O- Overfull \hbox (422.74239pt too wide) in paragraph at lines 16568--16568 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H](Cc 2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CCSC)NC(=O)[C@H](CC( C)C)NC(=O)[C@H](CC[S+](C)[O- Overfull \hbox (249.49289pt too wide) in paragraph at lines 16569--16569 []\T1/txtt/m/n/10 ])NC(=O)[C@H](C(C)C)NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H] (Cc2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CC[S+](C)[O- Overfull \hbox (522.4921pt too wide) in paragraph at lines 16570--16570 []\T1/txtt/m/n/10 CC[C@H](C)[C@H](N)C(=O)N[C@H](C(=O)N[C@@H](CC(C)C)C(=O)N[C@H] (C(=O)N1CCC[C@H]1C(=O)N1CCC[C@H]1C(=O)N[C@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CC(C )C)C(=O)O)Cc1ccccc1)Cc1ccccc1)C(C)C)[C@@H](C)CC| [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] Chapter 8. [229] [230] [231] Underfull \hbox (badness 10000) in paragraph at lines 17791--17795 \T1/qtm/m/n/10 Un-charger::uncharge() will now neu-tral-ize \T1/txtt/m/n/10 [Cl ,Br,I][O[]], [Cl,Br,I](=O)[O[]], [Cl, Underfull \hbox (badness 10000) in paragraph at lines 17791--17795 \T1/txtt/m/n/10 Br,I](=O)(=O)[O[]], [Cl,Br,I](=O)(=O)(=O)[O[]], [O[]]N=N[O[]], [N,P](=O)[O[]], Underfull \hbox (badness 10000) in paragraph at lines 17791--17795 \T1/txtt/m/n/10 [N+](=O)([O[]])[O[]], P(=O)([O[]])[O[]], P(=O)([O[]])([O[]])[O[ ]], S([O[]])[O[]], S(=O)([O[]])[O[]], [232] [233] [234] Chapter 9. [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] Chapter 10. [247] [248] [249] Underfull \hbox (badness 10000) in paragraph at lines 19693--19697 \T1/qtm/m/n/10 Groups of molecules are read us-ing a Sup-plier (for ex-am-ple, an \T1/txtt/m/n/10 RDKit::SDMolSupplier \T1/qtm/m/n/10 or an [250] [251] [252] [253] [254] Overfull \vbox (0.8796pt too high) detected at line 20130 [255] [256] Underfull \hbox (badness 6691) in paragraph at lines 20233--20235 []\T1/qtm/m/n/10 The \T1/txtt/m/n/10 auto\TS1/txtt/m/n/10 ' \T1/txtt/m/n/10 key word here is hiding the fact that \T1/qtm/m/n/10 get-Bond-Be-tweenAtoms\T1/txtt /m/n/10 returns the index of the [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] [268] Overfull \vbox (1.8739pt too high) detected at line 21250 [269] [270] [271] [272] Chapter 11. [273] [274] Chapter 12. (./RDKit.ind) [275] (./RDKit.aux) ) (see the transcript file for additional information) Output written on RDKit.pdf (279 pages, 2962396 bytes). Transcript written on RDKit.log. Latexmk: Getting log file 'RDKit.log' Latexmk: Examining 'RDKit.fls' Latexmk: Examining 'RDKit.log' Latexmk: Index file 'RDKit.idx' was written Latexmk: Log file says output to 'RDKit.pdf' Have index file 'RDKit.idx', RDKit.ind RDKit Latexmk: All targets (RDKit.pdf) are up-to-date make[3]: Leaving directory '/build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex' pdflatex finished; the PDF files are in _build/latex. make[2]: Leaving directory '/build/reproducible-path/rdkit-202503.1/Docs/Book' make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' cp -r rdkit obj-*/ find /build/reproducible-path/rdkit-202503.1 -name rdchem.so /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so PYTHONPATH=/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/:/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib:" dh_auto_test cd obj-x86_64-linux-gnu && make -j6 test ARGS\+=--verbose ARGS\+=-j6 make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j6 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end Connected to MAKE jobserver test 1 Start 1: testCoordGen 1: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/testCoordGen 1: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen 1: Test timeout computed to be: 1500 test 2 Start 2: pyCoordGen 2: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/External/CoordGen/Wrap/testCoordGen.py" 2: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/Wrap 2: Test timeout computed to be: 1500 test 3 Start 3: testDict 3: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/testDict 3: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral 3: Test timeout computed to be: 1500 test 4 Start 4: testRDValue 4: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/testRDValue 4: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral 4: Test timeout computed to be: 1500 test 5 Start 5: testConcurrentQueue 5: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/testConcurrentQueue 5: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral 5: Test timeout computed to be: 1500 test 6 Start 6: dictTestsCatch 6: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/dictTestsCatch 6: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral 6: Test timeout computed to be: 1500 3: [09:34:55] Testing Github940: property dictionaries leaking memory 3: [09:34:55] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect 3: static boost any:0.000287 s 3: dynamic boost any:0.00081 s 3: static RDAny:0.000122 s 3: dynamic RDAny:0.000751 s 3: static RDValue:1e-06 s 3: dynamic RDValue:0.000121 s 3: deleted! 3: [09:34:55] ------------------------------------- 3: [09:34:55] Testing String Pickle Roundtrips. 3: [09:34:55] done 3: [09:34:55] ------------------------------------- 3: [09:34:55] Testing conversion of vect to string. 3: [09:34:55] done 3: [09:34:55] ------------------------------------- 3: [09:34:55] Testing returning const references. 3: [09:34:55] any cast 3: [09:34:55] done: 0.00073 300000 3: [09:34:55] copy 4: -- running tests -- 4: min: -2147483648 -2147483648 4: min: 0 0 4: min: 2.22507e-308 2.22507e-308 4: min: 1.17549e-38 1.17549e-38 4: min: 0 0 4: == int 4: == double 4: == float 4: == unsigned int 4: == bool 4: == std::string 5: [09:34:55] 5: ----------------------------------------- 5: [09:34:55] Finished: testPushAndPop() 5: [09:34:55] 5: ----------------------------------------- 5: [09:34:55] 5: ----------------------------------------- 1/236 Test #4: testRDValue ............................ Passed 0.00 sec 3: [09:34:55] done: 0.000681 300000 3: [09:34:55] ref test 7 Start 7: logTestsCatch 7: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/logTestsCatch 7: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral 7: Test timeout computed to be: 1500 3: [09:34:55] done: 0.00068 300000 3: [09:34:55] dict 6: Randomness seeded to: 2454182210 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: 2/236 Test #6: dictTestsCatch ......................... Passed 0.00 sec test 8 Start 8: testDataStructs 8: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/testDataStructs 8: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs 8: Test timeout computed to be: 1500 3: [09:34:55] done: 0.001457 300000 3: [09:34:55] ref with hasVal 7: [09:34:55] should not be silent 7: [09:34:55] should not be silent 7: Randomness seeded to: 1697452930 7: [09:34:55] should not be silent 7: [09:34:55] should not be silent 7: [09:34:55] should not be silent 7: [09:34:55] should not be silent 7: [09:34:55] should not be silent 7: [09:34:55] should not be silent 7: [09:34:55] should not be silent 7: [09:34:55] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: 1: core 1: RDKit 2D 1: 1: 4 4 0 0 0 0 0 0 0 0999 V2000 1: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 1 1 0 1: M END 1: 3: [09:34:55] done: 0.001412 300000 3: [09:34:55] done 3: [09:34:55] ------------------------------------- 3: [09:34:55] Testing dict update. 3: [09:34:55] done 3: deleted! 3: deleted! 3: deleted! 3: deleted! 3: deleted! 3: deleted! 3/236 Test #7: logTestsCatch .......................... Passed 0.00 sec 1: core+sidechain 1: RDKit 2D 1: 1: 7 7 0 0 0 0 0 0 0 0999 V2000 1: 0.6496 0.9080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3926 -0.0584 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4726 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3396 -0.0616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2048 -0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.3590 -0.3156 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.6160 0.6508 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 1 1 0 1: M END 1: test 9 Start 9: testFPB 9: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/testFPB 9: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs 9: Test timeout computed to be: 1500 4/236 Test #3: testDict ............................... Passed 0.01 sec 1: templated 1: RDKit 2D 1: 1: 7 7 0 0 0 0 0 0 0 0999 V2000 1: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 10 10 0 0 0 0 0 0 0 0999 V2000 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 1 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 12 12 0 0 0 0 0 0 0 0999 V2000 1: 0.2846 -0.7516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2790 -1.7516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5898 -2.2466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4530 -1.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4476 -0.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5788 -0.2468 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5732 0.7532 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2956 1.2484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3012 2.2482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1700 2.7434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1590 0.7434 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1534 -0.2564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 8 11 1 0 1: 11 12 1 0 1: 12 1 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 12 12 0 0 0 0 0 0 0 0999 V2000 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 8 11 1 0 1: 11 12 1 0 1: 12 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 10 10 0 0 0 0 0 0 0 0999 V2000 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 1 1 0 1: M END 1: test 10 Start 10: testMultiFPB 10: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/testMultiFPB 10: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs 10: Test timeout computed to be: 1500 1: core+sidechain 1: RDKit 2D 1: 1: 16 16 0 0 0 0 0 0 0 0999 V2000 1: 1.7868 0.7799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.6532 1.2791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.5187 0.7785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.5180 -0.2215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.6515 -0.7209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7860 -0.2201 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.9195 -0.7195 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0539 -0.2189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8124 -0.7181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.6780 -0.2175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5445 -0.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.4101 -0.2161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.2764 -0.7153 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.1421 -0.2147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0547 0.7811 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.9211 1.2805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 8 15 1 0 1: 15 16 1 0 1: 16 1 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 16 16 0 0 0 0 0 0 0 0999 V2000 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 8 15 1 0 1: 15 16 1 0 1: 16 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 9 10 0 0 0 0 0 0 0 0999 V2000 1: 0.6718 -0.9994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5374 -0.4988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5366 0.5012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6702 1.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1954 0.4998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1946 -0.5002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1454 -0.8098 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7338 -0.0014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1466 0.8082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 6 1 1 0 1: 9 5 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 19 21 0 0 0 0 0 0 0 0999 V2000 1: -0.5657 -0.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4321 -0.4294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2977 -0.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2969 -1.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.1625 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4329 0.5708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5673 1.0714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5681 2.0714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2975 2.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2975 2.5728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.7969 3.4386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2991 0.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2999 -0.4278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2513 -0.7362 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5609 -1.6870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5393 -1.8942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8923 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.8381 0.0734 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2499 0.8820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 7 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 15 17 1 0 1: 14 18 1 0 1: 18 19 1 0 1: 13 1 1 0 1: 19 12 1 0 1: 11 9 1 0 1: M END 1: 8: [09:34:55] pass 8: [09:34:55] v3 4 8: [09:34:55] v4 5 8: [09:34:55] SPARSE ----------------------------------- 8: [09:34:55] Set 10: 0 8: [09:34:55] Set 11: 0 8: [09:34:55] Set 14: 0 8: [09:34:55] Set 10: 1 8: [09:34:55] Get 14: 1 8: [09:34:55] Num: 20 8: [09:34:55] NumOn: 3 8: [09:34:55] NumOff: 17 8: 10, 11, 14, 8: [09:34:55] t2[19]: 0 8: [09:34:55] t2[14]: 1 8: [09:34:55] t2[19]: 0 8: [09:34:55] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, 8: t1&t2: 10, 11, 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except 8: [09:34:55] Explicit ---------------------------------- 8: [09:34:55] Set 10: 0 8: [09:34:55] Set 11: 0 8: [09:34:55] Set 14: 0 8: [09:34:55] Set 10: 1 8: [09:34:55] Get 14: 1 8: [09:34:55] Num: 20 8: [09:34:55] NumOn: 3 8: [09:34:55] NumOff: 17 8: 10, 11, 14, 8: [09:34:55] t2[19]: 0 8: [09:34:55] t2[14]: 1 8: [09:34:55] t2[19]: 0 8: [09:34:55] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, 8: t1&t2: 10, 11, 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except 8: [09:34:55] Done 8: [09:34:55] Test DiscreteValue Vectors 1 ---------------------------- 8: [09:34:55] Expected failure: Value out of range 8: [09:34:55] Expected failure: Value out of range 8: [09:34:55] Expected failure: Value out of range 8: [09:34:55] Expected failure: Value out of range 8: [09:34:55] Expected failure: Value out of range 8: [09:34:55] Test DiscreteValue Vectors 2 ------------------------------ 8: [09:34:55] Test DiscreteValue Vectors 3 --------------------------- 8: [09:34:55] Test DiscreteValue Operations ----------------------------- 8: [09:34:55] Test DiscreteValue Operations 2 -------------------------- 8: [09:34:55] Test SparseIntVect ------------------------------------ 8: [09:34:55] Test SparseIntVect Serialization -------------------------- 8: [09:34:55] Test BitVect Serialization ------------------------------- 8: [09:34:55] Test BitVect to FPS ------------------------------- 8: [09:34:55] Test BitVect to binary string ------------------------------- 8: [09:34:55] Test Similarity Measures BitVect ------------------------------- 8: [09:34:55] Test Similarity Measures SparseBitVect ------------------------------- 8: [09:34:55] Test BitVect with all ones ------------------------------- 8: [09:34:55] Test Explicit BitVects: Concatenation Operation ------------------------------- 8: [09:34:55] Test bitmap operations ------------------------------- 8: [09:34:55] Test bitmaps as properties ------------------------------- 8: [09:34:55] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- 8: [09:34:55] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- 8: [09:34:55] Test RealValue Vectors 2: L1Norm ------------------------------- 8: [09:34:55] Test RealValue Vectors 3: Pickles ------------------------------- 8: [09:34:55] Test RealValue Vectors 4: Vector Operations ------------------------------- 5/236 Test #8: testDataStructs ........................ Passed 0.01 sec test 11 Start 11: catchDataStructs 11: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/catchDataStructs 11: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs 11: Test timeout computed to be: 1500 1: templated 1: RDKit 2D 1: 1: 19 21 0 0 0 0 0 0 0 0999 V2000 1: 0.5360 -0.9365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4021 -0.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2680 -0.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2680 -1.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4020 -2.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4021 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5360 1.0633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5360 2.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8300 3.4295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 -0.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2812 -0.7457 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.5900 -1.6966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9208 -2.4398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5682 -1.9046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8686 0.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2812 0.8725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 7 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 15 17 1 0 1: 14 18 1 0 1: 18 19 1 0 1: 13 1 1 0 1: 19 12 1 0 1: 11 9 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 5 4 0 0 0 0 0 0 0 0999 V2000 1: 1.2134 -0.4976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3464 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3444 1.0006 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5186 -0.5010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3856 -0.0028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 4 5 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 7 6 0 0 0 0 0 0 0 0999 V2000 1: -1.7333 -0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8661 -0.0697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8641 0.9303 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0011 -0.5713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8659 -0.0731 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8679 0.9269 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7309 -0.5749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 5 7 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 7 6 0 0 0 0 0 0 0 0999 V2000 1: 1.2227 -0.4921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3464 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3350 1.0058 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5185 -0.5117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3902 -0.0216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2506 -0.5314 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4014 0.9784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 5 7 1 0 1: M END 1: 1: test1 1: RDKit 2D 1: 1: 12 12 0 0 0 0 0 0 0 0999 V2000 1: -0.2902 0.4155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5740 0.9187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4418 0.4219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3060 0.9249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3024 1.9249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4454 -0.5781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5812 -1.0813 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2866 -0.5843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1508 -1.0875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.0186 -0.5905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.0222 0.4095 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.8828 -1.0937 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 2 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 3 6 2 0 1: 6 7 1 0 1: 7 8 2 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 2 0 1: 10 12 1 0 1: 8 1 1 0 1: M END 1: 1: test2 1: RDKit 2D 1: 1: 5 4 0 0 0 0 0 0 0 0999 V2000 1: -0.4980 0.7210 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0004 -0.1464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8678 -0.6440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5020 0.7182 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8642 -0.6488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 2 5 1 0 1: M END 1: 6/236 Test #9: testFPB ................................ Passed 0.01 sec test 12 Start 12: pyBV 12: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testBV.py" 12: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/Wrap 12: Test timeout computed to be: 1500 11: Randomness seeded to: 1232352749 11: =============================================================================== 11: All tests passed (3 assertions in 1 test case) 11: 7/236 Test #10: testMultiFPB ........................... Passed 0.01 sec test 13 Start 13: pyDiscreteValueVect 13: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testDiscreteValueVect.py" 13: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/Wrap 13: Test timeout computed to be: 1500 8/236 Test #11: catchDataStructs ....................... Passed 0.01 sec test 14 Start 14: pyRealValueVect 14: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testRealValueVect.py" 14: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/Wrap 14: Test timeout computed to be: 1500 1: cyclosporine a 1: RDKit 2D 1: 1: 85 85 0 0 0 0 0 0 0 0999 V2000 1: 1.4840 -0.8529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6174 -1.3521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6176 -2.3509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4860 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4912 -3.8491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3504 -2.3385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3352 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.1902 -0.7993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.1580 0.1961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0642 -1.2607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.9260 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.9144 0.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.7766 0.8337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0008 0.8409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.8596 1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.8162 2.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2038 1.4219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2560 3.1855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5280 4.2325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7128 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.8530 5.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.7676 4.5077 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0820 5.0835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9744 4.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8344 5.1337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9792 3.6203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8192 3.0813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7974 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7998 4.5809 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7790 3.0789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8812 2.0705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.1202 1.6015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.4194 2.0931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.0590 0.6211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8626 0.0983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8096 -0.8961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6470 -1.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.9122 -1.3587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.8776 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9982 -2.8425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1382 -2.3311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9886 -3.8459 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1202 -4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2526 -3.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6116 -4.3521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2494 -2.8505 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1228 -5.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2584 -5.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6092 -5.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2624 -6.8511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6018 -7.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5982 -8.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4624 -8.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9906 -5.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.8520 -4.3501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7288 -2.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7098 -3.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6032 -2.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.0646 -0.8235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.7362 0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5794 0.0605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5618 -0.9361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.4498 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.1628 0.1727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.7698 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5952 2.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.4896 1.7311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5292 3.1711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6054 3.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7186 2.0867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0328 6.0847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4396 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4580 5.6909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.3220 6.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5836 6.2065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2682 3.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.6630 2.5215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.5876 2.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.5648 3.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.7968 -1.2481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.6786 -0.7913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 7.5218 -1.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.7252 0.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0970 -2.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.2220 -2.8307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 3 2 1 1 1: 3 4 1 0 1: 4 5 2 0 1: 4 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 2 0 1: 8 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 2 0 1: 12 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 16 17 2 0 1: 16 18 1 0 1: 18 19 1 0 1: 19 20 1 0 1: 20 21 2 0 1: 20 22 1 0 1: 22 23 1 0 1: 23 24 1 0 1: 24 25 2 0 1: 24 26 1 0 1: 26 27 1 0 1: 27 28 1 0 1: 28 29 2 0 1: 28 30 1 0 1: 30 31 1 0 1: 31 32 1 0 1: 32 33 2 0 1: 32 34 1 0 1: 34 35 1 0 1: 35 36 1 0 1: 36 37 2 0 1: 36 38 1 0 1: 38 39 1 0 1: 39 40 1 0 1: 40 41 2 0 1: 40 42 1 0 1: 43 42 1 6 1: 43 44 1 0 1: 44 45 2 0 1: 44 46 1 0 1: 43 47 1 0 1: 47 48 1 0 1: 48 49 1 6 1: 48 50 1 0 1: 50 51 1 0 1: 51 52 2 0 1: 52 53 1 0 1: 47 54 1 1 1: 42 55 1 0 1: 39 56 1 6 1: 56 57 1 0 1: 56 58 1 0 1: 38 59 1 0 1: 35 60 1 6 1: 60 61 1 0 1: 61 62 1 0 1: 61 63 1 0 1: 34 64 1 0 1: 31 65 1 6 1: 65 66 1 0 1: 66 67 1 0 1: 66 68 1 0 1: 30 69 1 0 1: 27 70 1 6 1: 23 71 1 6 1: 19 72 1 6 1: 72 73 1 0 1: 73 74 1 0 1: 73 75 1 0 1: 18 76 1 0 1: 15 77 1 6 1: 77 78 1 0 1: 77 79 1 0 1: 11 80 1 6 1: 80 81 1 0 1: 81 82 1 0 1: 81 83 1 0 1: 10 84 1 0 1: 6 85 1 0 1: 46 3 1 0 1: M END 1: 1: single-double 1: RDKit 2D 1: 1: 17 16 0 0 0 0 0 0 0 0999 V2000 1: -6.9282 -0.2298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.0618 0.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.1962 -0.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.3298 0.2682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.4642 -0.2326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5978 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7322 -0.2340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8658 0.2654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0002 -0.2352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8662 0.2640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7318 -0.2366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5982 0.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4638 -0.2380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.3302 0.2612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.1958 -0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.0622 0.2598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.9278 -0.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 2 3 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 2 3 1: 11 12 1 0 1: 12 13 2 3 1: 13 14 1 0 1: 14 15 2 3 1: 15 16 1 0 1: 16 17 1 0 1: M END 1: 1: cis-trans 1: RDKit 2D 1: 1: 10 9 0 0 0 0 0 0 0 0999 V2000 1: -3.6370 -0.2028 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7706 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9050 -0.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.0386 -0.7008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1730 -0.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6934 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5590 -0.1988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5582 0.8012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.4238 1.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.2902 0.8026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 2 0 1: 3 4 1 0 1: 4 5 2 0 1: 5 6 1 0 1: 6 7 2 0 1: 7 8 1 0 1: 8 9 2 0 1: 9 10 1 0 1: M END 1: 1: admntn 1: RDKit 2D 1: 1: 10 12 0 0 0 0 0 0 0 0999 V2000 1: 1.3505 -0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5267 -1.1020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4629 -1.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.7523 0.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4741 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4761 0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3505 1.0730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.0611 0.5080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0643 0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1877 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 6 10 1 0 1: 8 1 1 0 1: 9 4 1 0 1: 10 2 1 0 1: M END 1: 1: github 4845 - nan coordinates but no crash 1: RDKit 2D 1: 1: 42 44 0 0 0 0 0 0 0 0999 V2000 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 2 0 1: 4 5 1 0 1: 5 6 3 0 1: 6 7 1 0 1: 7 8 2 0 1: 8 9 1 0 1: 9 10 3 0 1: 10 11 1 0 1: 11 12 2 0 1: 12 13 1 0 1: 13 14 3 0 1: 14 15 1 0 1: 15 16 2 0 1: 16 17 1 0 1: 16 18 1 0 1: 12 19 1 0 1: 19 20 2 0 1: 20 21 1 0 1: 20 22 1 0 1: 19 23 1 0 1: 23 24 3 0 1: 24 25 1 0 1: 25 26 1 0 1: 26 27 2 0 1: 27 28 2 0 1: 26 29 1 0 1: 29 30 3 0 1: 8 31 1 0 1: 31 32 2 0 1: 32 33 1 0 1: 32 34 1 0 1: 31 35 1 0 1: 35 36 3 0 1: 36 37 1 0 1: 37 38 2 0 1: 37 39 1 0 1: 39 40 2 0 1: 40 41 1 0 1: 40 42 1 0 1: 39 4 1 0 1: 15 7 1 0 1: 30 11 1 0 1: M END 1: 9/236 Test #1: testCoordGen ........................... Passed 0.09 sec test 15 Start 15: pySparseIntVect 15: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testSparseIntVect.py" 15: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/Wrap 15: Test timeout computed to be: 1500 13: ...... 13: ---------------------------------------------------------------------- 13: Ran 6 tests in 0.001s 13: 13: OK 14: ...... 14: ---------------------------------------------------------------------- 14: Ran 6 tests in 0.001s 14: 14: OK 10/236 Test #13: pyDiscreteValueVect .................... Passed 0.11 sec test 16 Start 16: pyFPB 16: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testFPB.py" 16: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/Wrap 16: Test timeout computed to be: 1500 2: .... 2: ---------------------------------------------------------------------- 2: Ran 4 tests in 0.012s 2: 2: OK 11/236 Test #14: pyRealValueVect ........................ Passed 0.11 sec test 17 Start 17: testTransforms 17: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/testTransforms 17: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry 17: Test timeout computed to be: 1500 17: **************************************** 17: testPointND 17: **************************************** 17: testPointOps3D 17: **************************************** 17: testPointOps2D 17: **************************************** 17: test12D 17: ref1: 0.300196 2.33799 ref2: 0.171289 1.46683 17: pt1: 0.977717 0.985104 pt2: 2.15922 1.67611 17: **************************************** 17: test23D 17: **************************************** 17: test3MatMultiply 17: Pt1: 1 0 0 Pt2: 2 0 0 17: -Pt1: -1 -0 -0 17: tp1: 0 0 0 tp2: 0 0 0 17: tp1: 0 0 0 tp2: 0 0 0 17: tp1: 0 0 3 tp2: 0 0 3 17: npt1: 0 0 3 npt2: 0 0 4 17: Pt1: 0 0 3 Pt2: 6.12323e-17 0 4 17: **************************************** 17: testFromQuaternion 17: **************************************** 12/236 Test #17: testTransforms ......................... Passed 0.01 sec test 18 Start 18: testGrid 18: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/testGrid 18: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry 18: Test timeout computed to be: 1500 13/236 Test #2: pyCoordGen ............................. Passed 0.15 sec test 19 Start 19: testRealValueGrid 19: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/testRealValueGrid 19: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry 19: Test timeout computed to be: 1500 18: *********************************************************** 18: Testing Grid 18: --------------------------------- 18: testUniformGrid1 18: 18: --------------------------------- 18: testUniformGrid2 18: 18: --------------------------------- 18: testUniformGridPickling 18: 18: --------------------------------- 18: testGridOps 18: 18: --------------------------------- 18: testUniformGridIndexing 18: 14/236 Test #18: testGrid ............................... Passed 0.02 sec test 20 Start 20: geometryTestsCatch 20: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/geometryTestsCatch 20: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry 20: Test timeout computed to be: 1500 20: Randomness seeded to: 394216319 20: =============================================================================== 20: All tests passed (50 assertions in 5 test cases) 20: 15/236 Test #20: geometryTestsCatch ..................... Passed 0.00 sec test 21 Start 21: testPyGeometry 21: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap/testGeometry.py" 21: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/Wrap 21: Test timeout computed to be: 1500 19: *********************************************************** 19: Testing RealValueGrid3D 19: --------------------------------- 19: test1UniformRealValueGrid3D 19: 19: --------------------------------- 19: test2UniformRealValueGrid3DPickling 19: 19: --------------------------------- 19: test3UniformRealValueGrid3DIndexing 19: 19: --------------------------------- 19: test4UniformRealValueGrid3DOps 19: 16/236 Test #19: testRealValueGrid ...................... Passed 0.02 sec test 22 Start 22: testMatrices 22: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/testMatrices 22: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics 22: Test timeout computed to be: 1500 22: [09:34:55] ----------------------------------------- 22: [09:34:55] Testing RDNumerics: vectors and matrices Code 22: [09:34:55] --------------------------------------- 22: [09:34:55] test1Vector 22: [09:34:55] --------------------------------------- 22: [09:34:55] test2Matrix 22: [09:34:55] --------------------------------------- 22: [09:34:55] test3SquareMatrix 22: [09:34:55] --------------------------------------- 22: [09:34:55] test4SymmMatrix 17/236 Test #22: testMatrices ........................... Passed 0.00 sec test 23 Start 23: testConrec 23: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/testConrec 23: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics 23: Test timeout computed to be: 1500 15: ......... 15: ---------------------------------------------------------------------- 15: Ran 9 tests in 0.003s 15: 15: OK 23: Randomness seeded to: 612668932 23: =============================================================================== 23: All tests passed (76 assertions in 3 test cases) 23: 18/236 Test #23: testConrec ............................. Passed 0.03 sec test 24 Start 24: testAlignment 24: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment/testAlignment 24: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment 24: Test timeout computed to be: 1500 19/236 Test #15: pySparseIntVect ........................ Passed 0.12 sec test 25 Start 25: pyAlignment 25: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/Wrap/testAlignment.py" 25: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap 25: Test timeout computed to be: 1500 24: ----------------------------------------- 24: Testing Alignment Code 24: --------------------------------------- 24: testBasic 24: --------------------------------------- 24: testTriangle 24: --------------------------------------- 24: testFourPts 24: --------------------------------------- 24: testReflection 24: --------------------------------------- 20/236 Test #24: testAlignment .......................... Passed 0.01 sec test 26 Start 26: testOptimizer 26: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/testOptimizer 26: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer 26: Test timeout computed to be: 1500 26: ------------------------------------- 26: Testing linear search. 26: done 26: ------------------------------------- 26: Testing BFGS optimization. 26: done 21/236 Test #26: testOptimizer .......................... Passed 0.00 sec test 27 Start 27: ForceFieldsCatch 27: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/ForceFieldsCatch 27: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField 27: Test timeout computed to be: 1500 27: Randomness seeded to: 260184753 27: =============================================================================== 27: All tests passed (20 assertions in 2 test cases) 27: 22/236 Test #27: ForceFieldsCatch ....................... Passed 0.02 sec test 28 Start 28: testUFFForceField 28: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/UFF/testUFFForceField 28: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/UFF 28: Test timeout computed to be: 1500 16: ......... 16: ---------------------------------------------------------------------- 16: Ran 9 tests in 0.003s 16: 16: OK 28: ------------------------------------- 28: Unit tests for force field basics. 28: done 28: ------------------------------------- 28: Unit tests for basics of UFF bond-stretch terms. 28: done 28: ------------------------------------- 28: Unit tests for UFF bond-stretch terms. 28: done 28: ------------------------------------- 28: Unit tests for basics of UFF angle terms. 28: done 28: ------------------------------------- 28: Unit tests for UFF angle-bend terms. 28: theta = 3.14159; theta0 = 3.14159 28: theta = 2.094395, param1.theta0 = 2.094395 28: done 28: ------------------------------------- 28: Test Simple UFF molecule optimizations. 28: done 28: ------------------------------------- 28: Unit tests for UFF nonbonded terms. 28: done 28: ------------------------------------- 28: Test UFF torsional terms. 28: done 28: ------------------------------------- 28: Test UFF Parameter objects 28: ------------------------------------- 28: Test Simple UFF molecule optimization, part 2. 28: done 28: ------------------------------------- 28: Test UFF Torsion Conflicts. 28: C 0.4783 -0.7477 -0.0753 28: C -0.5465 -0.0176 0.3519 28: C -0.5114 1.4472 0.0870 28: H -1.5201 -0.4838 0.2485 28: H 0.4696 1.8363 0.3367 28: O -1.2618 1.9423 0.6934 28: F -0.7163 1.6298 -0.9622 28: done 28: ------------------------------------- 28: Unit tests for UFF distance constraint terms. 28: done 28: ------------------------------------- 28: Unit tests for all UFF constraint terms. 23/236 Test #16: pyFPB .................................. Passed 0.12 sec test 29 Start 29: testMMFFForceField 29: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField 29: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/MMFF 29: Test timeout computed to be: 1500 28: done 28: ------------------------------------- 28: Unit tests for copying UFF ForceFields. 29: ------------------------------------- 29: Official MMFF validation suite. 28: done 28: ------------------------------------- 28: Unit test for UFF butane scan. 25: ..... 25: ---------------------------------------------------------------------- 25: Ran 5 tests in 0.001s 25: 25: OK 25: Testing Alignment Wrapper code: 24/236 Test #25: pyAlignment ............................ Passed 0.11 sec test 30 Start 30: pyForceFieldConstraints 30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ForceField/Wrap/testConstraints.py" 30: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/Wrap 30: Test timeout computed to be: 1500 29: 29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... 21: .................... 21: ---------------------------------------------------------------------- 21: Ran 20 tests in 0.036s 21: 21: OK 21: Testing Geometry wrapper 25/236 Test #21: testPyGeometry ......................... Passed 0.17 sec test 31 Start 31: testDistGeom 31: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom/testDistGeom 31: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom 31: Test timeout computed to be: 1500 31: *********************************************************** 31: test1 31: *********************************************************** 31: testIssue216 31: Rows: 4 Columns: 4 31: 0 1 1 1 31: 1 0 1 1 31: 1 1 0 1 31: 1 1 1 0 31: *********************************************************** 31: 26/236 Test #31: testDistGeom ........................... Passed 0.01 sec test 32 Start 32: pyDistGeom 32: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DistGeom/Wrap/rough_test.py" 32: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom/Wrap 32: Test timeout computed to be: 1500 28: done 27/236 Test #28: testUFFForceField ...................... Passed 0.13 sec test 33 Start 33: graphmolcpTest 33: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolcpTest 33: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 33: Test timeout computed to be: 1500 33: 33: 33: 33: COPY 28/236 Test #33: graphmolcpTest ......................... Passed 0.01 sec test 34 Start 34: graphmolqueryTest 34: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest 34: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 34: Test timeout computed to be: 1500 34: [09:34:56] ---------------------- Test1 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Test2 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Test3 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Test4 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Test5 34: [09:34:56] Done! 34: [09:34:56] 34: 34: **** 34: Pre-condition Violation 34: Can't expand empty query 34: Violation occurred on line 30 in file ./Code/GraphMol/QueryAtom.cpp 34: Failed Expression: dp_query 34: ---------- 34: Stacktrace: 34: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 34: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 34: 2# RDKit::QueryAtom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 34: 3# 0x000055AD1BB7C7EB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest 34: 4# 0x000055AD1BB7A0AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest 34: 5# 0x00007F14B5A33CA8 in /lib/x86_64-linux-gnu/libc.so.6 34: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 34: 7# 0x000055AD1BB7A121 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest 34: ---------- 34: **** 34: 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Test issue 2892580 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Test github issue 53: query molecules not matching [R] 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Test queries using qualifiers instead of == 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Test Github issue 165: radicals not used in atom-atom matching 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Test extra atom queries 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Test extra bond queries 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Test num heteroatom neighbor queries 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Test atom type queries 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Test Github #2471: dummy atom queries are flagged as complex 34: [09:34:56] Done! 34: [09:34:56] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() 34: [09:34:56] Done! 29/236 Test #34: graphmolqueryTest ...................... Passed 0.01 sec test 35 Start 35: graphmolMolOpsTest 35: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMolOpsTest 35: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 35: Test timeout computed to be: 1500 35: 1 1 2 35: 1 1 1 35: 2 1 0.75 35: path: 2 35: [09:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored 35: [09:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored 35: [09:34:56] Explicit valence for atom # 0 B, 5, is greater than permitted 35: [09:34:56] Explicit valence for atom # 1 C, 5, is greater than permitted 35: [09:34:56] Explicit valence for atom # 1 C, 5, is greater than permitted 35: [09:34:56] Explicit valence for atom # 1 C, 5, is greater than permitted 35: [09:34:56] Explicit valence for atom # 1 Si, 7, is greater than permitted 35: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 35: [09:34:56] non-ring atom 0 marked aromatic 35: [09:34:56] non-ring atom 0 marked aromatic 35: [09:34:56] Conflicting single bond directions around double bond at index 17. 35: [09:34:56] BondStereo set to STEREONONE and single bond directions set to NONE. 32: ...... 32: ---------------------------------------------------------------------- 32: Ran 6 tests in 0.000s 32: 32: OK 35: starting ring finding 35: done 35: starting ring finding 35: done 35: starting ring finding 35: done 35: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C 35: starting sanitization 30/236 Test #32: pyDistGeom ............................. Passed 0.12 sec test 36 Start 36: graphmoltestChirality 36: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestChirality 36: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 36: Test timeout computed to be: 1500 35: done 35: starting sanitization 30: ...[09:34:56] Molecule does not have explicit Hs. Consider calling AddHs() 35: done 35: starting ring finding 35: done 35: starting ring finding 35: done 35: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 36: -------------------------- 36: -------------------------- 36: C/C=C/C(C)Cl 35: [09:34:56] WARNING: not removing hydrogen atom with dummy atom neighbors 35: ------------------------------- 35: [09:34:56] Explicit valence for atom # 0 N, 4, is greater than permitted 36: [09:34:56] Conflicting single bond directions around double bond at index 2. 36: [09:34:56] BondStereo set to STEREONONE and single bond directions set to NONE. 36: [09:34:56] Conflicting single bond directions around double bond at index 4. 36: [09:34:56] BondStereo set to STEREONONE and single bond directions set to NONE. 36: [09:34:56] Conflicting single bond directions around double bond at index 15. 36: [09:34:56] BondStereo set to STEREONONE and single bond directions set to NONE. 36: [09:34:56] Conflicting single bond directions around double bond at index 2. 36: [09:34:56] BondStereo set to STEREONONE and single bond directions set to NONE. 36: [09:34:56] Conflicting single bond directions around double bond at index 1. 36: [09:34:56] BondStereo set to STEREONONE and single bond directions set to NONE. 35: [09:34:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 35: [09:34:56] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 35: [09:34:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 35: [09:34:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 35: [09:34:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 35: [09:34:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 35: [09:34:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 35: [09:34:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 35: 36: -------------------------------------------------- 35: [09:34:56] WARNING: not removing hydrogen atom with dummy atom neighbors 31/236 Test #36: graphmoltestChirality .................. Passed 0.03 sec test 37 Start 37: graphmoltestPickler 37: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPickler 37: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 37: Test timeout computed to be: 1500 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing String Pickle Roundtrips. 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing reading existing pickle file (v2). 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing combining molecules using pickles. 37: Atoms: 37: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 37: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 37: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 37: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 37: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 37: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: SP3 37: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 37: Bonds: 37: 0 0->1 order: 1 37: 1 1->2 order: 1 37: 2 2->0 order: 1 37: 3 3->4 order: 1 37: 4 4->5 order: 1 37: 5 5->6 order: 1 37: 6 6->3 order: 1 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing Issue164: Roundtrip Pickle Failure. 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing Issue219: Pickle Failure with Conformations. 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing Issue220: Pickle problems with bond stereochemistry. 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing query serialization. 37: [09:34:56] C=[$(C=O)] 37: [09:34:56] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing radical handling in pickles. 37: [09:34:56] done 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing sf.net issue 2788233. 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing sf.net issue 3202580. 37: mass! 13.0034 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing sf.net issue 3316407. 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing sf.net issue 3496759. 37: smi match: *C *C 37: smi match: **=* **=* 37: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O 37: smi match: *OS(=O)OC *OS(=O)OC 37: smi match: *S(=O)(=O)OC *S(=O)(=O)OC 37: smi match: O=COC=O O=COC=O 37: smi match: OO OO 37: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 37: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 37: smi match: nnnOC=O nnnOC=O 37: smi match: *=C=N *=C=N 37: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F 37: smi match: SP(S)=S SP(S)=S 37: smi match: NP(N)(N)=O NP(N)(N)=O 37: smi match: cN=[N+]=[N-] cN=[N+]=[N-] 37: smi match: *CC=O *CC=O 37: smi match: NNC=O NNC=O 37: smi match: * * 37: smi match: C=P C=P 37: smi match: CC(=N)Cl CC(=N)Cl 37: smi match: N=O N=O 37: smi match: ** ** 37: smi match: N=C=N N=C=N 37: smi match: [C-]#[NH+] [C-]#[NH+] 37: smi match: O=CON(C=O)C=O O=CON(C=O)C=O 37: smi match: N#CC[OH] N#CC[OH] 37: smi match: N#CC=O N#CC=O 37: smi match: N#CS(=O)=O N#CS(=O)=O 37: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC 37: smi match: N#CN=N N#CN=N 37: smi match: N=NCC=O N=NCC=O 37: smi match: CCCCCCC CCCCCCC 37: smi match: OCCOCCO OCCOCCO 37: smi match: SS SS 37: smi match: [SH] [SH] 37: smi match: *1CC1 *1CC1 37: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH] 37: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH] 37: smi match: NC(=S)N=N NC(=S)N=N 37: smi match: N#CS N#CS 37: smi match: cC[N+] cC[N+] 37: smi match: C*C=S C*C=S 37: smi match: N[CH2]C#N N[CH2]C#N 37: smi match: O=C1CCO1 O=C1CCO1 37: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] 37: smi match: O=C1CCN1 O=C1CCN1 37: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 37: smi match: C=CC=CC=CC=C C=CC=CC=CC=C 37: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 37: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 37: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 37: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 37: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 37: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 37: smi match: cN(=O)~O cN(=O)~O 37: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O 37: smi match: N~NC=O N~NC=O 37: smi match: *=N~C *=N~C 37: smi match: CO*(=O)=O CO*(=O)=O 37: smi match: * * 37: smi match: * * 37: smi match: *C=C *C=C 37: smi match: N#CS N#CS 37: smi match: *C=S *C=S 37: smi match: *N *N 37: smi match: *C(=C)C=O *C(=C)C=O 37: smi match: *C#C *C#C 37: smi match: N#CCO N#CCO 37: smi match: O=N(=O)CCO O=N(=O)CCO 37: smi match: N=CS N=CS 37: smi match: O=CNC(O)C=O O=CNC(O)C=O 37: smi match: C=C(C=O)C=O C=C(C=O)C=O 37: smi match: N=CC=O N=CC=O 37: smi match: *C(C=O)C=O *C(C=O)C=O 37: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O 37: smi match: O=CC=CC=O O=CC=CC=O 37: smi match: O=CN(O)C=O O=CN(O)C=O 37: smi match: O=CN(S)C=O O=CN(S)C=O 37: smi match: O=CNC=O O=CNC=O 37: smi match: O=CNN=O O=CNN=O 37: smi match: O=CNNC=O O=CNNC=O 37: smi match: O=CNOC=O O=CNOC=O 37: smi match: O=CS O=CS 37: smi match: O=CSC=S O=CSC=S 37: smi match: S=CS S=CS 37: smi match: C=O C=O 37: smi match: *C=N *C=N 37: smi match: CCCCCCC CCCCCCC 37: smi match: CN=O CN=O 37: smi match: CS(=O)(=O)O CS(=O)(=O)O 37: smi match: O=C1CCO1 O=C1CCO1 37: smi match: C=C(S)[SH]=O C=C(S)[SH]=O 37: smi match: C=CCO C=CCO 37: smi match: C=CC=N C=CC=N 37: smi match: C=CC=O C=CC=O 37: smi match: C=CC(=O)C=C C=CC(=O)C=C 37: smi match: C=CC=S C=CC=S 37: smi match: C=CC(=S)S C=CC(=S)S 37: smi match: *C=C(*)C=C *C=C(*)C=C 37: smi match: C=CC=N C=CC=N 37: smi match: *N(*)C=C *N(*)C=C 37: smi match: C=CN(=O)=O C=CN(=O)=O 37: smi match: C=CN(O)=O C=CN(O)=O 37: smi match: C=CO C=CO 37: smi match: C=COC=O C=COC=O 37: smi match: C=CS C=CS 37: smi match: C=C[SH](=O)=O C=C[SH](=O)=O 37: smi match: C=NCO C=NCO 37: smi match: C=NC=O C=NC=O 37: smi match: C=NN C=NN 37: smi match: C=NN=C C=NN=C 37: smi match: C=NO C=NO 37: smi match: C=NOC=O C=NOC=O 37: smi match: C=N=O C=N=O 37: smi match: N#CS N#CS 37: smi match: *CN=O *CN=O 37: smi match: NCN NCN 37: smi match: ON=CCN=O ON=CCN=O 37: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O 37: smi match: N=C(N)S N=C(N)S 37: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 37: smi match: NC=S NC=S 37: smi match: NC(N)=S NC(N)=S 37: smi match: C=CN C=CN 37: smi match: NOC=O NOC=O 37: smi match: C1CN1 C1CN1 37: smi match: O=C1NNNN1 O=C1NNNN1 37: smi match: N=C(N)C(=N)N N=C(N)C(=N)N 37: smi match: N=C(N)O N=C(N)O 37: smi match: N=C(N)C(=N)S N=C(N)C(=N)S 37: smi match: *C=N *C=N 37: smi match: N=CC=O N=CC=O 37: smi match: N=CS N=CS 37: smi match: N=C=N N=C=N 37: smi match: N=C=O N=C=O 37: smi match: N=C=S N=C=S 37: smi match: NOC(=O)O NOC(=O)O 37: smi match: *C(O)=S *C(O)=S 37: smi match: C=CO C=CO 37: smi match: ON=CC=NO ON=CC=NO 37: smi match: *C[SH](=O)=O *C[SH](=O)=O 37: smi match: OS(=O)=O OS(=O)=O 37: smi match: N#CS N#CS 37: smi match: C=C(S)S C=C(S)S 37: smi match: N=C(N)S N=C(N)S 37: smi match: N=C(S)S N=C(S)S 37: smi match: NC(=S)S NC(=S)S 37: smi match: O=CNS O=CNS 37: smi match: S S 37: smi match: [SiH4] [SiH4] 37: smi match: NS NS 37: smi match: NCN NCN 37: smi match: cC(c)(O)O cC(c)(O)O 37: smi match: *C(c)O *C(c)O 37: smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O 37: smi match: cS(=O)(=O)O cS(=O)(=O)O 37: smi match: *c1ccccn1=O *c1ccccn1=O 37: smi match: *c1ccccn1 *c1ccccn1 37: smi match: *c1nccccn1 *c1nccccn1 37: smi match: C1COCOC1 C1COCOC1 37: smi match: C=S C=S 37: smi match: c=S c=S 37: smi match: S=CS S=CS 37: smi match: C=CN(=O)=O C=CN(=O)=O 37: smi match: C=CN(=O)O C=CN(=O)O 37: smi match: N=CC=O N=CC=O 37: smi match: C=CS C=CS 37: smi match: SC(S)(S)S SC(S)(S)S 37: smi match: OS(O)(O)O OS(O)(O)O 37: smi match: O=N(=O)C[SH](=O)=O O=N(=O)C[SH](=O)=O 37: smi match: O=N(O)C[SH](=O)=O O=N(O)C[SH](=O)=O 37: smi match: N#CS N#CS 37: smi match: C=NO C=NO 37: smi match: C=N[SH]=N C=N[SH]=N 37: smi match: O=C(S)S O=C(S)S 37: smi match: N=C(S)S N=C(S)S 37: smi match: N=C(=N)S N=C(=N)S 37: smi match: O=N=O O=N=O 37: smi match: O=NO O=NO 37: smi match: ONO ONO 37: smi match: C1SCS1 C1SCS1 37: smi match: N=C=S N=C=S 37: smi match: N=C=N N=C=N 37: smi match: C1N=N1 C1N=N1 37: smi match: *CS *CS 37: smi match: SC(S)=C(S)S SC(S)=C(S)S 37: smi match: N=CC=NO N=CC=NO 37: smi match: N#CCC#N N#CCC#N 37: smi match: CON=O CON=O 37: smi match: C=CN C=CN 37: smi match: C=N[SH](=O)=O C=N[SH](=O)=O 37: smi match: NN=O NN=O 37: smi match: NC(=O)S NC(=O)S 37: smi match: N#CS N#CS 37: smi match: NC(=O)C(N)=O NC(=O)C(N)=O 37: smi match: c=N c=N 37: smi match: C1COCO1 C1COCO1 37: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O 37: smi match: O=CC=O O=CC=O 37: smi match: O=CNOC=O O=CNOC=O 37: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 37: smi match: ONO ONO 37: smi match: ON(~O)~O ON(~O)~O 37: smi match: OC1COC(O)C1 OC1COC(O)C1 37: smi match: OC1CCOC1O OC1CCOC1O 37: smi match: OC1CCOC(O)C1 OC1CCOC(O)C1 37: smi match: N=[N+]=N N=[N+]=N 37: smi match: N#CN N#CN 37: smi match: C=NN=C C=NN=C 37: smi match: *CCN(C)C *CCN(C)C 37: smi match: CNN CNN 37: smi match: *CC *CC 37: smi match: OCS OCS 37: smi match: C1NO1 C1NO1 37: smi match: COS(C)(=O)=O COS(C)(=O)=O 37: smi match: C1CO1 C1CO1 37: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 37: smi match: *C(*)=C *C(*)=C 37: smi match: N#[NH+] N#[NH+] 37: smi match: C#NO C#NO 37: smi match: OOO OOO 37: smi match: OO OO 37: smi match: O~Cl(~O)~O O~Cl(~O)~O 37: smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O 37: smi match: [OH]~C(~O)~O [OH]~C(~O)~O 37: smi match: *N *N 37: smi match: *P *P 37: smi match: *S *S 37: smi match: *C(*)(*)C=C *C(*)(*)C=C 37: smi match: *C(*)(*)C=C *C(*)(*)C=C 37: smi match: *C(*)C=C *C(*)C=C 37: smi match: *CC=C *CC=C 37: smi match: CN=C=O CN=C=O 37: smi match: CN=C=S CN=C=S 37: smi match: *C=O *C=O 37: smi match: N=N N=N 37: smi match: SS SS 37: smi match: O=C1CCNC(=O)O1 O=C1CCNC(=O)O1 37: smi match: CSC(C)=N CSC(C)=N 37: smi match: COC(C)=N COC(C)=N 37: smi match: C=C=C C=C=C 37: smi match: *C(=O)OC=O *C(=O)OC=O 37: smi match: C=CC#N C=CC#N 37: smi match: C=CC=O C=CC=O 37: smi match: CC=CC(C)=O CC=CC(C)=O 37: smi match: CC=CC(=O)OCC CC=CC(=O)OCC 37: smi match: C#CC#N C#CC#N 37: smi match: C#CC=O C#CC=O 37: smi match: C#CC(=O)OCC C#CC(=O)OCC 37: smi match: C#CC=O C#CC=O 37: smi match: *C(=O)C#C *C(=O)C#C 37: smi match: C=CC=O C=CC=O 37: smi match: *C(*)(*)O *C(*)(*)O 37: smi match: COS(O)(=O)=O COS(O)(=O)=O 37: smi match: CS(=O)(=O)[O-] CS(=O)(=O)[O-] 37: smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-] 37: smi match: *C(*)(*)C=O *C(*)(*)C=O 37: smi match: *C(*)(*)C=O *C(*)(*)C=O 37: smi match: *C(*)C=O *C(*)C=O 37: smi match: *CC=O *CC=O 37: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 37: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 37: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O 37: smi match: *C[SH](=O)=O *C[SH](=O)=O 37: smi match: * * 37: smi match: *1CC1 *1CC1 37: smi match: O=COC=O O=COC=O 37: smi match: N=C=O N=C=O 37: smi match: N=C=S N=C=S 37: smi match: O~O O~O 37: smi match: N~[SiH4] N~[SiH4] 37: smi match: *P *P 37: smi match: C=N=N C=N=N 37: smi match: *N#[NH+] *N#[NH+] 37: smi match: *S* *S* 37: smi match: ** ** 37: smi match: *CC* *CC* 37: smi match: *O[SiH3] *O[SiH3] 37: smi match: *OS(*)~O *OS(*)~O 37: smi match: N~N~O N~N~O 37: smi match: *N(~O)(~O)~O *N(~O)(~O)~O 37: smi match: *[N+](=C)[O-] *[N+](=C)[O-] 37: smi match: * * 37: smi match: *C(*)NCN(*)* *C(*)NCN(*)* 37: smi match: *OCC#N *OCC#N 37: smi match: **C=C **C=C 37: smi match: C=C[O-] C=C[O-] 37: smi match: C=CO C=CO 37: smi match: * * 37: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O 37: smi match: O=COn1ccnc1 O=COn1ccnc1 37: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 37: smi match: CC(C)(C)S CC(C)(C)S 37: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C 37: smi match: [CH]=O [CH]=O 37: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C 37: smi match: SS SS 37: smi match: [SH] [SH] 37: smi match: *C* *C* 37: smi match: * * 37: smi match: C[nH3+] C[nH3+] 37: smi match: cC(=N)[NH2] cC(=N)[NH2] 37: smi match: O=CN[OH] O=CN[OH] 37: smi match: NN NN 37: smi match: * * 37: smi match: *OP(=O)O* *OP(=O)O* 37: smi match: * * 37: smi match: * * 37: smi match: * * 37: smi match: *N=C(*)* *N=C(*)* 37: smi match: *C(*)(*)C=O *C(*)(*)C=O 37: smi match: CSC=O CSC=O 37: smi match: * * 37: smi match: O=CCl O=CCl 37: smi match: *** *** 37: smi match: *C=O *C=O 37: smi match: C[OH] C[OH] 37: smi match: C[OH] C[OH] 37: smi match: C[OH] C[OH] 37: smi match: C[OH] C[OH] 37: smi match: C[CH]=O C[CH]=O 37: smi match: *=* *=* 37: smi match: *C *C 37: smi match: C#C C#C 37: smi match: *[CH]C=C *[CH]C=C 37: smi match: cCC(=O)[OH] cCC(=O)[OH] 37: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] 37: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] 37: smi match: C=CC(=O)[OH] C=CC(=O)[OH] 37: smi match: N#CC(=O)[OH] N#CC(=O)[OH] 37: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O 37: smi match: *N(*)C*=O *N(*)C*=O 37: smi match: O=*C[OH] O=*C[OH] 37: smi match: *=C*=O *=C*=O 37: smi match: *=CC#N *=CC#N 37: smi match: *C[OH] *C[OH] 37: smi match: ** ** 37: smi match: *C[OH] *C[OH] 37: smi match: *C(*)=O *C(*)=O 37: smi match: * * 37: smi match: *CC(=O)[OH] *CC(=O)[OH] 37: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O 37: smi match: *c *c 37: smi match: CN(C)c CN(C)c 37: smi match: c c 37: smi match: *c *c 37: smi match: *c *c 37: smi match: **:*cF **:*cF 37: smi match: cB([OH])[OH] cB([OH])[OH] 37: smi match: N~N~N N~N~N 37: smi match: *N=N* *N=N* 37: smi match: *CC[OH] *CC[OH] 37: smi match: *CC[OH] *CC[OH] 37: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] 37: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] 37: smi match: *CCC(=O)[OH] *CCC(=O)[OH] 37: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] 37: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O 37: smi match: *OC(*)=O *OC(*)=O 37: smi match: *C(=O)[OH] *C(=O)[OH] 37: smi match: O=C[OH] O=C[OH] 37: smi match: *OC(=O)O* *OC(=O)O* 37: smi match: * * 37: smi match: *OC(=O)Cl *OC(=O)Cl 37: smi match: *C#N *C#N 37: smi match: NCC(=O)NCC=O NCC(=O)NCC=O 37: smi match: SS SS 37: smi match: * * 37: smi match: *=* *=* 37: smi match: *=* *=* 37: smi match: *=* *=* 37: smi match: *=* *=* 37: smi match: C1CO1 C1CO1 37: smi match: *OC(*)=O *OC(*)=O 37: smi match: * * 37: smi match: *O*[OH] *O*[OH] 37: smi match: COC(C)(C)O COC(C)(C)O 37: smi match: *[OH] *[OH] 37: smi match: ** ** 37: smi match: C=N[NH2] C=N[NH2] 37: smi match: C=NC=O C=NC=O 37: smi match: * * 37: smi match: C#NC C#NC 37: smi match: CN=C=O CN=C=O 37: smi match: CN=C=S CN=C=S 37: smi match: *OC(*)(*)O* *OC(*)(*)O* 37: smi match: *C(*)=O *C(*)=O 37: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C 37: smi match: *~*=O *~*=O 37: smi match: *~*=O *~*=O 37: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] 37: smi match: * * 37: smi match: *C#N *C#N 37: smi match: *N(=O)~O *N(=O)~O 37: smi match: N N 37: smi match: OC(=O)C(O)=O OC(=O)C(O)=O 37: smi match: C=NO C=NO 37: smi match: O~O O~O 37: smi match: c[OH] c[OH] 37: smi match: O=P(~[OH])~O O=P(~[OH])~O 37: smi match: CO~P(=O)~O CO~P(=O)~O 37: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O 37: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O 37: smi match: O=P(~O)~O O=P(~O)~O 37: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O 37: smi match: C[NH2] C[NH2] 37: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 37: smi match: * * 37: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 37: smi match: CS(C)~O CS(C)~O 37: smi match: CS(C)(~O)~O CS(C)(~O)~O 37: smi match: CS(N)(~O)~O CS(N)(~O)~O 37: smi match: CS([OH])(~O)~O CS([OH])(~O)~O 37: smi match: COS(C)(~O)~O COS(C)(~O)~O 37: smi match: *S(C)(~O)~O *S(C)(~O)~O 37: smi match: CN(C)C CN(C)C 37: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 37: smi match: *C(*)=S *C(*)=S 37: smi match: *OC(*)=S *OC(*)=S 37: smi match: * * 37: smi match: C[SH] C[SH] 37: smi match: c[SH] c[SH] 37: smi match: NC(N)=S NC(N)=S 37: smi match: * * 37: smi match: ***** ***** 37: smi match: NC(N)=O NC(N)=O 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing sf.net issue 280. 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing sf.net issue 285. 37: [09:34:56] done 37: [09:34:56] done 37: [09:34:56] done 37: [09:34:56] done 37: [09:34:56] done 37: [09:34:56] done 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing Github2441: Add RDProps interface to Conformers. 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing Issue2510: Pickle Confs as double. 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing Github #2465: Negative atom-map numbers cause depickling to fail. 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing loading pickled mols with conformers 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing conformer reading/writing options 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing property reading options 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing property reading options 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing boost::serialization integration 37: [09:34:56] done 37: [09:34:56] ------------------------------------- 37: [09:34:56] Testing github issue 6036 32/236 Test #37: graphmoltestPickler .................... Passed 0.13 sec test 38 Start 38: graphmoltestPicklerGlobalSetting 38: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting 38: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 38: Test timeout computed to be: 1500 35: [09:34:56] Maximum BFS search size exceeded. 35: This is likely due to a highly symmetric fused ring system. 38: [09:34:56] done 33/236 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.01 sec test 39 Start 39: graphmolIterTest 39: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolIterTest 39: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 39: Test timeout computed to be: 1500 34/236 Test #39: graphmolIterTest ....................... Passed 0.01 sec test 40 Start 40: hanoiTest 40: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest 40: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 40: [09:34:56] Testing the hanoi sort 40: [09:34:56] populating vectors 30: ......[09:34:56] Molecule does not have explicit Hs. Consider calling AddHs() 35: [09:34:56] Maximum BFS search size exceeded. 35: This is likely due to a highly symmetric fused ring system. 35: F/C=C/Cl 35: [H]/C(F)=C(/[H])Cl 35: F/C=C/Cl 35: F/C=C/Cl 35: C/C(F)=C(/C)Cl 35: [09:34:56] ----------------------- 35: Testing isRingFused 35/236 Test #35: graphmolMolOpsTest ..................... Passed 0.41 sec test 41 Start 41: graphmolMemTest1 41: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 41: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 41: Test timeout computed to be: 1500 36/236 Test #41: graphmolMemTest1 ....................... Passed 0.01 sec test 42 Start 42: resMolSupplierTest 42: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest 42: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 42: Test timeout computed to be: 1500 40: [09:34:56] sorting (hanoi sort) vectors 30: ... 30: ---------------------------------------------------------------------- 30: Ran 12 tests in 0.460s 30: 30: OK 37/236 Test #30: pyForceFieldConstraints ................ Passed 0.61 sec test 43 Start 43: molBundleTest 43: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/molBundleTest 43: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 43: Test timeout computed to be: 1500 38/236 Test #43: molBundleTest .......................... Passed 0.01 sec test 44 Start 44: testSGroup 44: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/testSGroup 44: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 44: Test timeout computed to be: 1500 39/236 Test #44: testSGroup ............................. Passed 0.02 sec test 45 Start 45: test-valgrind 45: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/test-valgrind 45: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 45: Test timeout computed to be: 1500 40/236 Test #45: test-valgrind .......................... Passed 0.01 sec test 46 Start 46: graphmolTestsCatch 46: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 46: Test timeout computed to be: 1500 46: Randomness seeded to: 1902068438 46: [09:34:56] WARNING: not removing hydrogen atom without neighbors 46: [09:34:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 46: [09:34:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 46: [09:34:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 46: [09:34:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 46: [09:34:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 46: [09:34:56] Explicit valence for atom # 1 N, 5, is greater than permitted 46: [09:34:56] Explicit valence for atom # 1 N, 6, is greater than permitted 46: [09:34:56] Explicit valence for atom # 1 N, 5, is greater than permitted 46: [09:34:56] Explicit valence for atom # 1 N, 5, is greater than permitted 46: [09:34:56] Explicit valence for atom # 2 O, 3, is greater than permitted 46: [09:34:56] Explicit valence for atom # 2 O, 3, is greater than permitted 46: [09:34:56] non-ring atom 2 marked aromatic 46: [09:34:56] non-ring atom 2 marked aromatic 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 1 2 3 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 1 2 3 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 46: [09:34:56] Explicit valence for atom # 1 O, 3, is greater than permitted 46: [09:34:56] Explicit valence for atom # 4 F, 2, is greater than permitted 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 6 7 8 46: [09:34:56] Explicit valence for atom # 1 C, 5, is greater than permitted 46: [09:34:56] WARNING: not removing hydrogen atom with dummy atom neighbors 46: [09:34:56] WARNING: not removing hydrogen atom with dummy atom neighbors 46: [09:34:56] WARNING: not removing hydrogen atom with wedged bond 46: [09:34:56] WARNING: not removing hydrogen atom without neighbors 46: [09:34:56] WARNING: not removing hydrogen atom without neighbors 46: [09:34:56] WARNING: not removing hydrogen atom without neighbors 46: [09:34:56] WARNING: not removing hydrogen atom without neighbors 46: [09:34:56] Unreasonable formal charge on atom # 0. 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: no atom 46: Violation occurred on line 181 in file ./Code/GraphMol/ROMol.cpp 46: Failed Expression: at 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F6E668 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: no owner 46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h 46: Failed Expression: dp_mol 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F6E6F2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: atom not associated with this molecule 46: Violation occurred on line 182 in file ./Code/GraphMol/ROMol.cpp 46: Failed Expression: &at->getOwningMol() == this 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F6E785 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: no atom 46: Violation occurred on line 364 in file ./Code/GraphMol/ROMol.cpp 46: Failed Expression: at 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F6E870 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: no owner 46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h 46: Failed Expression: dp_mol 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F6E901 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: atom not associated with this molecule 46: Violation occurred on line 365 in file ./Code/GraphMol/ROMol.cpp 46: Failed Expression: &at->getOwningMol() == this 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F6E99D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: no atom 46: Violation occurred on line 371 in file ./Code/GraphMol/ROMol.cpp 46: Failed Expression: at 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F6F2B9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: no owner 46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h 46: Failed Expression: dp_mol 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F6EB08 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: atom not associated with this molecule 46: Violation occurred on line 372 in file ./Code/GraphMol/ROMol.cpp 46: Failed Expression: &at->getOwningMol() == this 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F6EBA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: null atom passed in 46: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp 46: Failed Expression: atom_pin 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F6F291 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: cannot take ownership of an atom which already has an owner 46: Violation occurred on line 387 in file ./Code/GraphMol/ROMol.cpp 46: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F6EEB8 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: cannot take ownership of an bond which already has an owner 46: Violation occurred on line 412 in file ./Code/GraphMol/ROMol.cpp 46: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F6F26D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 46: [09:34:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 46: [09:34:56] WARNING: not removing hydrogen atom without neighbors 46: [09:34:56] Explicit valence for atom # 1 F greater than permitted 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: plain atoms have no Query 46: Violation occurred on line 697 in file ./Code/GraphMol/Atom.cpp 46: Failed Expression: 0 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F1614B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: plain atoms have no Query 46: Violation occurred on line 702 in file ./Code/GraphMol/Atom.cpp 46: Failed Expression: 0 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F161E0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: plain bonds have no Query 46: Violation occurred on line 207 in file ./Code/GraphMol/Bond.cpp 46: Failed Expression: 0 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F15E70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] 46: 46: **** 46: Pre-condition Violation 46: plain bonds have no query 46: Violation occurred on line 228 in file ./Code/GraphMol/Bond.cpp 46: Failed Expression: 0 46: ---------- 46: Stacktrace: 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 46: 3# 0x000055A530F15F05 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 4# 0x000055A530FBB938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 5# 0x000055A530FBC458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 6# 0x000055A530FBC8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 7# 0x000055A530F8DF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 8# 0x000055A530F8E2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 9# 0x000055A530F08DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: 10# 0x00007F8934433CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 46: 12# 0x000055A530F08E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 46: [09:34:56] Unusual charge on atom 0 number of radical electrons set to zero 46: [09:34:56] Unusual charge on atom 0 number of radical electrons set to zero 46: [09:34:56] Unusual charge on atom 0 number of radical electrons set to zero 46: [09:34:56] non-ring atom 0 marked aromatic 46: [09:34:56] non-ring atom 0 marked aromatic 46: [09:34:56] Explicit valence for atom # 1 C, 5, is greater than permitted 46: [09:34:56] Explicit valence for atom # 9 C, 5, is greater than permitted 46: [09:34:56] Explicit valence for atom # 3 N, 4, is greater than permitted 46: [09:34:56] Explicit valence for atom # 15 C, 5, is greater than permitted 46: [09:34:56] Explicit valence for atom # 11 C, 5, is greater than permitted 46: [09:34:56] Explicit valence for atom # 9 C, 5, is greater than permitted 46: [09:34:56] Explicit valence for atom # 9 C, 5, is greater than permitted 46: [09:34:56] Explicit valence for atom # 9 C, 6, is greater than permitted 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 7 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 3 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 3 7 46: [09:34:56] Can't kekulize mol. Unkekulized atoms: 3 7 46: [09:34:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 46: [09:34:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 46: [09:34:56] Explicit valence for atom # 1 O, 3, is greater than permitted 46: [09:34:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 46: [09:34:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 46: [09:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 46: [09:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 46: [09:34:56] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. 46: [09:34:56] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom 46: [09:34:56] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom 46: [09:34:56] non-ring atom 0 marked aromatic 46: [09:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 46: [09:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 46: [09:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 46: [09:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 46: [09:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 46: [09:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 46: [09:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 46: [09:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 46: [09:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 46: [09:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 46: [09:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 46: [09:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 46: [09:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 46: [09:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 46: [09:34:56] Explicit valence for atom # 0 Al, 6, is greater than permitted 46: [09:34:56] Explicit valence for atom # 0 Al, 6, is greater than permitted 46: [09:34:56] Explicit valence for atom # 1 Si, 6, is greater than permitted 46: [09:34:56] Explicit valence for atom # 1 Si, 6, is greater than permitted 46: [09:34:56] Explicit valence for atom # 0 P, 6, is greater than permitted 46: [09:34:56] Explicit valence for atom # 0 P, 6, is greater than permitted 46: [09:34:56] Explicit valence for atom # 0 P, 7, is greater than permitted 46: [09:34:56] Explicit valence for atom # 0 P, 7, is greater than permitted 46: [09:34:56] Explicit valence for atom # 1 As, 6, is greater than permitted 46: [09:34:56] Explicit valence for atom # 1 As, 6, is greater than permitted 46: [09:34:56] Explicit valence for atom # 1 As, 7, is greater than permitted 46: [09:34:56] Explicit valence for atom # 1 As, 7, is greater than permitted 46: [09:34:56] Explicit valence for atom # 0 Sb, 6, is greater than permitted 46: [09:34:56] Explicit valence for atom # 0 Sb, 6, is greater than permitted 46: [09:34:56] Explicit valence for atom # 0 Sb, 7, is greater than permitted 46: [09:34:56] Explicit valence for atom # 0 Sb, 7, is greater than permitted 46: [09:34:56] Explicit valence for atom # 1 Bi, 6, is greater than permitted 46: [09:34:56] Explicit valence for atom # 1 Bi, 6, is greater than permitted 46: [09:34:56] Explicit valence for atom # 1 Bi, 8, is greater than permitted 46: [09:34:56] Explicit valence for atom # 1 Bi, 8, is greater than permitted 46: =============================================================================== 46: All tests passed (4479 assertions in 107 test cases) 46: 41/236 Test #46: graphmolTestsCatch ..................... Passed 0.13 sec test 47 Start 47: graphmolOrganometallicsCatch 47: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch 47: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 47: Test timeout computed to be: 1500 47: Randomness seeded to: 3703970615 47: =============================================================================== 47: All tests passed (62 assertions in 6 test cases) 47: 42/236 Test #47: graphmolOrganometallicsCatch ........... Passed 0.06 sec test 48 Start 48: graphmolSGroupCatch 48: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolSGroupCatch 48: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 48: Test timeout computed to be: 1500 48: Randomness seeded to: 1388598896 48: =============================================================================== 48: All tests passed (136 assertions in 8 test cases) 48: 43/236 Test #48: graphmolSGroupCatch .................... Passed 0.02 sec test 49 Start 49: graphmolAdjustQueryCatch 49: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch 49: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 49: Test timeout computed to be: 1500 49: Randomness seeded to: 2026323765 49: =============================================================================== 49: All tests passed (292 assertions in 12 test cases) 49: 44/236 Test #49: graphmolAdjustQueryCatch ............... Passed 0.04 sec test 50 Start 50: chiralityTestsCatch 50: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/chiralityTestsCatch 50: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 50: Test timeout computed to be: 1500 50: Randomness seeded to: 2956258322 50: [09:34:56] unable to set wavy bonds for double bonds: 3 50: [09:34:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 50: [09:34:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 50: [09:34:56] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 50: [09:34:56] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 50: [09:34:57] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored 50: =============================================================================== 50: All tests passed (2295 assertions in 80 test cases) 50: 45/236 Test #50: chiralityTestsCatch .................... Passed 0.06 sec test 51 Start 51: canonTestsCatch 51: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/canonTestsCatch 51: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 51: Test timeout computed to be: 1500 29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 29: All 191 tests passed 29: 29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... 12: .................. 12: ---------------------------------------------------------------------- 12: Ran 18 tests in 1.457s 12: 12: OK 46/236 Test #12: pyBV ................................... Passed 1.57 sec test 52 Start 52: moliteratorTestsCatch 52: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/moliteratorTestsCatch 52: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 52: Test timeout computed to be: 1500 52: Randomness seeded to: 3857407103 52: =============================================================================== 52: All tests passed (14 assertions in 4 test cases) 52: 47/236 Test #52: moliteratorTestsCatch .................. Passed 0.01 sec test 53 Start 53: queryTestsCatch 53: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/queryTestsCatch 53: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 53: Test timeout computed to be: 1500 53: Randomness seeded to: 86228484 53: =============================================================================== 53: All tests passed (10 assertions in 1 test case) 53: 48/236 Test #53: queryTestsCatch ........................ Passed 0.01 sec test 54 Start 54: molbundleTestsCatch 54: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/molbundleTestsCatch 54: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 54: Test timeout computed to be: 1500 54: Randomness seeded to: 2073856286 54: =============================================================================== 54: All tests passed (6 assertions in 1 test case) 54: 49/236 Test #54: molbundleTestsCatch .................... Passed 0.02 sec test 55 Start 55: pickleTestsCatch 55: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/pickleTestsCatch 55: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 55: Test timeout computed to be: 1500 55: Randomness seeded to: 2081976177 55: =============================================================================== 55: All tests passed (45 assertions in 4 test cases) 55: 50/236 Test #55: pickleTestsCatch ....................... Passed 0.02 sec test 56 Start 56: tableTestsCatch 56: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/tableTestsCatch 56: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 56: Test timeout computed to be: 1500 56: Randomness seeded to: 1040109436 56: =============================================================================== 56: All tests passed (7 assertions in 2 test cases) 56: 51/236 Test #56: tableTestsCatch ........................ Passed 0.01 sec test 57 Start 57: molopsTestsCatch 57: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/molopsTestsCatch 57: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 57: Test timeout computed to be: 1500 57: Randomness seeded to: 271990394 57: =============================================================================== 57: All tests passed (230 assertions in 7 test cases) 57: 52/236 Test #57: molopsTestsCatch ....................... Passed 0.02 sec test 58 Start 58: smiTest1 58: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 58: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 58: Test timeout computed to be: 1500 58: [09:34:57] WARNING: not removing hydrogen atom without neighbors 58: [09:34:57] WARNING: not removing hydrogen atom without neighbors 58: [09:34:57] WARNING: not removing hydrogen atom without neighbors 58: [09:34:57] WARNING: not removing hydrogen atom without neighbors 58: [09:34:57] WARNING: not removing hydrogen atom without neighbors 58: [09:34:57] WARNING: not removing hydrogen atom without neighbors 58: [09:34:57] WARNING: not removing hydrogen atom without neighbors 58: [09:34:57] WARNING: not removing hydrogen atom without neighbors 58: [09:34:57] WARNING: not removing hydrogen atom without neighbors 58: [09:34:57] WARNING: not removing hydrogen atom without neighbors 58: [09:34:57] WARNING: not removing hydrogen atom without neighbors 58: [09:34:57] Invalid chiral specification on atom 0 58: [09:34:57] Invalid chiral specification on atom 0 58: [09:34:57] Invalid chiral specification on atom 0 58: [09:34:57] Invalid chiral specification on atom 0 58: [09:34:57] Invalid chiral specification on atom 0 58: [09:34:57] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' 58: [09:34:57] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' 58: --C1CCC2(CC1)CCCCC2CCC1CCCC1 58: smi: ClC1CCCCC1 58: smi: ClC1CCCCC1 58: smi: ClC1CCCCC1Br 58: smi: c1ccccc1 58: smi: c1ccncc1 58: smi: c1cc[nH]c1 58: smi: c1cc[nH]c1 58: smi: c1cc[pH]c1 58: [09:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 58: [09:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 58: CbC(aC)aC 58: CaC(bC)aC 58: CbC(bC)aC 58: O.C 58: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O 58: [09:34:57] SMILES Parse Error: syntax error while parsing: c%()ccccc%() 58: [09:34:57] SMILES Parse Error: check for mistakes around position 4: 58: [09:34:57] c%()ccccc%() 58: [09:34:57] ~~~^ 58: [09:34:57] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' 58: [09:34:57] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) 58: [09:34:57] SMILES Parse Error: check for mistakes around position 9: 58: [09:34:57] c%(100000)ccccc%(100000) 58: [09:34:57] ~~~~~~~~^ 58: [09:34:57] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' 58: [09:34:57] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' 58: [09:34:57] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' 58: [09:34:57] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 58: [09:34:57] SMILES Parse Error: check for mistakes around position 14: 58: [09:34:57] COc(c1)cccc1C# 58: [09:34:57] ~~~~~~~~~~~~~^ 58: [09:34:57] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 58: [09:34:57] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 58: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 58: [09:34:57] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 58: [09:34:57] SMILES Parse Error: check for mistakes around position 14: 58: [09:34:57] COc(c1)cccc1C# 58: [09:34:57] ~~~~~~~~~~~~~^ 58: [09:34:57] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 58: [09:34:57] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 58: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 58: [09:34:57] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 58: [09:34:57] SMILES Parse Error: check for mistakes around position 14: 58: [09:34:57] COc(c1)cccc1C# 58: [09:34:57] ~~~~~~~~~~~~~^ 58: [09:34:57] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 58: [09:34:57] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 58: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 58: C=c1s/c2n(c1=O)CCCCCCC\N=2 58: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 58: [09:34:57] SMILES Parse Error: extra close parentheses while parsing: C) 58: [09:34:57] SMILES Parse Error: check for mistakes around position 2: 58: [09:34:57] C) 58: [09:34:57] ~^ 58: [09:34:57] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' 53/236 Test #58: smiTest1 ............................... Passed 0.11 sec test 59 Start 59: smiTest2 59: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 59: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 59: Test timeout computed to be: 1500 59: [09:34:57] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' 59: [09:34:57] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' 59: [09:34:57] SMILES Parse Error: syntax error while parsing: - 59: [09:34:57] SMILES Parse Error: check for mistakes around position 1: 59: [09:34:57] - 59: [09:34:57] ^ 59: [09:34:57] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' 59: [09:34:57] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' 59: [09:34:57] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' 59: [09:34:57] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' 59: [09:34:57] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' 59: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' 59: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' 59: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' 59: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' 59: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' 59: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' 59: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' 54/236 Test #59: smiTest2 ............................... Passed 0.01 sec test 60 Start 60: cxsmilesTest 60: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 60: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 60: Test timeout computed to be: 1500 60: Randomness seeded to: 3528530885 60: Test 60: 60: ShortAtropisomerNoCoords.cxsmi 60: 60: Test 60: 60: ShortAtropisomer.cxsmi 60: 60: Test 60: 60: ShortAtropisomerArom.cxsmi 60: 60: Test 60: 60: AtropManyChirals.cxsmi 60: 60: Test 60: 60: AtropManyChiralsEnhanced.cxsmi 60: 60: Test 60: 60: AtropManyChiralsEnhanced2.cxsmi 60: 60: Test 60: 60: AtropManyChiralsEnhanced3.cxsmi 60: 60: Test 60: 60: AtropManyChiralsEnhanced4.cxsmi 60: 60: Test 60: 60: BMS-986142_3d_chiral.cxsmi 60: 60: Test 60: 60: BMS-986142_3d.cxsmi 60: 60: Test 60: 60: BMS-986142_atrop1.cxsmi 60: 60: Test 60: 60: BMS-986142_atrop2.cxsmi 60: 60: Test 60: 60: BMS-986142_atrop3.cxsmi 60: 60: Test 60: 60: BMS-986142_atrop4.cxsmi 60: 60: Test 60: 60: BMS-986142_atrop5.cxsmi 60: 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: Test 60: 60: BMS-986142_atrop6.cxsmi 60: 60: Test 60: 60: BMS-986142_atropBad1.cxsmi 60: 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 60: Test 60: 60: BMS-986142_atropBad2.cxsmi 60: 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 60: Test 60: 60: JDQ443_3d.cxsmi 60: 60: Test 60: 60: JDQ443_atrop1.cxsmi 60: 60: Test 60: 60: JDQ443_atrop2.cxsmi 60: 60: Test 60: 60: JDQ443_atrop3.cxsmi 60: 60: Test 60: 60: JDQ443_atrop4.cxsmi 60: 60: Test 60: 60: JDQ443_atropBad1.cxsmi 60: 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 60: Test 60: 60: RP-6306_atrop1.cxsmi 60: 60: Test 60: 60: RP-6306_atrop2.cxsmi 60: 60: Test 60: 60: RP-6306_atrop3.cxsmi 60: 60: Test 60: 60: RP-6306_atrop4.cxsmi 60: 60: Test 60: 60: RP-6306_atrop5.cxsmi 60: 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: Test 60: 60: RP-6306_atrop6.cxsmi 60: 60: Test 60: 60: RP-6306_atropBad1.cxsmi 60: 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 60: Test 60: 60: RP-6306_atropBad2.cxsmi 60: 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 60: Test 60: 60: RP-6306_3d.cxsmi 60: 60: Test 60: 60: Sotorasib_atrop1.cxsmi 60: 60: Test 60: 60: Sotorasib_atrop2.cxsmi 60: 60: Test 60: 60: Sotorasib_atrop3.cxsmi 60: 60: Test 60: 60: Sotorasib_atrop4.cxsmi 60: 60: Test 60: 60: Sotorasib_atrop5.cxsmi 60: 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: [09:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: Test 60: 60: Sotorasib_atropBad1.cxsmi 60: 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 60: Test 60: 60: Sotorasib_atropBad2.cxsmi 60: 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 60: [09:34:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 60: Test 60: 60: Sotorasib_3d.cxsmi 60: 60: Test 60: 60: ZM374979_atrop1.cxsmi 60: 60: Test 60: 60: ZM374979_atrop2.cxsmi 60: 60: Test 60: 60: ZM374979_atrop3.cxsmi 60: 60: Test 60: 60: ZM374979_atrop4.cxsmi 60: 60: Test 60: 60: ZM374979_atropBad1.cxsmi 60: 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 60: Test 60: 60: Mrtx1719_3d.cxsmi 60: 60: Test 60: 60: Mrtx1719_atrop1.cxsmi 60: 60: Test 60: 60: Mrtx1719_atrop2.cxsmi 60: 60: Test 60: 60: Mrtx1719_atrop3.cxsmi 60: 60: Test 60: 60: Mrtx1719_atrop4.cxsmi 60: 60: Test 60: 60: Mrtx1719_atropBad1.cxsmi 60: 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 60: [09:34:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 55/236 Test #42: resMolSupplierTest ..................... Passed 1.27 sec test 61 Start 61: smaTest1 61: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 61: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 61: Test timeout computed to be: 1500 61: [09:34:57] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC 61: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' 61: [09:34:57] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON 61: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' 61: [09:34:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 61: [09:34:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 56/236 Test #61: smaTest1 ............................... Passed 0.07 sec test 62 Start 62: smiTestCatch 62: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 62: Test timeout computed to be: 1500 62: Randomness seeded to: 3539848527 62: [09:34:57] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 62: [09:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 62: [09:34:57] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' 62: [09:34:57] SMARTS Parse Error: unclosed ring for input: 'C1C' 62: [09:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 62: [09:34:57] SMARTS Parse Error: syntax error while parsing: C)foo 62: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' 62: [09:34:57] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| 62: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' 62: [09:34:57] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' 62: [09:34:57] w block attempts to set wedging on bond 0 more than once. 62: [09:34:57] improperly formatted w block 62: [09:34:57] atom 3 is not associated with bond 1(1-2) in w block 62: [09:34:57] 62: 62: **** 62: Range Error 62: idx 62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 62: Failed Expression: 20 < 20 62: ---------- 62: Stacktrace: 62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 62: 7# 0x0000563FBDBD7A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 8# 0x0000563FBDC28D28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 9# 0x0000563FBDC29848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 10# 0x0000563FBDC29CC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 11# 0x0000563FBDBFB303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 12# 0x0000563FBDBFB66C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 13# 0x0000563FBDB8CE1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 14# 0x00007FB555433CA8 in /lib/x86_64-linux-gnu/libc.so.6 62: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 62: 16# 0x0000563FBDB8CE61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: ---------- 62: **** 62: 62: [09:34:57] 62: 62: **** 62: Range Error 62: idx 62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 62: Failed Expression: 20 < 20 62: ---------- 62: Stacktrace: 62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 62: 7# 0x0000563FBDBD7A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 8# 0x0000563FBDC28D28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 9# 0x0000563FBDC29848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 10# 0x0000563FBDC29CC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 11# 0x0000563FBDBFB303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 12# 0x0000563FBDBFB66C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 13# 0x0000563FBDB8CE1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: 14# 0x00007FB555433CA8 in /lib/x86_64-linux-gnu/libc.so.6 62: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 62: 16# 0x0000563FBDB8CE61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: ---------- 62: **** 62: 62: [09:34:57] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' 62: [09:34:57] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' 62: [09:34:57] SMARTS Parse Error: syntax error while parsing: C1C)foo 62: [09:34:57] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' 62: [09:34:57] SMILES Parse Error: extra close parentheses while parsing: C1C)foo 62: [09:34:57] SMILES Parse Error: check for mistakes around position 4: 62: [09:34:57] C1C)foo 62: [09:34:57] ~~~^ 62: [09:34:57] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' 62: =============================================================================== 62: All tests passed (1588 assertions in 69 test cases) 62: 57/236 Test #62: smiTestCatch ........................... Passed 0.08 sec test 63 Start 63: nontetrahedralCatch 63: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 63: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 63: Test timeout computed to be: 1500 63: Randomness seeded to: 3913165327 63: [09:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 63: [09:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 63: [09:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 63: [09:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 63: [09:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 63: [09:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 63: [09:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 63: [09:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 63: [09:34:57] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. 63: =============================================================================== 63: All tests passed (308 assertions in 9 test cases) 63: 58/236 Test #63: nontetrahedralCatch .................... Passed 0.04 sec test 64 Start 64: v2smiTestCatch 64: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch 64: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 64: Test timeout computed to be: 1500 64: Randomness seeded to: 1588784308 64: =============================================================================== 64: All tests passed (14 assertions in 2 test cases) 64: 59/236 Test #64: v2smiTestCatch ......................... Passed 0.01 sec test 65 Start 65: testDepictor 65: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor 65: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor 65: Test timeout computed to be: 1500 40: [09:34:58] done: 500000 40: [09:34:58] Done 40: [09:34:58] Testing hanoi with a functor. 40: [09:34:58] Done 40: [09:34:58] Testing basic partition refinement. 40: [09:34:58] Done 40: [09:34:58] Testing partition refinement with neighbors. 40: [09:34:58] Done 40: [09:34:58] testing canonicalization via tie breaking. 40: [09:34:58] Done 40: [09:34:58] testing canonicalization using the wrapper. 40: [09:34:58] Done 40: [09:34:58] testing some specific ordering problems 40: [09:34:58] Finished 40: [09:34:58] testing chiral invariants. 40: [09:34:58] Finished 40: [09:34:58] testing unique ranks in w.r.t. renumbering. 40: [09:34:58] Finished 40: [09:34:58] testing mol fragments. 40: [09:34:58] Finished 40: [09:34:58] testing protein round-tripping. 29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 60: Test 60: 60: AtropCanon1.cxsmi 60: 60: Test 60: 60: AtropCanon2.cxsmi 60: 60: Test 60: 60: AtropCanon3.cxsmi 60: 60: Test 60: 60: BMS-986142_3d_chiral.cxsmi 60: 60: Test 60: 60: BMS-986142_3d.cxsmi 60: 60: =============================================================================== 60: All tests passed (2496 assertions in 31 test cases) 60: 60/236 Test #60: cxsmilesTest ........................... Passed 0.62 sec test 66 Start 66: depictorCatch 66: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch 66: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor 66: Test timeout computed to be: 1500 29: All 191 tests passed 66: Randomness seeded to: 1119231740 66: =============================================================================== 66: All tests passed (580 assertions in 18 test cases) 66: 65: [09:34:58] Warning: stereochemistry around double bond may be incorrect in depiction. 61/236 Test #66: depictorCatch .......................... Passed 0.07 sec test 67 Start 67: pyDepictor 67: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Wrap/testDepictor.py" 67: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap 67: Test timeout computed to be: 1500 29: 29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... 62/236 Test #65: testDepictor ........................... Passed 0.24 sec test 68 Start 68: testMrvToMol 68: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 68: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse 68: Test timeout computed to be: 1500 68: Using new chirality perception 68: Test 68: 68: rxnStereoMarkedCrossed.mrv 68: 68: Test 68: 68: 145323811.mol 68: 68: [09:34:58] unsupported number of radical electrons 5 68: Test 68: 68: NewChiralTest.sdf 68: 68: Test 68: 68: NewChiralTest.sdf 68: 68: Test 68: 68: NewChiralTestNoChiral.sdf 68: 68: Test 68: 68: NewChiralTestNoChiral.sdf 68: 68: Test 68: 68: NewChiralTestAllChiral.sdf 68: 68: Test 68: 68: NewChiralTestAllChiral.sdf 68: 68: Test 68: 68: vendor839.sdf 68: 68: Test 68: 68: ProblemShort.mol 68: 68: [09:34:58] For a MultipleSgroup expansion, the matching orphaned bond was not found 68: The multiple sgroup will be ignored 40: [09:34:58] Finished 40: [09:34:58] testing stability w.r.t. renumbering. 40: [09:34:58] Finished 40: [09:34:58] testing smiles round-tripping. 68: Test 68: 68: badWedgeError.sdf 68: 68: Test 68: 68: CrossedDoubleBondWithChiralNbr2.sdf 68: 68: Test 68: 68: CrossedDoubleBondWithChiralNbr.sdf 68: 68: Test 68: 68: SimpleWiggleDoubleBond.sdf 68: 68: Test 68: 68: lostStereoAnd.sdf 68: 68: Test 68: 68: DoubleBondChain.sdf 68: 68: Test 68: 68: UnitsError.sdf 68: 68: Test 68: 68: StarAtom.sdf 68: 68: Test 68: 68: nonProprietary.mol 68: 68: Test 68: 68: ChiralTest.sdf 68: 68: Test 68: 68: TestBond1.mol 68: 68: Test 68: 68: Sgroup_MUL_ParentInMiddle.sdf 68: 68: Test 68: 68: BadRxn.rxn 68: 68: Test 68: 68: FalseChiral.mrv 68: 68: Test 68: 68: FalseChiral.mrv 68: 68: Test 68: 68: Cubane.mrv 68: 68: Test 68: 68: NewChiralTest.mrv 68: 68: Test 68: 68: NewChiralTest.mrv 68: 68: Test 68: 68: NewChiralTestNoChiral.mrv 68: 68: Test 68: 68: NewChiralTestNoChiral.mrv 68: 68: Test 68: 68: NewChiralTestAllChiral.mrv 68: 68: Test 68: 68: NewChiralTestAllChiral.mrv 68: 68: Test 68: 68: DataSgroupMissingUnitsDisplayed.mrv 68: 68: Test 68: 68: lostStereoAnd.mrv 68: 68: Test 68: 68: DoubleBondChain.mrv 68: 68: Test 68: 68: WigglyAndCrossed.mrv 68: 68: Test 68: 68: BondTypes.mrv 68: 68: Test 68: 68: EmbeddedSGroupSUP_MUL.mrv 68: 68: Test 68: 68: EmbeddedSgroupCOP_SUP.mrv 68: 68: Test 68: 68: EmbeddedSgroupDAT_SUP.mrv 68: 68: Test 68: 68: EmbeddedSgroupMULTICENTER_SUP.mrv 68: 68: Test 68: 68: EmbeddedSgroupMUL_MUL.mrv 68: 68: Test 68: 68: EmbeddedSgroupMUL_MUL2.mrv 68: 68: Test 68: 68: EmbeddedSgroupMUL_SUP.mrv 68: 68: Test 68: 68: EmbeddedSgroupSRU_SUP.mrv 68: 68: Test 68: 68: EmbeddedSgroupSUPEXP_SUP.mrv 68: 68: Test 68: 68: EmbeddedSgroupSUPEXP_SUP2.mrv 68: 68: Test 68: 68: EmbeddedSgroupSUP_MULTICENTER.mrv 68: 68: Test 68: 68: EmbeddedSgroupSUP_SUP.mrv 68: 68: Test 68: 68: EmbeddedSgroupSUP_SUP2.mrv 68: 68: Test 68: 68: RgroupBad.mrv 68: 68: Test 68: 68: valenceLessThanDrawn.mrv 68: 68: Test 68: 68: data_sgroup_no_fieldname.mrv 68: 68: Test 68: 68: data_sgroup_empty_field_data.mrv 68: 68: Test 68: 68: radical_value.mrv 68: 68: Test 68: 68: emptyOneLineAtomList.mrv 68: 68: Test 68: 68: mrvValence_value.mrv 68: 68: Test 68: 68: ChiralTest2.mrv 68: 68: Test 68: 68: ChiralTest.mrv 68: 68: Test 68: 68: SnCl2.mrv 68: 68: Test 68: 68: SnH2Cl2.mrv 68: 68: Test 68: 68: marvin01.mrv 68: 68: Test 68: 68: marvin02.mrv 68: 68: Test 68: 68: marvin07.mrv 68: 68: Test 68: 68: marvin10.mrv 68: 68: Test 68: 68: marvin06.mrv 68: 68: Test 68: 68: marvin12.mrv 68: 68: Test 68: 68: EmptyMol.mrv 68: 68: Test 68: 68: Sparse.mrv 68: 68: Test 68: 68: Sparse2.mrv 68: 68: Test 68: 68: Sparse3.mrv 68: 68: Test 68: 68: MarvinNoCoords.mrv 68: 68: Test 68: 68: aspirin.mrv 68: 68: Test 68: 68: MarvinStereoGroupsZeros.mrv 68: 68: Test 68: 68: MarvinStereoGroupsAbs.mrv 68: 68: Test 68: 68: triphenylphosphine.mrv 68: 68: Test 68: 68: MarvinOldSuperGroupTest.mrv 68: 68: Test 68: 68: RadicalTests.mrv 68: 68: Test 68: 68: AnyBond.mrv 68: 68: Test 68: 68: cisBenzene.mrv 68: 68: Test 68: 68: DativeBond.mrv 68: 68: Test 68: 68: MultipleSgroup.mrv 68: 68: Test 68: 68: SgroupExpanded.mrv 68: 68: Test 68: 68: SgroupMultAttach.mrv 68: 68: Test 68: 68: MarvinMissingX2.mrv 68: 68: Test 68: 68: MarvinMissingY2.mrv 68: 68: Test 68: 68: DataSgroup.mrv 68: 68: Test 68: 68: MulticenterSgroup.mrv 68: 68: [09:34:58] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 68: [09:34:58] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 68: Test 68: 68: GenericSgroup.mrv 68: 68: Test 68: 68: MonomerSgroup.mrv 68: 68: Test 68: 68: modification_sgroup.mrv 68: 68: Test 68: 68: copolymer_sgroup.mrv 68: 68: Test 68: 68: MultipleSgroupParentInMiddleOfAtomBlock.mrv 68: 68: Test 68: 68: EmbeddedSgroups.mrv 68: 68: Test 68: 68: marvin03.mrv 68: 68: Test 68: 68: MarvinBadMissingMolID.mrv 68: 68: [09:34:58] 68: 68: **** 68: Test Assert 68: Expression Failed: 68: Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp 68: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr 68: ---------- 68: Stacktrace: 68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 2# 0x000055CEF1B9A99F in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 68: 3# 0x000055CEF1BA569C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 68: 4# 0x000055CEF1B92A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 68: 5# 0x00007F5A98A33CA8 in /lib/x86_64-linux-gnu/libc.so.6 68: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 68: 7# 0x000055CEF1B92BE1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 68: ---------- 68: **** 68: 68: Test 68: 68: MarvinBadMissingAtomID.mrv 68: 68: Expected id, elementType for an atom definition in MRV file 68: Test 68: 68: MarvinBadX2.mrv 68: 68: The values x2 and y2 must be large floats in MRV file 68: Test 68: 68: MarvinBadY2.mrv 68: 68: The values x2 and y2 must be large floats in MRV file 68: Test 68: 68: MarvinBadStereoGroupsAbs.mrv 68: 68: Unrecognized group definition 68: Test 68: 68: MarvinBadElementType.mrv 68: 68: Test 68: 68: MarvinBadMissingBondID.mrv 68: 68: Test 68: 68: MarvinBadMissingBondAtomRefs 68: 68: Test 68: 68: MarvinBadMissingBondOrder.mrv 68: 68: bond must have one of: order, queryType, or convention in MRV File 68: Test 68: 68: MarvinBadMissingSruMolID.mrv 68: 68: Expected a molID in MRV file 40: [09:34:58] Finished 40: [09:34:58] testing github #1567: Non-canonical result from MolFragmentToSmiles() 40: [09:34:58] Finished 68: Test 68: 68: MarvinBadMissingSruID.mrv 68: 68: Test 68: 68: MarvinBadMissingSruRole.mrv 68: 68: Test 68: 68: MarvinBadMissingSruAtomRef.mrv 68: 68: Test 68: 68: MarvinBadMissingSruTitle.mrv 68: 68: Test 68: 68: MarvinBadSruAtomRef.mrv 68: 68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 68: Test 68: 68: MarvinBadSruID.mrv 68: 68: Test 68: 68: MarvinBadSruRole.mrv 68: 68: Test 68: 68: MarvinBadSruAtomRef.mrv 68: 68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 68: Test 68: 68: MarvinBadSruAtomRef.mrv 68: 68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 63/236 Test #40: hanoiTest .............................. Passed 2.10 sec 68: Test 68: 68: MarvinBadSruConnect.mrv 68: 68: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file test 69 Start 69: fileParsersTest1 69: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 69: Test timeout computed to be: 1500 68: Test 68: 68: MarvinBadSupAttachAtom.mrv 68: 68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 68: Test 68: 68: MarvinBadSupAttachBond.mrv 68: 68: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file 68: Test 68: 68: MarvinBadSupAttachOrder.mrv 68: 68: Order for an AttachmentPoint definition must be an integer in MRV file 68: Test 68: 68: MarvinBadSupAttachAtom.mrv 68: 68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 68: Test 68: 68: MarvinBadSupAttachAtom.mrv 68: 68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 68: Test 68: 68: MarvinBadSupAttachAtom.mrv 68: 68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 68: Test 68: 68: MarvinBadSupMissingAttachBond.mrv 68: 68: No attachment point found for bond to the condensed atom in a superatomSgroup 68: Test 68: 68: MarvinBadSupMissingAttachOrder.mrv 68: 68: Expected atom, order and bond, for an AttachmentPoint definition in MRV file 69: *************************************** 69: *************************************** 69: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: marvin03.mrv 68: 68: Test 68: 68: Cubane.mrv 68: 68: Test 68: 68: FalseAtropisomer.mrv 68: 68: Test 68: 68: AtropEnhancedStereo.mrv 68: 68: Test 68: 68: AtropManyChirals.mrv 68: 68: Test 68: 68: AtropManyChiralsEnhanced.mrv 68: 68: Test 68: 68: AtropManyChiralsEnhanced2.mrv 68: 68: Test 68: 68: AtropManyChiralsEnhanced3.mrv 68: 68: Test 68: 68: AtropManyChiralsEnhanced4.mrv 68: 68: Test 68: 68: BMS-986142_3d_chiral.mrv 68: 68: Test 68: 68: BMS-986142_3d.mrv 68: 68: Test 68: 68: BMS-986142_atrop1.mrv 68: 68: Test 68: 68: BMS-986142_atrop2.mrv 68: 68: Test 68: 68: BMS-986142_atrop3.mrv 68: 68: Test 68: 68: BMS-986142_atrop4.mrv 68: 68: Test 68: 68: BMS-986142_atrop5.mrv 68: 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:34:58] bond with order 0 found on line 7. This is not part of the MDL specification. 67: ..............[09:34:58] SMILES Parse Error: syntax error while parsing: invalidsmiles 67: [09:34:58] SMILES Parse Error: check for mistakes around position 1: 67: [09:34:58] invalidsmiles 67: [09:34:58] ^ 67: [09:34:58] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' 68: Test 68: 68: BMS-986142_atrop6.mrv 68: 68: Test 68: 68: BMS-986142_atrop7.mrv 68: 68: Test 68: 68: BMS-986142_atrop8.mrv 68: 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: 68: BMS-986142_atropBad2.mrv 68: 68: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 69: [09:34:58] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) 69: [09:34:58] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) 69: [09:34:58] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 69: generating smiles 69: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 69: converting back 68: Test 68: 68: JDQ443_3d.mrv 68: 68: Test 68: 68: JDQ443_atrop1.mrv 68: 68: Test 68: 68: JDQ443_atrop2.mrv 68: 68: Test 68: 68: JDQ443_atrop3.mrv 68: 68: Test 68: 68: JDQ443_atropBad1.mrv 68: 68: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 69: check isomorphism 68: Test 68: 68: RP-6306_atrop1.mrv 68: 68: Test 68: 68: RP-6306_atrop2.mrv 68: 68: Test 68: 68: RP-6306_atrop3.mrv 68: 68: Test 68: 68: RP-6306_atrop4.mrv 68: 68: Test 68: 68: RP-6306_atrop5.mrv 68: 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: Test 68: 68: RP-6306_atropBad1.mrv 68: 68: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 68: Test 68: 68: RP-6306_atropBad2.mrv 68: 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 68: Test 68: 68: RP-6306_3d.mrv 68: 68: Test 68: 68: Sotorasib_atrop1.mrv 68: 68: Test 68: 68: Sotorasib_atrop2.mrv 68: 68: Test 68: 68: Sotorasib_atrop3.mrv 68: 68: Test 68: 68: Sotorasib_atrop4.mrv 68: 68: Test 68: 68: Sotorasib_atrop5.mrv 68: 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: 68: Sotorasib_atropBad1.mrv 68: 68: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 68: Test 68: 68: Sotorasib_atropBad2.mrv 68: 68: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 67: ..... 67: ---------------------------------------------------------------------- 67: Ran 19 tests in 0.213s 67: 67: OK 68: Test 68: 68: Sotorasib_3d.mrv 68: 68: Test 68: 68: ZM374979_atrop1.mrv 68: 68: Test 68: 68: ZM374979_atrop2.mrv 68: 68: Test 68: 68: ZM374979_atrop3.mrv 68: 68: Test 68: 68: ZM374979_atropBad1.mrv 68: 68: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 64/236 Test #67: pyDepictor ............................. Passed 0.40 sec 68: Test 68: 68: mrtx1719_3d.mrv 68: 68: Test 68: 68: mrtx1719_atrop1.mrv 68: 68: Test 68: 68: mrtx1719_atrop2.mrv 68: 68: Test 68: 68: mrtx1719_atrop3.mrv 68: 68: Test 68: 68: mrtx1719_atropBad1.mrv 68: 68: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 test 70 Start 70: testAtropisomers 70: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers 70: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 70: Test timeout computed to be: 1500 70: [09:34:58] ---- Running with POSIX locale ----- 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: FalseAtropisomer.mrv 68: 68: Test 68: 68: AtropEnhancedStereo.mrv 68: 68: Test 68: 68: AtropManyChirals.mrv 68: 68: Test 68: 68: AtropManyChiralsEnhanced.mrv 68: 68: Test 68: 68: AtropManyChiralsEnhanced2.mrv 68: 68: Test 68: 68: AtropManyChiralsEnhanced3.mrv 68: 68: Test 68: 68: AtropManyChiralsEnhanced4.mrv 68: 68: Test 68: 68: BMS-986142_3d_chiral.mrv 68: 68: Test 68: 68: BMS-986142_3d.mrv 68: 68: Test 68: 68: BMS-986142_atrop1.mrv 68: 68: Test 68: 68: BMS-986142_atrop2.mrv 68: 68: Test 68: 68: BMS-986142_atrop3.mrv 68: 68: Test 68: 68: BMS-986142_atrop4.mrv 68: 68: Test 68: 68: BMS-986142_atrop5.mrv 68: 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: BMS-986142_atrop6.mrv 68: 68: Test 68: 68: BMS-986142_atrop7.mrv 68: 68: Test 68: 68: BMS-986142_atrop8.mrv 68: 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: 68: BMS-986142_atropBad2.mrv 68: 68: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 70: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 70: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 68: Test 68: 68: JDQ443_3d.mrv 68: 68: Test 68: 68: JDQ443_atrop1.mrv 68: 68: Test 68: 68: JDQ443_atrop2.mrv 68: 68: Test 68: 68: JDQ443_atrop3.mrv 68: 68: Test 68: 68: JDQ443_atropBad1.mrv 68: 68: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 68: Test 68: 68: RP-6306_atrop1.mrv 68: 68: Test 68: 68: RP-6306_atrop2.mrv 68: 68: Test 68: 68: RP-6306_atrop3.mrv 68: 68: Test 68: 68: RP-6306_atrop4.mrv 68: 68: Test 68: 68: RP-6306_atrop5.mrv 68: 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 70: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 70: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 70: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 68: Test 68: 68: RP-6306_atropBad1.mrv 68: 68: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: RP-6306_atropBad2.mrv 68: 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 70: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 70: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 70: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: RP-6306_3d.mrv 68: 68: Test 68: 68: Sotorasib_atrop1.mrv 68: 68: Test 68: 68: Sotorasib_atrop2.mrv 68: 68: Test 68: 68: Sotorasib_atrop3.mrv 68: 68: Test 68: 68: Sotorasib_atrop4.mrv 68: 68: Test 68: 68: Sotorasib_atrop5.mrv 68: 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: Sotorasib_atropBad1.mrv 68: 68: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 70: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 68: Test 68: 68: Sotorasib_atropBad2.mrv 68: 68: [09:34:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 68: Test 68: 68: Sotorasib_3d.mrv 68: 68: Test 68: 68: ZM374979_atrop1.mrv 68: 68: Test 68: 68: ZM374979_atrop2.mrv 68: 68: Test 68: 68: ZM374979_atrop3.mrv 68: 68: Test 68: 68: ZM374979_atropBad1.mrv 68: 68: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 68: Test 68: 68: mrtx1719_3d.mrv 68: 68: Test 68: 68: mrtx1719_atrop1.mrv 68: 68: Test 68: 68: mrtx1719_atrop2.mrv 68: 68: Test 68: 68: mrtx1719_atrop3.mrv 68: 68: Test 68: 68: mrtx1719_atropBad1.mrv 68: 68: [09:34:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: AlexRxn.mrv 68: 68: Test 68: 68: BadReactionSign.mrv 68: 68: Test 68: 68: bondArray_node.mrv 68: 68: Test 68: 68: marvin03.mrv 68: 68: Test 68: 68: marvin04.mrv 68: 68: Test 68: 68: marvin08.mrv 68: 68: Test 68: 68: marvin09.mrv 68: 68: Test 68: 68: marvin11.mrv 68: 68: Test 68: 68: marvin05.mrv 68: 68: Test 68: 68: EmptyRxn.mrv 68: 68: [09:34:58] initialization failed 70: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: Atropisomers- 1 hits 3 misses 70: Final results: 70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses 65/236 Test #70: testAtropisomers ....................... Passed 0.15 sec test 71 Start 71: testSquiggleDoubleBonds 71: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds 71: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 71: Test timeout computed to be: 1500 71: Randomness seeded to: 3440564348 71: =============================================================================== 71: All tests passed (15 assertions in 3 test cases) 71: 66/236 Test #71: testSquiggleDoubleBonds ................ Passed 0.02 sec test 72 Start 72: testMolSupplier 72: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 72: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 72: Test timeout computed to be: 1500 68: Test 68: 68: RxnNoCoords.mrv 68: 68: Test 68: 68: mrvValenceZero.mrv 68: 68: Test 68: 68: condition_coordinates_mpoint.mrv 68: 68: Test 68: 68: marvin01.mrv 68: 68: Test 68: 68: aspirineSynthesisWithAttributes.mrv 68: 68: Test 68: 68: marvin01.mrv 68: 68: Test 68: 68: NewChiralTest 68: 68: Test 68: 68: NewChiralTest 68: 68: Test 68: 68: NewChiralTestNoChiral 68: 68: Test 68: 68: NewChiralTestNoChiral 68: 68: Test 68: 68: NewChiralTest2 68: 68: Test 68: 68: NewChiralTest2 68: 68: Test 68: 68: NewChiralTest2AllChiral 68: 68: Test 68: 68: NewChiralTest2AllChiral 68: 68: Test 68: 68: Vendor839 68: 68: Test 68: 68: DoubleBondChain 68: 68: Test 68: 68: Na_Mg_Al_OH 68: 68: Test 68: 68: Pb 68: 68: Test 68: 68: O_Mg_Si 68: 68: Test 68: 68: SquiggleBond 68: 68: Test 68: 68: BigMacrocycle 68: 68: Test 68: 68: Smiles1 68: 67/236 Test #68: testMrvToMol ........................... Passed 0.54 sec test 73 Start 73: testGeneralFileReader 73: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader 73: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 73: Test timeout computed to be: 1500 72: [09:34:58] 72: ----------------------------------------- 73: [09:34:58] 73: ----------------------------------------- 73: [09:34:58] Finished: testDetermineFormat() 73: [09:34:58] ----------------------------------------- 73: 73: [09:34:58] 73: ----------------------------------------- 72: [09:34:58] Ignoring invalid chirality label: '2_bad_chirality' 73: [09:34:58] Finished: testSdf() 73: [09:34:58] ----------------------------------------- 73: 73: [09:34:58] 73: ----------------------------------------- 73: [09:34:58] Finished: testSmi() 73: [09:34:58] ----------------------------------------- 73: 73: [09:34:58] 73: ----------------------------------------- 72: [09:34:58] Finished: testMolSup() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testRandMolSup() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 73: [09:34:58] Finished: testMae() 73: [09:34:58] ----------------------------------------- 73: 73: [09:34:58] 73: ----------------------------------------- 73: [09:34:58] Finished: testTdt() 73: [09:34:58] ----------------------------------------- 73: 68/236 Test #73: testGeneralFileReader .................. Passed 0.05 sec test 74 Start 74: testMultithreadedMolSupplier 74: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier 74: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 74: Test timeout computed to be: 1500 72: [09:34:58] Finished: testSmilesSup() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] ------------------------------------------------------ 72: [09:34:58] SMILES Parse Error: syntax error while parsing: fail 72: [09:34:58] SMILES Parse Error: check for mistakes around position 1: 72: [09:34:58] fail 72: [09:34:58] ^ 72: [09:34:58] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' 72: [09:34:58] ERROR: Smiles parse error on line 3 72: [09:34:58] ERROR: Cannot create molecule from : 'fail' 72: [09:34:58] ------------------------------------------------------ 72: [09:34:58] ------------------------------------------------------ 72: [09:34:58] >>> This may result in an infinite loop. It should finish almost immediately: 72: [09:34:58] <<< done. 72: [09:34:58] Finished: testSmilesSupFromText() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testSmilesWriter() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 74: [09:34:58] 74: ----------------------------------------- 72: [09:34:58] Finished: testSDWriter() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testSDSupplierEnding() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testSuppliersEmptyFile() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testCisTrans() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testStereoRound() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 72: [09:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 72: [09:34:58] Finished: testIssue226() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testTDTSupplier1() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testTDTSupplier2() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testTDTSupplier3() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testSDSupplierFromText() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] ERROR: Problems encountered parsing data fields 72: [09:34:58] ERROR: moving to the beginning of the next molecule 72: [09:34:58] ERROR: Problems encountered parsing data fields 72: [09:34:58] ERROR: moving to the beginning of the next molecule 72: [09:34:58] Spurious data before the first property will be ignored 72: [09:34:58] Property will be truncated after the first blank line 72: [09:34:58] Property will be truncated after the first blank line 72: [09:34:58] Property will be truncated after the first blank line 72: [09:34:58] Finished: testSDSupplierStrLax1() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] ERROR: Problems encountered parsing data fields 72: [09:34:58] ERROR: moving to the beginning of the next molecule 72: [09:34:58] Property will be truncated after the first blank line 72: [09:34:58] Finished: testSDSupplierStrLax2() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] ERROR: Problems encountered parsing data fields 72: [09:34:58] ERROR: moving to the beginning of the next molecule 72: [09:34:58] ERROR: Problems encountered parsing data fields 72: [09:34:58] ERROR: moving to the beginning of the next molecule 72: [09:34:58] Spurious data before the first property will be ignored 72: [09:34:58] Property will be truncated after the first blank line 72: [09:34:58] Property will be truncated after the first blank line 72: [09:34:58] Property will be truncated after the first blank line 72: [09:34:58] Finished: testSDSupplierFromTextStrLax1() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] ERROR: Problems encountered parsing data fields 72: [09:34:58] ERROR: moving to the beginning of the next molecule 72: [09:34:58] Property will be truncated after the first blank line 72: [09:34:58] Finished: testSDSupplierFromTextStrLax2() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testIssue265() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] ERROR: End of data field name not found 72: [09:34:58] ERROR: moving to the beginning of the next molecule 72: [09:34:58] Explicit valence for atom # 0 F, 2, is greater than permitted 72: [09:34:58] ERROR: Could not sanitize molecule ending on line 16 72: [09:34:58] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted 72: [09:34:58] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 72: [09:34:58] ERROR: moving to the beginning of the next molecule 72: [09:34:58] ERROR: Bond line too short: 'M END' on line 18 72: [09:34:58] ERROR: moving to the beginning of the next molecule 72: [09:34:58] Finished: testSDErrorHandling() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testIssue381() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testSetStreamIndices() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testMixIterAndRandom() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: build: 72: [09:34:58] Finished: testRemoveHs() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testGetItemText() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testForwardSDSupplier() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testMissingCRSDSupplier() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testIssue3482695() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] ERROR: Cannot convert 'foo' to unsigned int on line 557 72: [09:34:58] ERROR: moving to the beginning of the next molecule 72: [09:34:58] Finished: testIssue3525673() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testBlankLinesInProps() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testSkipLines() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testGitHub23() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testGitHub88() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testGitHub2285() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 72: [09:34:58] ERROR: Smiles parse error on line 1 72: [09:34:58] ERROR: Cannot create molecule from : 'c1ccccc' 72: [09:34:58] SMILES Parse Error: extra open parentheses while parsing: C(C 72: [09:34:58] SMILES Parse Error: check for mistakes around position 2: 72: [09:34:58] C(C 72: [09:34:58] ~^ 72: [09:34:58] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' 72: [09:34:58] ERROR: Smiles parse error on line 3 72: [09:34:58] ERROR: Cannot create molecule from : 'C(C' 72: [09:34:58] Explicit valence for atom # 1 C, 5, is greater than permitted 72: [09:34:58] ERROR: Could not sanitize molecule on line 5 72: [09:34:58] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted 72: [09:34:58] Explicit valence for atom # 1 F, 2, is greater than permitted 72: [09:34:58] ERROR: Could not sanitize molecule ending on line 21 72: [09:34:58] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 72: [09:34:58] Explicit valence for atom # 1 F, 2, is greater than permitted 72: [09:34:58] ERROR: Could not sanitize molecule ending on line 21 72: [09:34:58] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 72: [09:34:58] Explicit valence for atom # 1 F, 2, is greater than permitted 72: [09:34:58] ERROR: Could not sanitize molecule ending on line 21 72: [09:34:58] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 72: [09:34:58] ERROR: Atom line too short: ' -9.6' on line 28 72: [09:34:58] ERROR: moving to the beginning of the next molecule 72: [09:34:58] Explicit valence for atom # 1 F, 2, is greater than permitted 72: [09:34:58] ERROR: Could not sanitize molecule ending on line 21 72: [09:34:58] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 72: [09:34:58] ERROR: Atom line too short: ' -9.6' on line 28 72: [09:34:58] ERROR: moving to the beginning of the next molecule 72: [09:34:58] Finished: testGitHub2479() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Ignoring invalid chirality label: '7_S_8_9_6_10' 72: [09:34:58] Finished: testGitHub2881() 72: [09:34:58] ----------------------------------------- 72: 72: [09:34:58] ----------------------------------------- 72: [09:34:58] Finished: testGitHub3517() 72: [09:34:58] ----------------------------------------- 72: 69/236 Test #72: testMolSupplier ........................ Passed 0.13 sec 69: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 69: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 69: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 69: [09:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored test 75 Start 75: testMolWriter 75: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter 75: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 75: Test timeout computed to be: 1500 69: [09:34:58] deprecated group abbreviation ignored on line 24 69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] 69: [09:34:58] 69: 69: **** 69: Post-condition Violation 69: Element 'Mv' not found 69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 69: Failed Expression: anum > -1 69: ---------- 69: Stacktrace: 69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 3# 0x00007F9056AC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 4# 0x00007F9056AD1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 5# 0x00007F9056AD217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 9# 0x0000557205694C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: 10# 0x00005572056FB372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: 11# 0x000055720567B923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: 12# 0x00007F9056033CA8 in /lib/x86_64-linux-gnu/libc.so.6 69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 69: 14# 0x000055720567BAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: ---------- 69: **** 69: 69: [09:34:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 69: [09:34:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 69: ---------------------------------- 69: ---------------------------------- 69: [09:34:59] 69: 69: **** 69: Pre-condition Violation 69: rlabel out of range for MDL files 69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp 69: Failed Expression: rlabel >= 0 && rlabel < 100 69: ---------- 69: Stacktrace: 69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 69: 3# 0x00005572056A1FFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: 4# 0x00005572056FB3EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: 5# 0x000055720567B923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: 6# 0x00007F9056033CA8 in /lib/x86_64-linux-gnu/libc.so.6 69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 69: 8# 0x000055720567BAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: ---------- 69: **** 69: 69: [09:34:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 75: [09:34:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 75: 0.40201265 0.40201265 75: -0.13299436 -0.13299436 75: 1.00000017 1.00000017 75: 0.8762226 0.8762226 75: 0.9973909 0.9973909 75: 1.00000003 1.00000003 75: 0.36613799 0.36613799 75: 2.1107185 2.1107185 75: 0.99999982 0.99999982 75: 2.48696157 2.48696157 75: 1.00479935 1.00479935 75: 0.99999999 0.99999999 75: 3.03311841 3.03311841 75: 2.23739955 2.23739955 75: 1.0000001 1.0000001 75: 3.00772337 3.00772337 75: 0.37399294 0.37399294 75: 2.07713325 2.07713325 75: 3.0077234 3.0077234 75: 0.37399312 0.37399312 75: -0.07713336 -0.07713336 75: [09:34:59] bond with order 0 found on line 11. This is not part of the MDL specification. 75: [09:34:59] bond with order 0 found on line 16. This is not part of the MDL specification. 70/236 Test #75: testMolWriter .......................... Passed 0.21 sec test 76 Start 76: testTplParser 76: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser 76: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 76: Test timeout computed to be: 1500 71/236 Test #76: testTplParser .......................... Passed 0.05 sec test 77 Start 77: testMol2ToMol 77: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol 77: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 77: Test timeout computed to be: 1500 72/236 Test #77: testMol2ToMol .......................... Passed 0.02 sec test 78 Start 78: testSequence 78: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence 78: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 78: Test timeout computed to be: 1500 69: [09:34:59] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas 69: [09:34:59] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 78: Sequence: GREG 78: HELM: PEPTIDE1{G.R.E.G}$$$$ 78: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O 78: PDB: 78: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 78: CONECT 1 2 78: CONECT 2 3 78: CONECT 3 4 4 5 78: CONECT 5 6 78: CONECT 6 7 9 78: CONECT 7 8 8 16 78: CONECT 9 10 78: CONECT 10 11 78: CONECT 11 12 78: CONECT 12 13 78: CONECT 13 14 14 15 78: CONECT 16 17 78: CONECT 17 18 20 78: CONECT 18 19 19 25 78: CONECT 20 21 78: CONECT 21 22 78: CONECT 22 23 23 24 78: CONECT 25 26 78: CONECT 26 27 78: CONECT 27 28 28 29 78: END 78: 78: Sequence: TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN 78: HELM: PEPTIDE1{T.T.C.C.P.S.I.V.A.R.S.N.F.N.V.C.R.L.P.G.T.P.E.A.I.C.A.T.Y.T.G.C.I.I.I.P.G.A.T.C.P.G.D.Y.A.N}$$$$ 78: Smiles: CC[C@H](C)[C@H](NC(=O)[C@H](C)NC(=O)[C@H](CCC(=O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H](NC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCNC(=N)N)NC(=O)[C@H](CS)NC(=O)[C@@H](NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CO)NC(=O)[C@H](CCCNC(=N)N)NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](CO)NC(=O)[C@@H]1CCCN1C(=O)[C@H](CS)NC(=O)[C@H](CS)NC(=O)[C@@H](NC(=O)[C@@H](N)[C@@H](C)O)[C@@H](C)O)[C@@H](C)CC)C(C)C)C(C)C)[C@@H](C)O)C(=O)N[C@@H](CS)C(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)NCC(=O)N[C@@H](CS)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N1CCC[C@H]1C(=O)NCC(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@@H](CS)C(=O)N1CCC[C@H]1C(=O)NCC(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(N)=O)C(=O)O)[C@@H](C)O)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)O)[C@@H](C)O 78: PDB: 78: ATOM 1 N THR A 1 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 2 CA THR A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 3 C THR A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 4 O THR A 1 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 5 CB THR A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 6 OG1 THR A 1 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 7 CG2 THR A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 8 N THR A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 9 CA THR A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 10 C THR A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 11 O THR A 2 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 12 CB THR A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 13 OG1 THR A 2 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 14 CG2 THR A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 15 N CYS A 3 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 16 CA CYS A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 17 C CYS A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 18 O CYS A 3 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 19 CB CYS A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 20 SG CYS A 3 0.000 0.000 0.000 1.00 0.00 S 78: ATOM 21 N CYS A 4 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 22 CA CYS A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 23 C CYS A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 24 O CYS A 4 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 25 CB CYS A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 26 SG CYS A 4 0.000 0.000 0.000 1.00 0.00 S 78: ATOM 27 N PRO A 5 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 28 CA PRO A 5 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 29 C PRO A 5 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 30 O PRO A 5 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 31 CB PRO A 5 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 32 CG PRO A 5 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 33 CD PRO A 5 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 34 N SER A 6 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 35 CA SER A 6 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 36 C SER A 6 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 37 O SER A 6 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 38 CB SER A 6 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 39 OG SER A 6 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 40 N ILE A 7 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 41 CA ILE A 7 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 42 C ILE A 7 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 43 O ILE A 7 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 44 CB ILE A 7 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 45 CG1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 46 CG2 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 47 CD1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 48 N VAL A 8 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 49 CA VAL A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 50 C VAL A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 51 O VAL A 8 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 52 CB VAL A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 53 CG1 VAL A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 54 CG2 VAL A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 55 N ALA A 9 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 56 CA ALA A 9 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 57 C ALA A 9 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 58 O ALA A 9 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 59 CB ALA A 9 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 60 N ARG A 10 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 61 CA ARG A 10 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 62 C ARG A 10 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 63 O ARG A 10 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 64 CB ARG A 10 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 65 CG ARG A 10 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 66 CD ARG A 10 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 67 NE ARG A 10 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 68 CZ ARG A 10 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 69 NH1 ARG A 10 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 70 NH2 ARG A 10 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 71 N SER A 11 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 72 CA SER A 11 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 73 C SER A 11 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 74 O SER A 11 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 75 CB SER A 11 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 76 OG SER A 11 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 77 N ASN A 12 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 78 CA ASN A 12 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 79 C ASN A 12 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 80 O ASN A 12 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 81 CB ASN A 12 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 82 CG ASN A 12 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 83 OD1 ASN A 12 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 84 ND2 ASN A 12 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 85 N PHE A 13 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 86 CA PHE A 13 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 87 C PHE A 13 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 88 O PHE A 13 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 89 CB PHE A 13 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 90 CG PHE A 13 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 91 CD1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 92 CD2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 93 CE1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 94 CE2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 95 CZ PHE A 13 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 96 N ASN A 14 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 97 CA ASN A 14 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 98 C ASN A 14 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 99 O ASN A 14 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 100 CB ASN A 14 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 101 CG ASN A 14 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 102 OD1 ASN A 14 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 103 ND2 ASN A 14 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 104 N VAL A 15 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 105 CA VAL A 15 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 106 C VAL A 15 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 107 O VAL A 15 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 108 CB VAL A 15 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 109 CG1 VAL A 15 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 110 CG2 VAL A 15 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 111 N CYS A 16 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 112 CA CYS A 16 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 113 C CYS A 16 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 114 O CYS A 16 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 115 CB CYS A 16 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 116 SG CYS A 16 0.000 0.000 0.000 1.00 0.00 S 78: ATOM 117 N ARG A 17 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 118 CA ARG A 17 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 119 C ARG A 17 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 120 O ARG A 17 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 121 CB ARG A 17 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 122 CG ARG A 17 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 123 CD ARG A 17 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 124 NE ARG A 17 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 125 CZ ARG A 17 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 126 NH1 ARG A 17 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 127 NH2 ARG A 17 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 128 N LEU A 18 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 129 CA LEU A 18 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 130 C LEU A 18 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 131 O LEU A 18 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 132 CB LEU A 18 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 133 CG LEU A 18 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 134 CD1 LEU A 18 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 135 CD2 LEU A 18 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 136 N PRO A 19 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 137 CA PRO A 19 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 138 C PRO A 19 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 139 O PRO A 19 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 140 CB PRO A 19 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 141 CG PRO A 19 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 142 CD PRO A 19 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 143 N GLY A 20 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 144 CA GLY A 20 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 145 C GLY A 20 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 146 O GLY A 20 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 147 N THR A 21 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 148 CA THR A 21 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 149 C THR A 21 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 150 O THR A 21 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 151 CB THR A 21 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 152 OG1 THR A 21 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 153 CG2 THR A 21 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 154 N PRO A 22 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 155 CA PRO A 22 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 156 C PRO A 22 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 157 O PRO A 22 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 158 CB PRO A 22 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 159 CG PRO A 22 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 160 CD PRO A 22 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 161 N GLU A 23 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 162 CA GLU A 23 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 163 C GLU A 23 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 164 O GLU A 23 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 165 CB GLU A 23 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 166 CG GLU A 23 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 167 CD GLU A 23 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 168 OE1 GLU A 23 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 169 OE2 GLU A 23 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 170 N ALA A 24 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 171 CA ALA A 24 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 172 C ALA A 24 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 173 O ALA A 24 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 174 CB ALA A 24 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 175 N ILE A 25 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 176 CA ILE A 25 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 177 C ILE A 25 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 178 O ILE A 25 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 179 CB ILE A 25 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 180 CG1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 181 CG2 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 182 CD1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 183 N CYS A 26 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 184 CA CYS A 26 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 185 C CYS A 26 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 186 O CYS A 26 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 187 CB CYS A 26 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 188 SG CYS A 26 0.000 0.000 0.000 1.00 0.00 S 78: ATOM 189 N ALA A 27 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 190 CA ALA A 27 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 191 C ALA A 27 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 192 O ALA A 27 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 193 CB ALA A 27 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 194 N THR A 28 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 195 CA THR A 28 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 196 C THR A 28 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 197 O THR A 28 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 198 CB THR A 28 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 199 OG1 THR A 28 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 200 CG2 THR A 28 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 201 N TYR A 29 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 202 CA TYR A 29 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 203 C TYR A 29 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 204 O TYR A 29 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 205 CB TYR A 29 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 206 CG TYR A 29 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 207 CD1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 208 CD2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 209 CE1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 210 CE2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 211 CZ TYR A 29 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 212 OH TYR A 29 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 213 N THR A 30 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 214 CA THR A 30 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 215 C THR A 30 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 216 O THR A 30 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 217 CB THR A 30 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 218 OG1 THR A 30 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 219 CG2 THR A 30 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 220 N GLY A 31 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 221 CA GLY A 31 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 222 C GLY A 31 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 223 O GLY A 31 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 224 N CYS A 32 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 225 CA CYS A 32 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 226 C CYS A 32 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 227 O CYS A 32 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 228 CB CYS A 32 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 229 SG CYS A 32 0.000 0.000 0.000 1.00 0.00 S 78: ATOM 230 N ILE A 33 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 231 CA ILE A 33 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 232 C ILE A 33 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 233 O ILE A 33 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 234 CB ILE A 33 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 235 CG1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 236 CG2 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 237 CD1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 238 N ILE A 34 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 239 CA ILE A 34 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 240 C ILE A 34 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 241 O ILE A 34 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 242 CB ILE A 34 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 243 CG1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 244 CG2 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 245 CD1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 246 N ILE A 35 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 247 CA ILE A 35 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 248 C ILE A 35 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 249 O ILE A 35 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 250 CB ILE A 35 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 251 CG1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 252 CG2 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 253 CD1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 254 N PRO A 36 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 255 CA PRO A 36 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 256 C PRO A 36 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 257 O PRO A 36 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 258 CB PRO A 36 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 259 CG PRO A 36 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 260 CD PRO A 36 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 261 N GLY A 37 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 262 CA GLY A 37 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 263 C GLY A 37 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 264 O GLY A 37 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 265 N ALA A 38 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 266 CA ALA A 38 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 267 C ALA A 38 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 268 O ALA A 38 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 269 CB ALA A 38 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 270 N THR A 39 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 271 CA THR A 39 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 272 C THR A 39 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 273 O THR A 39 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 274 CB THR A 39 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 275 OG1 THR A 39 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 276 CG2 THR A 39 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 277 N CYS A 40 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 278 CA CYS A 40 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 279 C CYS A 40 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 280 O CYS A 40 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 281 CB CYS A 40 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 282 SG CYS A 40 0.000 0.000 0.000 1.00 0.00 S 78: ATOM 283 N PRO A 41 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 284 CA PRO A 41 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 285 C PRO A 41 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 286 O PRO A 41 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 287 CB PRO A 41 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 288 CG PRO A 41 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 289 CD PRO A 41 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 290 N GLY A 42 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 291 CA GLY A 42 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 292 C GLY A 42 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 293 O GLY A 42 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 294 N ASP A 43 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 295 CA ASP A 43 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 296 C ASP A 43 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 297 O ASP A 43 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 298 CB ASP A 43 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 299 CG ASP A 43 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 300 OD1 ASP A 43 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 301 OD2 ASP A 43 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 302 N TYR A 44 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 303 CA TYR A 44 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 304 C TYR A 44 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 305 O TYR A 44 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 306 CB TYR A 44 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 307 CG TYR A 44 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 308 CD1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 309 CD2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 310 CE1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 311 CE2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 312 CZ TYR A 44 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 313 OH TYR A 44 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 314 N ALA A 45 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 315 CA ALA A 45 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 316 C ALA A 45 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 317 O ALA A 45 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 318 CB ALA A 45 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 319 N ASN A 46 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 320 CA ASN A 46 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 321 C ASN A 46 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 322 O ASN A 46 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 323 CB ASN A 46 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 324 CG ASN A 46 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 325 OD1 ASN A 46 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 326 ND2 ASN A 46 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 327 OXT ASN A 46 0.000 0.000 0.000 1.00 0.00 O 78: CONECT 1 2 78: CONECT 2 3 5 78: CONECT 3 4 4 8 78: CONECT 5 6 7 78: CONECT 8 9 78: CONECT 9 10 12 78: CONECT 10 11 11 15 78: CONECT 12 13 14 78: CONECT 15 16 78: CONECT 16 17 19 78: CONECT 17 18 18 21 78: CONECT 19 20 78: CONECT 21 22 78: CONECT 22 23 25 78: CONECT 23 24 24 27 78: CONECT 25 26 78: CONECT 27 28 33 78: CONECT 28 29 31 78: CONECT 29 30 30 34 78: CONECT 31 32 78: CONECT 32 33 78: CONECT 34 35 78: CONECT 35 36 38 78: CONECT 36 37 37 40 78: CONECT 38 39 78: CONECT 40 41 78: CONECT 41 42 44 78: CONECT 42 43 43 48 78: CONECT 44 45 46 78: CONECT 46 47 78: CONECT 48 49 78: CONECT 49 50 52 78: CONECT 50 51 51 55 78: CONECT 52 53 54 78: CONECT 55 56 78: CONECT 56 57 59 78: CONECT 57 58 58 60 78: CONECT 60 61 78: CONECT 61 62 64 78: CONECT 62 63 63 71 78: CONECT 64 65 78: CONECT 65 66 78: CONECT 66 67 78: CONECT 67 68 78: CONECT 68 69 69 70 78: CONECT 71 72 78: CONECT 72 73 75 78: CONECT 73 74 74 77 78: CONECT 75 76 78: CONECT 77 78 78: CONECT 78 79 81 78: CONECT 79 80 80 85 78: CONECT 81 82 78: CONECT 82 83 83 84 78: CONECT 85 86 78: CONECT 86 87 89 78: CONECT 87 88 88 96 78: CONECT 89 90 78: CONECT 90 91 91 92 78: CONECT 91 93 78: CONECT 92 94 94 78: CONECT 93 95 95 78: CONECT 94 95 78: CONECT 96 97 78: CONECT 97 98 100 78: CONECT 98 99 99 104 78: CONECT 100 101 78: CONECT 101 102 102 103 78: CONECT 104 105 78: CONECT 105 106 108 78: CONECT 106 107 107 111 78: CONECT 108 109 110 78: CONECT 111 112 78: CONECT 112 113 115 78: CONECT 113 114 114 117 78: CONECT 115 116 78: CONECT 117 118 78: CONECT 118 119 121 78: CONECT 119 120 120 128 78: CONECT 121 122 78: CONECT 122 123 78: CONECT 123 124 78: CONECT 124 125 78: CONECT 125 126 126 127 78: CONECT 128 129 78: CONECT 129 130 132 78: CONECT 130 131 131 136 78: CONECT 132 133 78: CONECT 133 134 135 78: CONECT 136 137 142 78: CONECT 137 138 140 78: CONECT 138 139 139 143 78: CONECT 140 141 78: CONECT 141 142 78: CONECT 143 144 78: CONECT 144 145 78: CONECT 145 146 146 147 78: CONECT 147 148 78: CONECT 148 149 151 78: CONECT 149 150 150 154 78: CONECT 151 152 153 78: CONECT 154 155 160 78: CONECT 155 156 158 78: CONECT 156 157 157 161 78: CONECT 158 159 78: CONECT 159 160 78: CONECT 161 162 78: CONECT 162 163 165 78: CONECT 163 164 164 170 78: CONECT 165 166 78: CONECT 166 167 78: CONECT 167 168 168 169 78: CONECT 170 171 78: CONECT 171 172 174 78: CONECT 172 173 173 175 78: CONECT 175 176 78: CONECT 176 177 179 78: CONECT 177 178 178 183 78: CONECT 179 180 181 78: CONECT 181 182 78: CONECT 183 184 78: CONECT 184 185 187 78: CONECT 185 186 186 189 78: CONECT 187 188 78: CONECT 189 190 78: CONECT 190 191 193 78: CONECT 191 192 192 194 78: CONECT 194 195 78: CONECT 195 196 198 78: CONECT 196 197 197 201 78: CONECT 198 199 200 78: CONECT 201 202 78: CONECT 202 203 205 78: CONECT 203 204 204 213 78: CONECT 205 206 78: CONECT 206 207 207 208 78: CONECT 207 209 78: CONECT 208 210 210 78: CONECT 209 211 211 78: CONECT 210 211 78: CONECT 211 212 78: CONECT 213 214 78: CONECT 214 215 217 78: CONECT 215 216 216 220 78: CONECT 217 218 219 78: CONECT 220 221 78: CONECT 221 222 78: CONECT 222 223 223 224 78: CONECT 224 225 78: CONECT 225 226 228 78: CONECT 226 227 227 230 78: CONECT 228 229 78: CONECT 230 231 78: CONECT 231 232 234 78: CONECT 232 233 233 238 78: CONECT 234 235 236 78: CONECT 236 237 78: CONECT 238 239 78: CONECT 239 240 242 78: CONECT 240 241 241 246 78: CONECT 242 243 244 78: CONECT 244 245 78: CONECT 246 247 78: CONECT 247 248 250 78: CONECT 248 249 249 254 78: CONECT 250 251 252 78: CONECT 252 253 78: CONECT 254 255 260 78: CONECT 255 256 258 78: CONECT 256 257 257 261 78: CONECT 258 259 78: CONECT 259 260 78: CONECT 261 262 78: CONECT 262 263 78: CONECT 263 264 264 265 78: CONECT 265 266 78: CONECT 266 267 269 78: CONECT 267 268 268 270 78: CONECT 270 271 78: CONECT 271 272 274 78: CONECT 272 273 273 277 78: CONECT 274 275 276 78: CONECT 277 278 78: CONECT 278 279 281 78: CONECT 279 280 280 283 78: CONECT 281 282 78: CONECT 283 284 289 78: CONECT 284 285 287 78: CONECT 285 286 286 290 78: CONECT 287 288 78: CONECT 288 289 78: CONECT 290 291 78: CONECT 291 292 78: CONECT 292 293 293 294 78: CONECT 294 295 78: CONECT 295 296 298 78: CONECT 296 297 297 302 78: CONECT 298 299 78: CONECT 299 300 300 301 78: CONECT 302 303 78: CONECT 303 304 306 78: CONECT 304 305 305 314 78: CONECT 306 307 78: CONECT 307 308 308 309 78: CONECT 308 310 78: CONECT 309 311 311 78: CONECT 310 312 312 78: CONECT 311 312 78: CONECT 312 313 78: CONECT 314 315 78: CONECT 315 316 318 78: CONECT 316 317 317 319 78: CONECT 319 320 78: CONECT 320 321 323 78: CONECT 321 322 322 327 78: CONECT 323 324 78: CONECT 324 325 325 326 78: END 78: 78: Sequence: GREG 78: HELM: PEPTIDE1{G.R.E.G}$$$$ 78: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O 78: PDB: 78: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 78: CONECT 1 2 78: CONECT 2 3 78: CONECT 3 4 4 5 78: CONECT 5 6 78: CONECT 6 7 9 78: CONECT 7 8 8 16 78: CONECT 9 10 78: CONECT 10 11 78: CONECT 11 12 78: CONECT 12 13 78: CONECT 13 14 14 15 78: CONECT 16 17 78: CONECT 17 18 20 78: CONECT 18 19 19 25 78: CONECT 20 21 78: CONECT 21 22 78: CONECT 22 23 23 24 78: CONECT 25 26 78: CONECT 26 27 78: CONECT 27 28 28 29 78: END 78: 78: Sequence: CYIQNCPLG 78: HELM: PEPTIDE1{C.Y.I.Q.N.C.P.L.G.[am]}$PEPTIDE1,PEPTIDE1,1:R3-6:R3$$$ 78: Smiles: CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccc(O)cc2)NC(=O)[C@@H](N)CSSC[C@@H](C(=O)N2CCC[C@H]2C(=O)N[C@@H](CC(C)C)C(=O)NCC(N)=O)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCC(N)=O)NC1=O 78: PDB: 78: ATOM 1 N CYS A 1 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 2 CA CYS A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 3 C CYS A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 4 O CYS A 1 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 5 CB CYS A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 6 SG CYS A 1 0.000 0.000 0.000 1.00 0.00 S 78: ATOM 7 N TYR A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 8 CA TYR A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 9 C TYR A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 10 O TYR A 2 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 11 CB TYR A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 12 CG TYR A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 13 CD1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 14 CD2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 15 CE1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 16 CE2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 17 CZ TYR A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 18 OH TYR A 2 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 19 N ILE A 3 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 20 CA ILE A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 21 C ILE A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 22 O ILE A 3 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 23 CB ILE A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 24 CG1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 25 CG2 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 26 CD1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 27 N GLN A 4 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 28 CA GLN A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 29 C GLN A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 30 O GLN A 4 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 31 CB GLN A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 32 CG GLN A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 33 CD GLN A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 34 OE1 GLN A 4 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 35 NE2 GLN A 4 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 36 N ASN A 5 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 37 CA ASN A 5 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 38 C ASN A 5 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 39 O ASN A 5 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 40 CB ASN A 5 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 41 CG ASN A 5 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 42 OD1 ASN A 5 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 43 ND2 ASN A 5 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 44 N CYS A 6 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 45 CA CYS A 6 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 46 C CYS A 6 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 47 O CYS A 6 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 48 CB CYS A 6 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 49 SG CYS A 6 0.000 0.000 0.000 1.00 0.00 S 78: ATOM 50 N PRO A 7 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 51 CA PRO A 7 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 52 C PRO A 7 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 53 O PRO A 7 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 54 CB PRO A 7 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 55 CG PRO A 7 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 56 CD PRO A 7 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 57 N LEU A 8 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 58 CA LEU A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 59 C LEU A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 60 O LEU A 8 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 61 CB LEU A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 62 CG LEU A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 63 CD1 LEU A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 64 CD2 LEU A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 65 N GLY A 9 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 66 CA GLY A 9 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 67 C GLY A 9 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 68 O GLY A 9 0.000 0.000 0.000 1.00 0.00 O 78: HETATM 69 N NH2 A 10 0.000 0.000 0.000 1.00 0.00 N 78: CONECT 1 2 78: CONECT 2 3 5 78: CONECT 3 4 4 7 78: CONECT 5 6 78: CONECT 6 49 78: CONECT 7 8 78: CONECT 8 9 11 78: CONECT 9 10 10 19 78: CONECT 11 12 78: CONECT 12 13 13 14 78: CONECT 13 15 78: CONECT 14 16 16 78: CONECT 15 17 17 78: CONECT 16 17 78: CONECT 17 18 78: CONECT 19 20 78: CONECT 20 21 23 78: CONECT 21 22 22 27 78: CONECT 23 24 25 78: CONECT 25 26 78: CONECT 27 28 78: CONECT 28 29 31 78: CONECT 29 30 30 36 78: CONECT 31 32 78: CONECT 32 33 78: CONECT 33 34 34 35 78: CONECT 36 37 78: CONECT 37 38 40 78: CONECT 38 39 39 44 78: CONECT 40 41 78: CONECT 41 42 42 43 78: CONECT 44 45 78: CONECT 45 46 48 78: CONECT 46 47 47 50 78: CONECT 48 49 78: CONECT 50 51 56 78: CONECT 51 52 54 78: CONECT 52 53 53 57 78: CONECT 54 55 78: CONECT 55 56 78: CONECT 57 58 78: CONECT 58 59 61 78: CONECT 59 60 60 65 78: CONECT 61 62 78: CONECT 62 63 64 78: CONECT 65 66 78: CONECT 66 67 78: CONECT 67 68 68 69 78: END 78: 78: Sequence: LfPVXLfPVX 78: HELM: PEPTIDE1{L.[dF].P.V.[Orn].L.[dF].P.V.[Orn]}$PEPTIDE1,PEPTIDE1,10:R2-1:R1$$$ 78: Smiles: CC(C)C[C@@H]1NC(=O)[C@H](CCCN)NC(=O)[C@H](C(C)C)NC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCN)NC(=O)[C@H](C(C)C)NC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc2ccccc2)NC1=O 78: PDB: 78: ATOM 1 N LEU A 1 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 2 CA LEU A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 3 C LEU A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 4 O LEU A 1 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 5 CB LEU A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 6 CG LEU A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 7 CD1 LEU A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 8 CD2 LEU A 1 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 9 N DPN A 2 0.000 0.000 0.000 1.00 0.00 N 78: HETATM 10 CA DPN A 2 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 11 C DPN A 2 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 12 O DPN A 2 0.000 0.000 0.000 1.00 0.00 O 78: HETATM 13 CB DPN A 2 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 14 CG DPN A 2 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 15 CD1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 16 CD2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 17 CE1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 18 CE2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 19 CZ DPN A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 20 N PRO A 3 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 21 CA PRO A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 22 C PRO A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 23 O PRO A 3 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 24 CB PRO A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 25 CG PRO A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 26 CD PRO A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 27 N VAL A 4 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 28 CA VAL A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 29 C VAL A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 30 O VAL A 4 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 31 CB VAL A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 32 CG1 VAL A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 33 CG2 VAL A 4 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 34 N ORN A 5 0.000 0.000 0.000 1.00 0.00 N 78: HETATM 35 CA ORN A 5 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 36 C ORN A 5 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 37 O ORN A 5 0.000 0.000 0.000 1.00 0.00 O 78: HETATM 38 CB ORN A 5 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 39 CG ORN A 5 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 40 CD ORN A 5 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 41 NE ORN A 5 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 42 N LEU A 6 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 43 CA LEU A 6 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 44 C LEU A 6 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 45 O LEU A 6 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 46 CB LEU A 6 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 47 CG LEU A 6 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 48 CD1 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 49 CD2 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 50 N DPN A 7 0.000 0.000 0.000 1.00 0.00 N 78: HETATM 51 CA DPN A 7 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 52 C DPN A 7 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 53 O DPN A 7 0.000 0.000 0.000 1.00 0.00 O 78: HETATM 54 CB DPN A 7 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 55 CG DPN A 7 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 56 CD1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 57 CD2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 58 CE1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 59 CE2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 60 CZ DPN A 7 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 61 N PRO A 8 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 62 CA PRO A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 63 C PRO A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 64 O PRO A 8 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 65 CB PRO A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 66 CG PRO A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 67 CD PRO A 8 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 68 N VAL A 9 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 69 CA VAL A 9 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 70 C VAL A 9 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 71 O VAL A 9 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 72 CB VAL A 9 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 73 CG1 VAL A 9 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 74 CG2 VAL A 9 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 75 N ORN A 10 0.000 0.000 0.000 1.00 0.00 N 78: HETATM 76 CA ORN A 10 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 77 C ORN A 10 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 78 O ORN A 10 0.000 0.000 0.000 1.00 0.00 O 78: HETATM 79 CB ORN A 10 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 80 CG ORN A 10 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 81 CD ORN A 10 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 82 NE ORN A 10 0.000 0.000 0.000 1.00 0.00 N 78: CONECT 1 2 77 78: CONECT 2 3 5 78: CONECT 3 4 4 9 78: CONECT 5 6 78: CONECT 6 7 8 78: CONECT 9 10 78: CONECT 10 11 13 78: CONECT 11 12 12 20 78: CONECT 13 14 78: CONECT 14 15 15 16 78: CONECT 15 17 78: CONECT 16 18 18 78: CONECT 17 19 19 78: CONECT 18 19 78: CONECT 20 21 26 78: CONECT 21 22 24 78: CONECT 22 23 23 27 78: CONECT 24 25 78: CONECT 25 26 78: CONECT 27 28 78: CONECT 28 29 31 78: CONECT 29 30 30 34 78: CONECT 31 32 33 78: CONECT 34 35 78: CONECT 35 36 38 78: CONECT 36 37 37 42 78: CONECT 38 39 78: CONECT 39 40 78: CONECT 40 41 78: CONECT 42 43 78: CONECT 43 44 46 78: CONECT 44 45 45 50 78: CONECT 46 47 78: CONECT 47 48 49 78: CONECT 50 51 78: CONECT 51 52 54 78: CONECT 52 53 53 61 78: CONECT 54 55 78: CONECT 55 56 56 57 78: CONECT 56 58 78: CONECT 57 59 59 78: CONECT 58 60 60 78: CONECT 59 60 78: CONECT 61 62 67 78: CONECT 62 63 65 78: CONECT 63 64 64 68 78: CONECT 65 66 78: CONECT 66 67 78: CONECT 68 69 78: CONECT 69 70 72 78: CONECT 70 71 71 75 78: CONECT 72 73 74 78: CONECT 75 76 78: CONECT 76 77 79 78: CONECT 77 78 78 78: CONECT 79 80 78: CONECT 80 81 78: CONECT 81 82 78: END 78: 78: Sequence: GREG 78: HELM: PEPTIDE1{G.R.E.G}$$$$ 78: Smiles: N=C(N)NCCCC(NC(=O)CN)C(=O)NC(CCC(=O)O)C(=O)NCC(=O)O 78: PDB: 78: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 23 OD1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 24 OD2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 78: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 78: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 78: CONECT 1 2 78: CONECT 2 3 78: CONECT 3 4 4 5 78: CONECT 5 6 78: CONECT 6 7 9 78: CONECT 7 8 8 16 78: CONECT 9 10 78: CONECT 10 11 78: CONECT 11 12 78: CONECT 12 13 78: CONECT 13 14 14 15 78: CONECT 16 17 78: CONECT 17 18 20 78: CONECT 18 19 19 25 78: CONECT 20 21 78: CONECT 21 22 78: CONECT 22 23 23 24 78: CONECT 25 26 78: CONECT 26 27 78: CONECT 27 28 28 29 78: END 78: 73/236 Test #78: testSequence ........................... Passed 0.03 sec test 79 Start 79: testExtendedStereoParsing 79: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing 79: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 79: Test timeout computed to be: 1500 74/236 Test #79: testExtendedStereoParsing .............. Passed 0.05 sec test 80 Start 80: fileParsersCatchTest 80: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 80: Test timeout computed to be: 1500 69: [09:34:59] Empty atom list: 'M ALS 1 0 F' on line 8. 69: C 69: [09:34:59] ------------------------------------- 69: [09:34:59] Test multithreading Locale Switching 69: [09:34:59] Test multithreading (Done) 69: [09:34:59] ------------------------------------- 80: Randomness seeded to: 2772408113 80: [09:34:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 80: [09:34:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 80: [09:34:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 80: [09:34:59] SGroup 1 is invalid and will be ignored 80: [09:34:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 80: [09:34:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 80: [09:34:59] SGroup 1 is invalid and will be ignored 80: [09:34:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 80: [09:34:59] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 80: [09:34:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 80: [09:34:59] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 80: [09:34:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 80: [09:34:59] SGroup 1 is invalid and will be ignored 80: [09:34:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 80: [09:34:59] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 80: [09:34:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 80: [09:34:59] SGroup 1 is invalid and will be ignored 80: [09:34:59] SGroup 3 referenced on line 40 not found. 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: no bonds 80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp 80: Failed Expression: !d_bonds.empty() 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 4# 0x00007F8995EDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# 0x00005566F54676A9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 8# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 16# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] SGroup 3 referenced on line 40 not found. 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: no bonds 80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp 80: Failed Expression: !d_bonds.empty() 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 4# 0x00007F8995EDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# 0x00005566F5467752 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 8# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 16# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] no bonds 80: [09:34:59] SGroup 1 is invalid and will be ignored 80: [09:34:59] SGroup line too short: 'M SBV 1 6' on line 42 69: *************************************** 80: [09:34:59] SGroup 1 is invalid and will be ignored 69: *************************************** 80: [09:34:59] SGroup line too short: 'M SBL 2 3 9 10' on line 46 80: [09:34:59] SGroup 2 is invalid and will be ignored 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 80: Failed Expression: (lu != d_bondBookmarks.end()) 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# 0x00007F8995EDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# 0x00005566F5468312 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 17# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 80: Failed Expression: (lu != d_bondBookmarks.end()) 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# 0x00007F8995EDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# 0x00005566F54683BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 17# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] bookmark not found 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: bond is not part of the SubstanceGroup 80: Violation occurred on line 200 in file ./Code/GraphMol/SubstanceGroup.cpp 80: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# 0x00007F8995EDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# 0x00005566F54683BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 17# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] bond is not part of the SubstanceGroup 80: [09:34:59] SGroup 2 is invalid and will be ignored 80: [09:34:59] 80: 80: **** 69: [09:34:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: [09:34:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 80: Failed Expression: (lu != d_atomBookmarks.end()) 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# 0x00007F8995EDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# 0x00005566F5468729 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 17# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 80: Failed Expression: (lu != d_atomBookmarks.end()) 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# 0x00007F8995EDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# 0x00005566F54687D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 17# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] bookmark not found 80: [09:34:59] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. 80: [09:34:59] SGroup 2 is invalid and will be ignored 80: [09:34:59] WARNING: final character of V3000 array is not ')' 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 80: Failed Expression: (lu != d_bondBookmarks.end()) 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 9# 0x00005566F5466033 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 16# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 18# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] WARNING: final character of V3000 array is not ')' 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 80: Failed Expression: (lu != d_bondBookmarks.end()) 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 9# 0x00005566F54660CB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 16# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 18# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] bookmark not found 80: [09:34:59] SGroup 1 is invalid and will be ignored 80: [09:34:59] WARNING: final character of V3000 array is not ')' 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 80: Failed Expression: (lu != d_atomBookmarks.end()) 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 9# 0x00005566F5466434 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 16# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 18# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] WARNING: final character of V3000 array is not ')' 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 80: Failed Expression: (lu != d_atomBookmarks.end()) 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 9# 0x00005566F54664CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 16# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 18# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] bookmark not found 80: [09:34:59] SGroup 1 is invalid and will be ignored 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 80: Failed Expression: (lu != d_bondBookmarks.end()) 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 9# 0x00005566F5466833 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 16# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 18# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 80: Failed Expression: (lu != d_bondBookmarks.end()) 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 9# 0x00005566F54668CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 16# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 18# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] bookmark not found 80: [09:34:59] SGroup 2 is invalid and will be ignored 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 80: Failed Expression: (lu != d_atomBookmarks.end()) 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 9# 0x00005566F5466C32 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 16# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 18# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 80: Failed Expression: (lu != d_atomBookmarks.end()) 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 9# 0x00005566F5466CCC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 16# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 18# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] bookmark not found 80: [09:34:59] SGroup 2 is invalid and will be ignored 69: [09:34:59] bond with order 0 found on line 7. This is not part of the MDL specification. 80: [09:34:59] Explicit valence for atom # 2 O, 3, is greater than permitted 80: [09:34:59] Explicit valence for atom # 1 O, 3, is greater than permitted 80: [09:34:59] Explicit valence for atom # 1 C, 5, is greater than permitted 80: [09:34:59] sanitize [09:34:59] UNK: [09:34:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 69: [09:34:59] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) 69: [09:34:59] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) 69: [09:34:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 80: [09:34:59] skipping block at line 7: 'BEGIN ATOM' 80: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL 80: END 80: 80: [09:34:59] 80: 80: **** 69: generating smiles 80: Pre-condition Violation 80: no stream 80: Violation occurred on line 133 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp 80: Failed Expression: dp_inStream 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# 0x00005566F549B3C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 4# 0x00005566F5456CAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 5# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 6# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 7# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 8# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 13# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: no stream 80: Violation occurred on line 187 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp 80: Failed Expression: dp_inStream 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# 0x00005566F549B3C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 4# 0x00005566F5456E88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 5# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 6# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 7# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 8# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 13# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: no stream 80: Violation occurred on line 409 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp 80: Failed Expression: dp_inStream 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# 0x00005566F549B3C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 4# 0x00005566F54572C1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 5# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 6# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 7# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 8# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 13# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] 80: 80: **** 69: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 69: converting back 80: Pre-condition Violation 80: no stream 80: Violation occurred on line 264 in file ./Code/GraphMol/FileParsers/TDTMolSupplier.cpp 80: Failed Expression: dp_inStream 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# 0x00005566F549B3C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 4# 0x00005566F5457646 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 5# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 6# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 7# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 8# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 13# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: no stream 80: Violation occurred on line 593 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 80: Failed Expression: dp_sInStream != nullptr 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# 0x00005566F549B3C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 4# 0x00005566F54578C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 5# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 6# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 7# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 8# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 13# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] Found a SCD/SED line with missing/empty SDT specification at line 21 80: [09:34:59] Found a SCD/SED line with missing/empty SDT specification at line 20 80: [09:34:59] BEGIN SGROUP line not found on line 14 80: [09:34:59] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. 80: [09:34:59] END SGROUP line not found on line 14 80: [09:34:59] END SGROUP line not found on line 14 80: [09:34:59] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. 80: [09:34:59] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. 80: [09:34:59] 80: 80: **** 80: Range Error 80: idx 80: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp 80: Failed Expression: 99 < 9 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# 0x00005566F549AFDF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 7# 0x00005566F545CCC3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 8# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 16# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. 80: [09:34:59] Multiple ATTCHPT values for atom 2 on line 9 69: check isomorphism 80: [09:34:59] Found a SCD/SED line with missing/empty SDT specification at line 12 80: [09:34:59] SMARTS Parse Error: syntax error while parsing: [#6;R 80: [09:34:59] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' 80: [09:34:59] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. 80: [09:34:59] Skipping empty SMARTS value for SMARTSQ. 80: [09:34:59] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. 80: [09:34:59] Found a SCD/SED line with missing/empty SDT specification at line 12 80: [09:34:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 80: [09:34:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 80: [09:34:59] WARNING: Skipping property bar because the value includes an illegal blank line 80: [09:34:59] WARNING: Skipping property baz because the value includes an illegal blank line 80: [09:34:59] WARNING: Skipping property bletch 80: nope because the name includes a newline 80: [09:34:59] WARNING: Skipping property bletch 80: nope2 because the name includes a newline 80: [09:34:59] 80: 80: **** 80: Post-condition Violation 80: Element 'QQQ' not found 80: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 80: Failed Expression: anum > -1 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# 0x00007F8995EC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 4# 0x00007F8995ED3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# 0x00007F8995ED4FAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 9# 0x00005566F542E35C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 16# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 18# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] 80: 80: **** 80: Post-condition Violation 80: Element 'QQQ' not found 80: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 80: Failed Expression: anum > -1 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# 0x00007F8995EC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 4# 0x00007F8995ED3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# 0x00007F8995ED4FAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 9# 0x00005566F542DA3A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 16# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 18# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] 80: 80: **** 80: Post-condition Violation 80: Element 'QQQ' not found 80: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 80: Failed Expression: anum > -1 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# 0x00007F8995EC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 4# 0x00007F8995ED1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# 0x00007F8995ED217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 9# 0x00005566F542E304 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 16# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 18# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] 80: 80: **** 80: Post-condition Violation 80: Element 'QQQ' not found 80: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 80: Failed Expression: anum > -1 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# 0x00007F8995EC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 4# 0x00007F8995ED1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# 0x00007F8995ED217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 9# 0x00005566F542DFA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 12# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 13# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 14# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 15# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 16# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 18# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] atom 3 has a negative isotope value. line: 15 80: [09:34:59] Ignoring invalid chirality label: '2_bad_chirality' 80: [09:34:59] 80: 80: **** 80: Pre-condition Violation 80: no input stream 80: Violation occurred on line 560 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 80: Failed Expression: dp_sInStream 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 4# 0x00005566F54707A5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 5# 0x00005566F54DF228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 6# 0x00005566F54DFD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 7# 0x00005566F54E01C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 8# 0x00005566F54B18C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 9# 0x00005566F54B1C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 10# 0x00005566F5424C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: 11# 0x00007F8995433CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 80: 13# 0x00005566F5424C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: 80: [09:34:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 80: [09:34:59] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[09:34:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 80: [09:34:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 80: [09:34:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 80: [09:34:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: [09:34:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 69: [09:34:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 69: [09:34:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 69: [09:34:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 69: [09:34:59] deprecated group abbreviation ignored on line 24 69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] 69: [09:34:59] 69: 69: **** 69: Post-condition Violation 69: Element 'Mv' not found 69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 69: Failed Expression: anum > -1 69: ---------- 69: Stacktrace: 69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 3# 0x00007F9056AC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 4# 0x00007F9056AD1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 5# 0x00007F9056AD217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 69: 9# 0x0000557205694C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: 10# 0x00005572056FB372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: 11# 0x000055720567B9A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: 12# 0x00007F9056033CA8 in /lib/x86_64-linux-gnu/libc.so.6 69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 69: 14# 0x000055720567BAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: ---------- 69: **** 69: 69: [09:34:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 69: [09:34:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 69: ---------------------------------- 69: ---------------------------------- 69: [09:34:59] 69: 69: **** 69: Pre-condition Violation 69: rlabel out of range for MDL files 69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp 69: Failed Expression: rlabel >= 0 && rlabel < 100 69: ---------- 69: Stacktrace: 69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 69: 3# 0x00005572056A1FFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: 4# 0x00005572056FB3EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: 5# 0x000055720567B9A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: 6# 0x00007F9056033CA8 in /lib/x86_64-linux-gnu/libc.so.6 69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 69: 8# 0x000055720567BAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: ---------- 69: **** 69: 69: [09:34:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 69: [09:35:00] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas 69: [09:35:00] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 69: [09:35:00] Empty atom list: 'M ALS 1 0 F' on line 8. 75/236 Test #69: fileParsersTest1 ....................... Passed 1.71 sec test 81 Start 81: testPropertyLists 81: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists 81: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 81: Test timeout computed to be: 1500 81: Randomness seeded to: 3231395427 81: =============================================================================== 81: All tests passed (95 assertions in 4 test cases) 81: 76/236 Test #81: testPropertyLists ...................... Passed 0.02 sec test 82 Start 82: XYZFileParserCatchTest 82: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest 82: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 82: Test timeout computed to be: 1500 82: Randomness seeded to: 3174551436 82: =============================================================================== 82: All tests passed (100 assertions in 2 test cases) 82: 77/236 Test #82: XYZFileParserCatchTest ................. Passed 0.01 sec test 83 Start 83: cdxmlParserCatchTest 83: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest 83: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 83: Test timeout computed to be: 1500 83: Randomness seeded to: 2482281660 83: [09:35:00] Invalid or missing fragment id from CDXML fragment, assigning new one... 83: [09:35:00] Explicit valence for atom # 3 N, 4, is greater than permitted 83: [09:35:00] CDXMLParser: failed sanitizing skipping fragment 32 83: [09:35:00] Bad bond in CDXML skipping fragment 58... 83: [09:35:00] Invalid or missing fragment id from CDXML fragment, assigning new one... 83: [09:35:00] Bad bond in CDXML skipping fragment 58... 83: [09:35:00] WARNING: not removing hydrogen atom without neighbors 83: [09:35:00] WARNING: not removing hydrogen atom without neighbors 83: [09:35:00] WARNING: not removing hydrogen atom without neighbors 83: [09:35:00] WARNING: not removing hydrogen atom without neighbors 83: [09:35:00] WARNING: not removing hydrogen atom without neighbors 83: [09:35:00] WARNING: not removing hydrogen atom without neighbors 83: [09:35:00] WARNING: not removing hydrogen atom without neighbors 83: [09:35:00] WARNING: not removing hydrogen atom without neighbors 83: [09:35:00] WARNING: not removing hydrogen atom without neighbors 83: [09:35:00] WARNING: not removing hydrogen atom without neighbors 83: [09:35:00] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. 83: [09:35:00] Incomplete atom labelling, cannot make bond 83: [09:35:00] Incomplete atom labelling, cannot make bond 83: [09:35:00] Incomplete atom labelling, cannot make bond 83: [09:35:00] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas 83: [09:35:00] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas 83: [09:35:00] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast 83: [09:35:00] Failed to parse XML fragment 5 node: b attribute: Order: 5 83: [09:35:00] Invalid or missing fragment id from CDXML fragment, assigning new one... 83: =============================================================================== 83: All tests passed (263 assertions in 7 test cases) 83: 78/236 Test #83: cdxmlParserCatchTest ................... Passed 0.09 sec test 84 Start 84: molfileStereoCatchTest 84: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest 84: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 84: Test timeout computed to be: 1500 84: Randomness seeded to: 11885800 84: [09:35:00] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 84: [09:35:00] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 84: [09:35:00] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 84: [09:35:00] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 84: =============================================================================== 84: All tests passed (142 assertions in 6 test cases) 84: 79/236 Test #84: molfileStereoCatchTest ................. Passed 0.05 sec test 85 Start 85: connectTheDotsTest 85: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest 85: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 85: Test timeout computed to be: 1500 85: Randomness seeded to: 2104980272 85: =============================================================================== 85: All tests passed (8 assertions in 1 test case) 85: 80/236 Test #85: connectTheDotsTest ..................... Passed 0.02 sec test 86 Start 86: v2MolSuppliers 86: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers 86: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 86: Test timeout computed to be: 1500 86: Randomness seeded to: 3093533266 86: [09:35:00] Ignoring invalid chirality label: '12_R_1_3_4_5' 86: [09:35:00] Ignoring invalid chirality label: '12_ANR_1_3_4_15' 86: [09:35:00] Ignoring invalid chirality label: '2_S_1_3_4' 86: [09:35:00] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' 86: =============================================================================== 86: All tests passed (24 assertions in 6 test cases) 86: 81/236 Test #86: v2MolSuppliers ......................... Passed 0.02 sec test 87 Start 87: v2FileParsersCatchTest 87: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest 87: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 87: Test timeout computed to be: 1500 87: Randomness seeded to: 4065709695 87: =============================================================================== 87: All tests passed (6 assertions in 1 test case) 87: 82/236 Test #87: v2FileParsersCatchTest ................. Passed 0.06 sec test 88 Start 88: atropisomersCatch 88: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/atropisomersCatch 88: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 88: Test timeout computed to be: 1500 88: Randomness seeded to: 1059961284 88: =============================================================================== 88: All tests passed (26 assertions in 2 test cases) 88: 83/236 Test #88: atropisomersCatch ...................... Passed 0.02 sec test 89 Start 89: multithreadedSupplierCatchTest 89: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest 89: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 89: Test timeout computed to be: 1500 89: Randomness seeded to: 3381119268 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [09:35:00] Explicit valence for atom # 9 N, 5, is greater than permitted 89: [09:35:00] Explicit valence for atom # 3 Al, 6, is greater than permitted 89: [09:35:00] Explicit valence for atom # 4 Al, 6, is greater than permitted 89: [09:35:00] Explicit valence for atom # 10 Si, 6, is greater than permitted 89: [09:35:00] Explicit valence for atom # 2 O, 4, is greater than permitted 89: [09:35:00] Explicit valence for atom # 3 Al, 6, is greater than permitted 89: [09:35:00] Explicit valence for atom # 3 Be, 4, is greater than permitted 89: [09:35:00] Explicit valence for atom # 27 P, 6, is greater than permitted 29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 29: All 191 tests passed 89: [09:35:01] Explicit valence for atom # 9 N, 5, is greater than permitted 89: [09:35:01] Explicit valence for atom # 3 Al, 6, is greater than permitted 29: 29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 89: [09:35:01] Explicit valence for atom # 4 Al, 6, is greater than permitted 89: [09:35:01] Explicit valence for atom # 10 Si, 6, is greater than permitted 89: [09:35:01] Explicit valence for atom # 2 O, 4, is greater than permitted 89: [09:35:01] Explicit valence for atom # 3 Be, 4, is greater than permitted 89: [09:35:01] Explicit valence for atom # 3 Al, 6, is greater than permitted 89: [09:35:01] Explicit valence for atom # 27 P, 6, is greater than permitted 89: =============================================================================== 89: All tests passed (21562 assertions in 3 test cases) 89: 84/236 Test #89: multithreadedSupplierCatchTest ......... Passed 0.90 sec test 90 Start 90: testSubstructMatch 90: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct 90: Test timeout computed to be: 1500 90: ----------------- Test 1 90: Done 90: 90: ----------------- Test 2 90: Done 90: 90: ----------------- Test 3 90: Done 90: 90: ----------------- Test 4 90: Done 90: 90: ----------------- Test 5 90: Done 90: 90: ----------------- Test 5 QueryRoot 90: Done 90: 90: ----------------- Test 6 (Issue71 related) 90: Done 90: 90: ----------------- Testing serial numbers on recursive queries 90: Done 90: 90: [09:35:01] ------------------------------------- 90: [09:35:01] Test multithreading 90: reading molecules 90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 90: processing 90: launch :0 90: launch :1 90: launch :2 90: launch :3 90: done 90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 90: processing2 90: launch2 :0 90: launch2 :1 90: launch2 :2 90: launch2 :3 90: done 90: preprocessing 3 90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 90: processing3 90: launch3 :0 90: launch3 :1 90: launch3 :2 90: launch3 :3 90: done 90: [09:35:01] done 90: [09:35:01] ------------------------------------- 90: [09:35:01] Test GitHub issue 15 90: [09:35:01] done 90: [09:35:01] ------------------------------------- 90: [09:35:01] Test GitHub issue 409 90: [09:35:01] done 90: [09:35:01] ------------------------------------- 90: [09:35:01] Test chiral matching 90: [09:35:01] done 90: [09:35:01] ------------------------------------- 90: [09:35:01] Test GitHub issue 688: partially specified chiral substructure queries don't work properly 90: [09:35:01] done 90: [09:35:01] ------------------------------------- 90: [09:35:01] Test dative-bond matching 90: [09:35:01] done 90: [09:35:01] ------------------------------------- 90: [09:35:01] Test cis/trans matching 90: [09:35:01] done 90: [09:35:01] ------------------------------------- 90: [09:35:01] Test cis/trans matching part 2 90: [09:35:01] done 90: [09:35:01] ------------------------------------- 90: [09:35:01] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS 90: [09:35:01] done 90: [09:35:01] ------------------------------------- 90: [09:35:01] Testing matching E/Z against Cis/Trans stereo bonds 90: [09:35:01] 90: 90: **** 90: Pre-condition Violation 90: matches must not be empty 90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 90: Failed Expression: !matches.empty() 90: ---------- 90: Stacktrace: 90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 4# 0x0000557E7373538A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: 5# 0x0000557E73725BF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: 6# 0x00007FB67CA33CA8 in /lib/x86_64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 90: 8# 0x0000557E73725D31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: 90: [09:35:01] 90: 90: **** 90: Pre-condition Violation 90: matches must not be empty 90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 90: Failed Expression: !matches.empty() 90: ---------- 90: Stacktrace: 90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 4# 0x0000557E73720420 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: 5# 0x0000557E73725BF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: 6# 0x00007FB67CA33CA8 in /lib/x86_64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 90: 8# 0x0000557E73725D31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: 90: [09:35:01] ------------------------------------- 90: [09:35:01] Test substructure matching with a pathological case for symmetric SSSR 90: [09:35:01] ------------------------------------- 90: [09:35:01] Test isAtomTerminalRGroupOrQueryHydrogen 85/236 Test #90: testSubstructMatch ..................... Passed 0.40 sec test 91 Start 91: substructTestCatch 91: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch 91: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct 91: Test timeout computed to be: 1500 91: Randomness seeded to: 2269921378 91: =============================================================================== 91: All tests passed (242 assertions in 12 test cases) 91: 86/236 Test #91: substructTestCatch ..................... Passed 0.21 sec test 92 Start 92: testGenericGroups 92: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups 92: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups 92: Test timeout computed to be: 1500 92: Randomness seeded to: 3637284961 92: =============================================================================== 92: All tests passed (11480 assertions in 38 test cases) 92: 87/236 Test #92: testGenericGroups ...................... Passed 0.41 sec test 93 Start 93: testReaction 93: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction 93: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 93: Test timeout computed to be: 1500 93: smi: O=C1CNC(=O)CN1 93: 1: O=C1CNC(=O)CN1 93: 2: COOC 93: [09:35:02] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] 93: [09:35:02] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 93: O=C1CNC(=O)CN1 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 93: [09:35:02] atom 0 in product 0 has multiple charge specifications. 93: mass: 15.0001 93: Oc1ccccn1 93: Oc1ccc[nH]1 93: [09:35:02] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] 93: [09:35:02] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' 93: [09:35:02] SMARTS Parse Error: syntax error while parsing: ([C:2] 93: [09:35:02] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' 93: [09:35:02] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] 93: [09:35:02] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' 93: [09:35:02] SMARTS Parse Error: syntax error while parsing: [C:2]) 93: [09:35:02] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' 93: [09:35:02] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] 93: [09:35:02] SMILES Parse Error: check for mistakes around position 2: 93: [09:35:02] [Q:1][C:2][C:3](=[O:4])[O:5] 93: [09:35:02] ~^ 93: [09:35:02] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 93: [09:35:02] reactant 2 has no mapped atoms. 93: [09:35:02] >> Atoms within one molecule have different RXN roles. 93: [09:35:02] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. 93: [09:35:02] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] 93: [09:35:02] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' 93: [09:35:02] SMARTS Parse Error: syntax error while parsing: ([C:2] 93: [09:35:02] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' 93: [09:35:02] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) 93: [09:35:02] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' 93: [09:35:02] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] 93: [09:35:02] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' 93: [09:35:02] reactant 0 has no mapped atoms. 93: [09:35:02] reactant 1 has no mapped atoms. 93: [09:35:02] reactant 3 has no mapped atoms. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 4 found multiple times. 93: [09:35:02] product atom-mapping number 5 found multiple times. 93: [09:35:02] product atom-mapping number 6 found multiple times. 93: [09:35:02] product atom-mapping number 7 found multiple times. 93: [09:35:02] product atom-mapping number 8 found multiple times. 93: [09:35:02] product atom-mapping number 12 found multiple times. 93: [09:35:02] product atom-mapping number 9 found multiple times. 93: [09:35:02] product atom-mapping number 10 found multiple times. 93: [09:35:02] product atom-mapping number 11 found multiple times. 93: [09:35:02] reactant 0 has no mapped atoms. 93: [09:35:02] reactant 1 has no mapped atoms. 93: [09:35:02] reactant 3 has no mapped atoms. 93: [09:35:02] reactant atom-mapping number 19 found multiple times. 93: [09:35:02] reactant atom-mapping number 25 found multiple times. 93: [09:35:02] reactant atom-mapping number 20 found multiple times. 93: [09:35:02] reactant atom-mapping number 21 found multiple times. 93: [09:35:02] reactant atom-mapping number 22 found multiple times. 93: [09:35:02] reactant atom-mapping number 23 found multiple times. 93: [09:35:02] reactant atom-mapping number 24 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br 93: [09:35:02] product atom-mapping number 5 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 4 found multiple times. 93: [09:35:02] product atom-mapping number 5 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br 93: [09:35:02] product atom-mapping number 5 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 4 found multiple times. 93: [09:35:02] product atom-mapping number 5 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 4 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 4 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)O[C@](F)(Cl)Br 93: [09:35:02] product atom-mapping number 4 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 4 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 4 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 4 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 93: [09:35:02] product atom-mapping number 3 found multiple times. 93: [09:35:02] product atom-mapping number 2 found multiple times. 93: [09:35:02] product atom-mapping number 1 found multiple times. 93: [09:35:02] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 93: [09:35:02] product atom-mapping number 6 not found in reactants. 93: [09:35:02] product atom-mapping number 7 not found in reactants. 93: [09:35:02] product atom-mapping number 8 not found in reactants. 93: [09:35:02] product atom-mapping number 7 not found in reactants. 93: [09:35:02] product atom-mapping number 8 not found in reactants. 93: [09:35:02] product atom-mapping number 9 not found in reactants. 93: [09:35:02] product atom-mapping number 10 not found in reactants. 93: [09:35:02] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 93: [09:35:02] product atom-mapping number 7 not found in reactants. 93: [09:35:02] product atom-mapping number 8 not found in reactants. 93: [09:35:02] product atom-mapping number 9 not found in reactants. 93: [09:35:02] product atom-mapping number 10 not found in reactants. 93: [09:35:02] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 93: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 93: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 93: [09:35:02] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 93: [09:35:02] product atom-mapping number 17 not found in reactants. 93: [09:35:02] product atom-mapping number 18 not found in reactants. 93: [09:35:02] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 12 93: [09:35:02] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 93: [09:35:02] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 93: 93: [09:35:02] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels 93: ------------- 93: CCOc1ccccc1 93: [09:35:02] reactant 0 has no mapped atoms. 93: [09:35:02] product 0 has no mapped atoms. 93: [09:35:02] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. 88/236 Test #93: testReaction ........................... Passed 0.29 sec test 94 Start 94: testReactionFingerprints 94: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints 94: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 94: Test timeout computed to be: 1500 94: [09:35:02] ------------------------------------- 94: [09:35:02] Test Reaction StructuralFingerprint 94: [09:35:02] ------------------------------------- 94: [09:35:02] Test Reaction DifferenceFingerprint 89/236 Test #94: testReactionFingerprints ............... Passed 0.02 sec test 95 Start 95: testEnumeration 95: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration 95: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 95: Test timeout computed to be: 1500 95: 30000000 30000000 80: =============================================================================== 80: All tests passed (1596 assertions in 100 test cases) 80: 90/236 Test #80: fileParsersCatchTest ................... Passed 3.73 sec test 96 Start 96: rxnTestCatch 96: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch 96: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 96: Test timeout computed to be: 1500 96: Randomness seeded to: 3729234988 96: [09:35:03] atom 0 in product 0 has multiple charge specifications. 96: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 34 96: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 36 96: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 38 96: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 40 96: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 42 96: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 87 96: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 89 96: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 91 96: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 93 96: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 95 96: [09:35:03] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 96: [09:35:03] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 96: [09:35:03] SMARTS Parse Error: unclosed ring for input: 'CC1' 96: [09:35:03] SMILES Parse Error: unclosed ring for input: 'CC1' 96: [09:35:03] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 96: [09:35:03] product atom-mapping number 2 not found in reactants. 96: [09:35:03] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 96: [09:35:03] product atom-mapping number 2 not found in reactants. 96: [09:35:03] CX Extensions: Substance group hierarchy is not always preserved. 96: [09:35:03] CX Extensions: Substance group hierarchy is not always preserved. 96: [09:35:03] reactant 0 has no mapped atoms. 96: [09:35:03] product 0 has no mapped atoms. 96: [09:35:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 96: [09:35:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 96: [09:35:03] Explicit valence for atom # 1 O, 5, is greater than permitted 96: =============================================================================== 96: All tests passed (722 assertions in 30 test cases) 96: 91/236 Test #96: rxnTestCatch ........................... Passed 0.09 sec test 97 Start 97: pyChemReactions 97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" 97: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 97: Test timeout computed to be: 1500 97: ...[09:35:03] 97: 97: **** 97: Pre-condition Violation 97: getNumImplicitHs() called without preceding call to calcImplicitValence() 97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp 97: Failed Expression: d_implicitValence > -1 97: ---------- 97: Stacktrace: 97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 25# 0x00007FE5B967962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 36# 0x00007FE5B73B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 37# 0x00007FE5B73B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 38# 0x00007FE5B73B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 39# 0x00007FE5B73B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 40# 0x00007FE5B73B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 46# 0x00007FE5B96763C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 47# _PyObject_MakeTpCall in /usr/bin/python3 97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 49# 0x00000000005C30D9 in /usr/bin/python3 97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 51# 0x000000000064B89F in /usr/bin/python3 97: 52# 0x000000000069ECA0 in /usr/bin/python3 97: 53# _PyObject_MakeTpCall in /usr/bin/python3 97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 55# 0x00000000005C30D9 in /usr/bin/python3 97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 57# 0x000000000064B89F in /usr/bin/python3 97: 58# 0x000000000069ECA0 in /usr/bin/python3 97: 59# _PyObject_MakeTpCall in /usr/bin/python3 97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 61# 0x00000000005C30D9 in /usr/bin/python3 97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 63# 0x000000000064B89F in /usr/bin/python3 97: 64# 0x000000000069ECA0 in /usr/bin/python3 97: 65# _PyObject_MakeTpCall in /usr/bin/python3 97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 67# 0x0000000000599DE7 in /usr/bin/python3 97: 68# _PyObject_MakeTpCall in /usr/bin/python3 97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 70# PyEval_EvalCode in /usr/bin/python3 97: 71# 0x000000000066DA21 in /usr/bin/python3 97: 72# 0x0000000000669A8C in /usr/bin/python3 97: 73# 0x0000000000682973 in /usr/bin/python3 97: 74# 0x0000000000682273 in /usr/bin/python3 97: 75# 0x00000000006820AE in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 97: 78# 0x00007FE5BA0DFCA8 in /lib/x86_64-linux-gnu/libc.so.6 97: 79# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 97: 80# _start in /usr/bin/python3 97: ---------- 97: **** 97: 97: [09:35:03] 97: 97: **** 97: Pre-condition Violation 97: getNumImplicitHs() called without preceding call to calcImplicitValence() 97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp 97: Failed Expression: d_implicitValence > -1 97: ---------- 97: Stacktrace: 97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 25# 0x00007FE5B967962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 36# 0x00007FE5B73B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 37# 0x00007FE5B73B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 38# 0x00007FE5B73B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 39# 0x00007FE5B73B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 40# 0x00007FE5B73B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 46# 0x00007FE5B96763C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 47# _PyObject_MakeTpCall in /usr/bin/python3 97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 49# 0x00000000005C30D9 in /usr/bin/python3 97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 51# 0x000000000064B89F in /usr/bin/python3 97: 52# 0x000000000069ECA0 in /usr/bin/python3 97: 53# _PyObject_MakeTpCall in /usr/bin/python3 97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 55# 0x00000000005C30D9 in /usr/bin/python3 97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 57# 0x000000000064B89F in /usr/bin/python3 97: 58# 0x000000000069ECA0 in /usr/bin/python3 97: 59# _PyObject_MakeTpCall in /usr/bin/python3 97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 61# 0x00000000005C30D9 in /usr/bin/python3 97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 63# 0x000000000064B89F in /usr/bin/python3 97: 64# 0x000000000069ECA0 in /usr/bin/python3 97: 65# _PyObject_MakeTpCall in /usr/bin/python3 97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 67# 0x0000000000599DE7 in /usr/bin/python3 97: 68# _PyObject_MakeTpCall in /usr/bin/python3 97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 70# PyEval_EvalCode in /usr/bin/python3 97: 71# 0x000000000066DA21 in /usr/bin/python3 97: 72# 0x0000000000669A8C in /usr/bin/python3 97: 73# 0x0000000000682973 in /usr/bin/python3 97: 74# 0x0000000000682273 in /usr/bin/python3 97: 75# 0x00000000006820AE in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 97: 78# 0x00007FE5BA0DFCA8 in /lib/x86_64-linux-gnu/libc.so.6 97: 79# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 97: 80# _start in /usr/bin/python3 97: ---------- 97: **** 97: 97: .........[09:35:03] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 97: [09:35:03] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 97: [09:35:03] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 97: [09:35:03] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 97: .[09:35:03] product atom-mapping number 1 found multiple times. 97: [09:35:03] product atom-mapping number 1 found multiple times. 97: ................[09:35:03] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 3 97: [09:35:03] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 3 97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. 97: [09:35:03] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 3 97: ..[09:35:03] reactant 2 has no mapped atoms. 97: [09:35:03] reactant 2 has no mapped atoms. 97: [09:35:03] product 1 has no mapped atoms. 97: ........[09:35:03] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q 97: [09:35:03] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' 97: [09:35:03] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q 97: [09:35:03] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' 97: .[09:35:03] reactant atom-mapping number 1 found multiple times. 97: [09:35:03] product atom-mapping number 2 not found in reactants. 97: [09:35:03] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 4 97: [09:35:03] product atom-mapping number 5 not found in reactants. 97: ........./build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> 97: png = open(fname, 'rb').read() 97: ResourceWarning: Enable tracemalloc to get the object allocation traceback 97: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 34 97: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 36 97: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 38 97: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 40 97: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 42 97: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 87 97: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 89 97: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 91 97: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 93 97: [09:35:03] Found a SCD/SED line with missing/empty SDT specification at line 95 97: ..[09:35:03] SMARTS Parse Error: syntax error while parsing: boromicacid 97: [09:35:03] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 97: [09:35:03] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 97: [09:35:03] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 97: [09:35:03] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 97: [09:35:03] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 97: [09:35:03] reaction has no reactants 97: [09:35:03] reaction has no products 97: [09:35:03] initialization failed 97: [09:35:03] reaction has no reactants 97: [09:35:03] reaction has no products 97: .[09:35:03] SMARTS Parse Error: syntax error while parsing: boromicacid 97: [09:35:03] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 97: [09:35:03] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 97: [09:35:03] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 97: [09:35:03] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 97: [09:35:03] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 97: [09:35:03] reaction has no reactants 97: [09:35:03] reaction has no products 97: [09:35:03] initialization failed 97: [09:35:03] reaction has no reactants 97: [09:35:03] reaction has no products 97: . 97: ---------------------------------------------------------------------- 97: Ran 54 tests in 0.115s 97: 97: OK 97: ******************************************** 97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn 97: 92/236 Test #97: pyChemReactions ........................ Passed 0.42 sec test 98 Start 98: pyChemReactionEnumerations 98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" 98: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 98: Test timeout computed to be: 1500 98: [09:35:03] == testCartesianProduct 98: .[09:35:03] == testEnumerateLibrary 98: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> 98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) 98: ResourceWarning: Enable tracemalloc to get the object allocation traceback 98: ..[09:35:03] == testRGroupState 98: .[09:35:03] == testRandomEnumerateAllBBsLibrary 98: ** [1, 1] 98: ** [0, 2] 98: ** [1, 0] 98: .[09:35:03] == testRandomEnumerateLibrary 98: .[09:35:03] == testRandomSample 98: .[09:35:03] == testRandomSampleAllBBs 98: .[09:35:03] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 98: [09:35:03] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 98: .[09:35:03] == testRemoveBadMatches 98: .[09:35:03] == testTimings 29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 29: All 191 tests passed 29: done 29: ------------------------------------- 29: Unit tests for all MMFF constraint terms. 29: 10.0003 29: done 29: ------------------------------------- 29: Unit test for MMFF TorsionConstraint close to 0 degrees. 29: done 29: ------------------------------------- 29: Unit tests for copying MMFF ForceFields. 29: done 29: ------------------------------------- 29: Unit test for MMFF butane scan. 98: . 98: ---------------------------------------------------------------------- 98: Ran 11 tests in 0.580s 98: 98: OK 98: True 98: == CartesianProductStrategy CartesianProductStrategy 98: 197 out of 300 98: 0 6 out of 10 98: 1 3 out of 5 98: 2 4 out of 6 98: 198 out of 300 98: 0 10 out of 10 98: 1 5 out of 5 98: 2 6 out of 6 98: Skipped 10000000 in 0.07596826553344727 seconds 98: Skipped 10000000 in 0.26769399642944336 seconds 98: Skipped 10000000 in 0.10884523391723633 seconds 93/236 Test #98: pyChemReactionEnumerations ............. Passed 0.81 sec test 99 Start 99: pyChemReactionSanitize 99: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" 99: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 99: Test timeout computed to be: 1500 29: done 94/236 Test #29: testMMFFForceField ..................... Passed 8.44 sec test 100 Start 100: testChemTransforms 100: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 100: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms 100: Test timeout computed to be: 1500 100: 1 smi: CC 100: 1 smi: CC 100: 2 smi: CCO[C@H](N)P 100: 2 smi: CC 100: replaceSub smi1:CCP(CC)[C@@H](N)O 100: replaceSub smi1:CCNCC 100: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 100: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O 100: [09:35:04] SMARTS Parse Error: syntax error while parsing: bar 100: [09:35:04] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' 95/236 Test #100: testChemTransforms ..................... Passed 0.07 sec test 101 Start 101: chemTransformsTestCatch 101: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms 101: Test timeout computed to be: 1500 101: Randomness seeded to: 1167661556 101: [09:35:04] Incomplete atom labelling, cannot make bond 101: [09:35:04] 101: 101: **** 101: Invariant Violation 101: molzip: bond info already exists for end atom with label:1 101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 101: Failed Expression: !bond.b 101: ---------- 101: Stacktrace: 101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# 0x00005569D95A8596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 5# 0x00005569D95FA168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 6# 0x00005569D95FAC88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 7# 0x00005569D95FB100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 8# 0x00005569D95CC903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 9# 0x00005569D95CCC6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 10# 0x00005569D959C75E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 11# 0x00007F2AF4633CA8 in /lib/x86_64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 101: 13# 0x00005569D959C7A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: [09:35:04] Incomplete atom labelling, cannot make bond 101: [09:35:04] 101: 101: **** 101: Invariant Violation 101: molzip: bond info already exists for end atom with label:1 101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 101: Failed Expression: !bond.b 101: ---------- 101: Stacktrace: 101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# 0x00005569D95A8596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 5# 0x00005569D95FA168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 6# 0x00005569D95FAC88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 7# 0x00005569D95FB100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 8# 0x00005569D95CC903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 9# 0x00005569D95CCC6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 10# 0x00005569D959C75E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 11# 0x00007F2AF4633CA8 in /lib/x86_64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 101: 13# 0x00005569D959C7A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: [09:35:04] Incomplete atom labelling, cannot make bond 101: [09:35:04] 101: 101: **** 101: Invariant Violation 101: molzip: bond info already exists for end atom with label:1 101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 101: Failed Expression: !bond.b 101: ---------- 101: Stacktrace: 101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# 0x00005569D95A8596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 5# 0x00005569D95FA168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 6# 0x00005569D95FAC88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 7# 0x00005569D95FB100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 8# 0x00005569D95CC903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 9# 0x00005569D95CCC6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 10# 0x00005569D959C75E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 11# 0x00007F2AF4633CA8 in /lib/x86_64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 101: 13# 0x00005569D959C7A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: [09:35:04] Incomplete atom labelling, cannot make bond 101: [09:35:04] Incomplete atom labelling, cannot make bond 101: [09:35:04] Incomplete atom labelling, cannot make bond 101: [09:35:04] 101: 101: **** 101: Invariant Violation 101: molzip: bond info already exists for end atom with label:1 101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 101: Failed Expression: !bond.b 101: ---------- 101: Stacktrace: 101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# 0x00005569D95A8596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 5# 0x00005569D95FA168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 6# 0x00005569D95FAC88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 7# 0x00005569D95FB100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 8# 0x00005569D95CC903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 9# 0x00005569D95CCC6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 10# 0x00005569D959C75E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 11# 0x00007F2AF4633CA8 in /lib/x86_64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 101: 13# 0x00005569D959C7A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: [09:35:04] Incomplete atom labelling, cannot make bond 101: [09:35:04] 101: 101: **** 101: Invariant Violation 101: molzip: bond info already exists for end atom with label:1 101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 101: Failed Expression: !bond.b 101: ---------- 101: Stacktrace: 101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# 0x00005569D95A8596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 5# 0x00005569D95FA168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 6# 0x00005569D95FAC88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 7# 0x00005569D95FB100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 8# 0x00005569D95CC903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 9# 0x00005569D95CCC6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 10# 0x00005569D959C75E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 11# 0x00007F2AF4633CA8 in /lib/x86_64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 101: 13# 0x00005569D959C7A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: [09:35:04] 101: 101: **** 101: Invariant Violation 101: molzip: zipped Bond already exists, perhaps labels are duplicated 101: Violation occurred on line 744 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 101: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) 101: ---------- 101: Stacktrace: 101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 5# 0x00005569D959D87D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 6# 0x00005569D95FA168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 7# 0x00005569D95FAC88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 8# 0x00005569D95FB100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 9# 0x00005569D95CC903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 10# 0x00005569D95CCC6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 11# 0x00005569D959C75E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 12# 0x00007F2AF4633CA8 in /lib/x86_64-linux-gnu/libc.so.6 101: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 101: 14# 0x00005569D959C7A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: =============================================================================== 101: All tests passed (675 assertions in 10 test cases) 101: 96/236 Test #101: chemTransformsTestCatch ................ Passed 0.09 sec test 102 Start 102: tautomerQueryTestCatch 102: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch 102: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery 102: Test timeout computed to be: 1500 99: .[09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: .[09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: () 99: ******************************************** 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 1 2 1 0 99: M RGP 1 2 1 99: V 1 halogen.bromine.aromatic 99: V 2 [*:1] 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M RGP 1 1 2 99: V 1 [*:2] 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 1 2 1 0 99: M RGP 2 1 1 2 2 99: V 1 [*:1] 99: V 2 [*:2] 99: M END 99: 99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 1 2 1 0 99: M RGP 1 2 1 99: V 1 halogen.bromine.aromatic 99: V 2 [*:1] 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M RGP 1 1 2 99: V 1 [*:2] 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 1 2 1 0 99: M RGP 2 1 1 2 2 99: V 1 [*:1] 99: V 2 [*:2] 99: M END 99: 99: ******************************************** 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M RGP 1 2 1 99: V 1 halogen.bromine.aromatic 99: V 2 * 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M RGP 1 1 2 99: V 1 * 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M RGP 2 1 1 2 2 99: V 1 * 99: V 2 * 99: M END 99: 99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 1 2 1 0 99: M RGP 1 2 1 99: V 1 halogen.bromine.aromatic 99: V 2 [*:1] 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M RGP 1 1 2 99: V 1 [*:2] 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 1 2 1 0 99: M RGP 2 1 1 2 2 99: V 1 [*:1] 99: V 2 [*:2] 99: M END 99: 99: ******************************************** 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M ISO 1 2 1 99: V 1 halogen.bromine.aromatic 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M ISO 1 1 2 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END 99: 99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 1 2 1 0 99: M RGP 1 2 1 99: V 1 halogen.bromine.aromatic 99: V 2 [*:1] 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M RGP 1 1 2 99: V 1 [*:2] 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 1 2 1 0 99: M RGP 2 1 1 2 2 99: V 1 [*:1] 99: V 2 [*:2] 99: M END 99: 99: ******************************************** 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M ISO 1 2 1 99: V 1 halogen.bromine.aromatic 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M ISO 1 1 3 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END 99: [09:35:04] reactant 0 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] product 0 has no mapped atoms. 99: [09:35:04] Could not find RLabel mapping for atom: 0 in template: 1 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: [09:35:04] reactant 1 has no mapped atoms. 99: .. 99: ---------------------------------------------------------------------- 99: Ran 4 tests in 0.014s 99: 99: OK 99: 99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 1 2 1 0 99: M RGP 1 2 1 99: V 1 halogen.bromine.aromatic 99: V 2 [*:1] 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M ISO 1 1 3 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M ISO 1 2 2 99: M RGP 1 1 1 99: V 1 [*:1] 99: M END 99: 99: $RXN Failed 97/236 Test #99: pyChemReactionSanitize ................. Passed 0.35 sec test 103 Start 103: pyTautomerQuery 103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" 103: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap 103: Test timeout computed to be: 1500 102: Randomness seeded to: 880740617 102: =============================================================================== 102: All tests passed (93 assertions in 13 test cases) 102: 98/236 Test #102: tautomerQueryTestCatch ................. Passed 0.18 sec test 104 Start 104: testSubgraphs1 104: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 104: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs 104: Test timeout computed to be: 1500 104: ----------------------- 104: Subgraph retrieval 104: Finished 104: ----------------------- 104: testSubgraphs2a 104: Finished 104: ----------------------- 104: testSubgraphs2 104: Finished 104: ----------------------- 104: Path retrieval 104: Finished 104: ----------------------- 104: Path retrieval2 104: Finished 104: ----------------------- 104: Unique Subgraph retrieval 104: Finished 104: ----------------------- 104: testUniqueSubgraphs2 103: ..... 103: ---------------------------------------------------------------------- 103: Ran 5 tests in 0.017s 103: 103: OK 99/236 Test #103: pyTautomerQuery ........................ Passed 0.24 sec test 105 Start 105: testSubgraphs2 105: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 105: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs 105: Test timeout computed to be: 1500 105: ----------------------- 105: Test1: pathToSubmol 105: Finished 105: ----------------------- 105: Test2: Atom Environments 105: Finished 105: ----------------------- 105: Test 3: Atom Environments (Extension) 105: Finished 105: ----------------------- 105: Testing github Issue103: stereochemistry and pathToSubmol 105: Finished 105: ----------------------- 105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 105: Finished 100/236 Test #105: testSubgraphs2 ......................... Passed 0.01 sec test 106 Start 106: subgraphsCatch 106: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch 106: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs 106: Test timeout computed to be: 1500 106: Randomness seeded to: 4262104933 106: --------- 106: =============================================================================== 106: All tests passed (11 assertions in 1 test case) 106: 101/236 Test #106: subgraphsCatch ......................... Passed 0.04 sec test 107 Start 107: filterCatalogTest 107: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest 107: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog 107: Test timeout computed to be: 1500 104: Finished 104: ----------------------- 104: testRootedSubgraphs 104: Finished 104: ----------------------- 104: testRootedPaths 104: Finished 102/236 Test #104: testSubgraphs1 ......................... Passed 0.22 sec test 108 Start 108: pyFilterCatalog 108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" 108: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap 108: Test timeout computed to be: 1500 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason hzone_phenol_A(479) 107: v = { 107: 0,23}, 107: 1,22}, 107: 2,20}, 107: 3,19}, 107: 4,25}, 107: 5,24}, 107: 6,18}, 107: 7,17}, 107: 8,16}, 107: 9,21}, 107: } 107: match = { 107: 0,23}, 107: 1,22}, 107: 2,20}, 107: 3,19}, 107: 4,25}, 107: 5,24}, 107: 6,18}, 107: 7,17}, 107: 8,16}, 107: 9,21}, 107: } 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason cyano_imine_B(17) 107: v = { 107: 0,11}, 107: 1,12}, 107: 2,13}, 107: 3,14}, 107: 4,15}, 107: 5,10}, 107: 6,9}, 107: 7,8}, 107: 8,7}, 107: 9,6}, 107: 10,5}, 107: 11,17}, 107: 12,16}, 107: } 107: match = { 107: 0,11}, 107: 1,12}, 107: 2,13}, 107: 3,14}, 107: 4,15}, 107: 5,10}, 107: 6,9}, 107: 7,8}, 107: 8,7}, 107: 9,6}, 107: 10,5}, 107: 11,17}, 107: 12,16}, 107: } 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason keto_keto_gamma(5) 107: v = { 107: 0,0}, 107: 1,1}, 107: 2,2}, 107: 3,4}, 107: 4,5}, 107: 5,6}, 107: 6,7}, 107: 7,8}, 107: 8,9}, 107: 9,14}, 107: 10,15}, 107: 11,16}, 107: } 107: match = { 107: 0,0}, 107: 1,1}, 107: 2,2}, 107: 3,4}, 107: 4,5}, 107: 5,6}, 107: 6,7}, 107: 7,8}, 107: 8,9}, 107: 9,14}, 107: 10,15}, 107: 11,16}, 107: } 103/236 Test #107: filterCatalogTest ...................... Passed 0.69 sec test 109 Start 109: testFragCatalog 109: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog 109: Test timeout computed to be: 1500 109: 21 108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. 74: [09:35:06] Finished: testSmiCorrectness() 74: [09:35:06] ----------------------------------------- 74: 74: [09:35:06] 74: ----------------------------------------- 74: [09:35:06] Spurious data before the first property will be ignored 74: [09:35:06] Property will be truncated after the first blank line 74: [09:35:06] Property will be truncated after the first blank line 74: [09:35:06] Property will be truncated after the first blank line 109: [09:35:06] 109: 109: **** 109: Invariant Violation 109: nonsense 109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 109: Failed Expression: token != tokens.end() 109: ---------- 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 2# 0x00007F7CFC248DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 4# 0x000055C51C70A1FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: 5# 0x000055C51C7076A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: 6# 0x00007F7CFB633CA8 in /lib/x86_64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 109: 8# 0x000055C51C7077D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: 109: [09:35:06] 109: 109: **** 109: Invariant Violation 109: nonsense no new line 109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 109: Failed Expression: token != tokens.end() 109: ---------- 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 2# 0x00007F7CFC248DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 4# 0x000055C51C70A1FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: 5# 0x000055C51C7076A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: 6# 0x00007F7CFB633CA8 in /lib/x86_64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 109: 8# 0x000055C51C7077D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: 109: [09:35:06] 109: 109: **** 109: Invariant Violation 109: nonsense with tab 109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 109: Failed Expression: token != tokens.end() 109: ---------- 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 2# 0x00007F7CFC248DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 4# 0x000055C51C70A1FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: 5# 0x000055C51C7076A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: 6# 0x00007F7CFB633CA8 in /lib/x86_64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 109: 8# 0x000055C51C7077D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: 104/236 Test #109: testFragCatalog ........................ Passed 0.72 sec test 110 Start 110: pyFragCatalog 110: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 110: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 110: Test timeout computed to be: 1500 51: Randomness seeded to: 2893107487 51: =============================================================================== 51: All tests passed (14835 assertions in 14 test cases) 51: 105/236 Test #51: canonTestsCatch ........................ Passed 9.38 sec test 111 Start 111: testDescriptors 111: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 111: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 111: [09:35:06] ------------------------------------- 111: [09:35:06] Test Crippen parameter acquisition. 111: [09:35:06] done 111: [09:35:06] ------------------------------------- 111: [09:35:06] Test Crippen calculation. 111: [09:35:06] done 111: [09:35:06] ------------------------------------- 111: [09:35:06] Test Issue262: problems with Crippen calculation from pickles. 111: [09:35:06] done 111: [09:35:06] ------------------------------------- 111: [09:35:06] Test AMW calculation. 111: [09:35:06] done 111: [09:35:06] ------------------------------------- 111: [09:35:06] Test Exact MW calculation. 111: [09:35:06] done 111: [09:35:06] ------------------------------------- 111: [09:35:06] Test Labute ASA descriptors. 111: [09:35:06] done 111: [09:35:06] ------------------------------------- 111: [09:35:06] Test TPSA descriptors. 111: [09:35:06] done 111: [09:35:06] ------------------------------------- 111: [09:35:06] Test Lipinski parameters. 110: ......... 110: ---------------------------------------------------------------------- 110: Ran 9 tests in 0.088s 110: 110: OK 111: [09:35:06] done 106/236 Test #110: pyFragCatalog .......................... Passed 0.49 sec test 112 Start 112: testAUTOCORR2D 112: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 112: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 111: [09:35:06] ------------------------------------- 111: [09:35:06] Test VSA descriptors. 111: [09:35:06] done 111: [09:35:06] ------------------------------------- 111: [09:35:06] Test molecular formula calculation. 111: [09:35:06] done 111: [09:35:06] ------------------------------------- 111: [09:35:06] Test Issue 3415534. 111: [09:35:06] done 111: [09:35:06] ------------------------------------- 111: [09:35:06] Test Issue3433771: Bad definition for Crippen atom type O11. 111: [09:35:06] done 111: [09:35:06] ------------------------------------- 111: [09:35:06] Test multithreading 111: reading molecules 111: processing 111: launch :0 111: launch :1 111: launch :2 111: launch :3 112: [09:35:06] ---------------------------- 112: start test autocorr2D 74: [09:35:06] Finished: testSDCorrectness() 74: [09:35:06] ----------------------------------------- 74: 107/236 Test #74: testMultithreadedMolSupplier ........... Passed 8.13 sec test 113 Start 113: testATF 113: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF 113: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 113: Test timeout computed to be: 1500 108/236 Test #113: testATF ................................ Passed 0.08 sec test 114 Start 114: testBCUT 114: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT 114: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 114: Test timeout computed to be: 1500 114: [09:35:07] ------------------------------------- 114: [09:35:07] Basic BCUT tests. 114: [09:35:07] done 114: [09:35:07] ------------------------------------- 114: [09:35:07] Larger BCUT tests. 108: .............[09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 108: [09:35:07] SMILES Parse Error: syntax error while parsing: --- 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] --- 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [09:35:07] dasfsadf 112: [09:35:07] done 112: [09:35:07] ------------------------------------- 112: [09:35:07] Test Github #3806: NaNs from AUTOCORR2D descriptor 112: [09:35:07] done 109/236 Test #112: testAUTOCORR2D ......................... Passed 0.61 sec test 115 Start 115: testEEM 115: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM 115: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 115: Test timeout computed to be: 1500 108: .[09:35:07] SMILES Parse Error: syntax error while parsing: mydoghasfleas 108: [09:35:07] SMILES Parse Error: check for mistakes around position 1: 108: [09:35:07] mydoghasfleas 108: [09:35:07] ^ 108: [09:35:07] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' 115: =>start test EEM 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 0 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 108: ....... 108: ---------------------------------------------------------------------- 108: Ran 21 tests in 1.895s 108: 108: OK 108: (Five aromatic carbons And (Not any of Five aromatic carbons)) 108: (Five aromatic carbons Or (Not any of Five aromatic carbons)) 108: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) 108: ******************************************** 108: Testing: PAINS_A 2 108: ******************************************** 108: Testing: PAINS_B 4 108: ******************************************** 108: Testing: PAINS_C 8 108: ******************************************** 108: Testing: PAINS 14 108: (Not FilterMatcher) 108: Bar 108: Count 1 108: ******************************************** 108: {'Cl,Br,I'} 108: 1 108: 2 108: running 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 100 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 110/236 Test #108: pyFilterCatalog ........................ Passed 2.79 sec test 116 Start 116: testPBF 116: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF 116: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 116: Test timeout computed to be: 1500 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 116: [09:35:07] ------------------------------------- 116: [09:35:07] Basic PBF tests. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 200 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 300 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 116: [09:35:08] done 116: [09:35:08] ------------------------------------- 116: [09:35:08] PBF edge cases. 116: [09:35:08] done 111/236 Test #116: testPBF ................................ Passed 0.31 sec test 117 Start 117: testRDFcustom 117: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom 117: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 117: Test timeout computed to be: 1500 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 400 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 114: [09:35:08] ------------------------------------- 114: [09:35:08] Test empty molecule BCUT. 112/236 Test #114: testBCUT ............................... Passed 1.21 sec test 118 Start 118: testRDF 118: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF 118: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 118: Test timeout computed to be: 1500 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [09:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: Elapsed time: 0.898815 s 115: Errors:0 115: [09:35:08] test on : 500 molecules done 113/236 Test #115: testEEM ................................ Passed 0.98 sec test 119 Start 119: testMORSE 119: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE 119: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 119: Test timeout computed to be: 1500 117: =>start test rdf custom 117: [09:35:08] test on : 365 molecules done 118: =>start test rdf 118: [09:35:09] test on : 365 molecules done 114/236 Test #118: testRDF ................................ Passed 0.79 sec test 120 Start 120: test3D 120: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D 120: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 120: Test timeout computed to be: 1500 120: [09:35:09] ------------------------------------- 120: [09:35:09] Basic PMI tests. 119: =>start test MORSE 119: =>read file 119: [09:35:09] test on : 365 molecules done 115/236 Test #119: testMORSE .............................. Passed 0.64 sec test 121 Start 121: testWHIM 121: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM 121: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 121: Test timeout computed to be: 1500 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test Issue252: Bad definitions for Crippen atom types. 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test calculation of ChiVs. 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test calculation of ChiNs. 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test calculation of HallKierAlpha. 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test calculation of Kappa1. 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test calculation of Kappa2. 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test calculation of Kappa3. 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test Crippen atom type calculations. 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test ring descriptors 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test other count descriptors. 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test MQN 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test GitHub Issue 56. 111: [09:35:09] WARNING: not removing hydrogen atom without neighbors 111: [09:35:09] WARNING: not removing hydrogen atom without neighbors 111: [09:35:09] WARNING: not removing hydrogen atom without neighbors 111: [09:35:09] WARNING: not removing hydrogen atom without neighbors 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test Github92: Bad Crippen atom type for pyrrole H. 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test Github362: order dependence in Kier-Hall descriptors. 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test calculation of spiro and bridgehead counts. 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test Github694: ExactMolWt ignoring the mass of the electron 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Testing Properties and KitchenSink 111: [09:35:09] ---Caught keyerror (bad property name)--- 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test USR Descriptor 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test Github #1973: support P and S terms for TPSA calculation 111: [09:35:09] done 111: [09:35:09] ------------------------------------- 111: [09:35:09] Test Github #2948: Empty molecule has non-zero LabuteASA 111: [09:35:09] done 116/236 Test #111: testDescriptors ........................ Passed 2.78 sec test 122 Start 122: testGETAWAY 122: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 122: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 122: Test timeout computed to be: 1500 120: [09:35:09] done 120: [09:35:09] ------------------------------------- 120: [09:35:09] More PMI/NPR tests. 120: [09:35:09] done 120: [09:35:09] ------------------------------------- 120: [09:35:09] Basic NPR tests. 117: =>start test morse custom 117: [09:35:09] test on : 365 molecules done 121: =>start test WHIM 121: [09:35:09] test on : 365 molecules done 117/236 Test #121: testWHIM ............................... Passed 0.20 sec test 123 Start 123: testAUTOCORR3D 123: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 123: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 123: Test timeout computed to be: 1500 120: [09:35:09] done 120: [09:35:09] ------------------------------------- 120: [09:35:09] PMI edge cases. 120: [09:35:09] done 120: [09:35:09] ------------------------------------- 120: [09:35:09] NPR edge cases. 120: [09:35:09] done 120: [09:35:09] ------------------------------------- 120: [09:35:09] 3D descriptors. 120: [09:35:09] done 120: [09:35:09] ------------------------------------- 120: [09:35:09] 3D descriptor edge cases. 120: [09:35:09] done 120: [09:35:09] ------------------------------------- 120: [09:35:09] Inertial shape factor. 120: [09:35:09] done 118/236 Test #120: test3D ................................. Passed 0.26 sec test 124 Start 124: testCoulombMat 124: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat 124: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 124: Test timeout computed to be: 1500 124: ===================== Testing CoulombMat ======================= 124: CM test 1 mat Done 119/236 Test #124: testCoulombMat ......................... Passed 0.04 sec test 125 Start 125: descriptorsTestCatch 125: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 125: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 125: Test timeout computed to be: 1500 125: Randomness seeded to: 2199828838 125: Warning: Atom Count for residue GLU5A does not match expected count 125: Warning: Atom Count for residue ASN39A does not match expected count 125: Warning: Atom Count for residue GLU53A does not match expected count 125: Warning: Atom Count for residue ARG64A does not match expected count 125: Warning: Atom Count for residue LYS80A does not match expected count 125: Warning: Atom Count for residue GLU150A does not match expected count 125: Warning: Atom Count for residue ASN157A does not match expected count 117: =>start test AUTOCORR3D custom 117: [09:35:09] test on : 365 molecules done 125: Warning: Atom Count for residue GLU5A does not match expected count 123: =>start test autocorr3D 123: [09:35:09] test on : 365 molecules done 120/236 Test #123: testAUTOCORR3D ......................... Passed 0.21 sec test 126 Start 126: pyMolDescriptors 126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 126: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap 126: Test timeout computed to be: 1500 117: =>start test 2 WHIM custom 117: [09:35:09] test on : 365 molecules done 125: Warning: Atom Count for residue ASN39A does not match expected count 125: Warning: Atom Count for residue GLU53A does not match expected count 125: Warning: Atom Count for residue ARG64A does not match expected count 117: =>start test 1 WHIM custom 117: [09:35:09] test on : 365 molecules done 125: Warning: Atom Count for residue LYS80A does not match expected count 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:09] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:09] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:09] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:09] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:09] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:09] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:09] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:09] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:09] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:09] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:09] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ..[09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: .[09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:09] DEPRECATION WARNING: please use AtomPairGenerator 126: ..[09:35:09] 126: 126: **** 126: Pre-condition Violation 126: Number of atom props not equal to number of atoms 126: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp 126: Failed Expression: atom_props.size() == num_atoms 126: ---------- 126: Stacktrace: 126: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitDescriptors.so.1 126: 3# 0x00007F728563443A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so 126: 4# 0x00007F7285644726 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so 126: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 126: 6# 0x00007F728963D62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 126: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 126: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 126: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 126: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 126: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 126: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 126: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 126: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 126: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 126: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 126: 17# 0x00007F72871B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 126: 18# 0x00007F72871B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 126: 19# 0x00007F72871B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 126: 20# 0x00007F72871B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 126: 21# 0x00007F72871B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 126: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 126: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 126: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 126: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 126: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 126: 27# 0x00007F728963A3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 126: 28# _PyObject_MakeTpCall in /usr/bin/python3 126: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 30# 0x00000000005C30D9 in /usr/bin/python3 126: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 32# 0x000000000064B89F in /usr/bin/python3 126: 33# 0x000000000069ECA0 in /usr/bin/python3 126: 34# _PyObject_MakeTpCall in /usr/bin/python3 126: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 36# 0x00000000005C30D9 in /usr/bin/python3 126: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 38# 0x000000000064B89F in /usr/bin/python3 126: 39# 0x000000000069ECA0 in /usr/bin/python3 126: 40# _PyObject_MakeTpCall in /usr/bin/python3 126: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 42# 0x00000000005C30D9 in /usr/bin/python3 126: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 44# 0x000000000064B89F in /usr/bin/python3 126: 45# 0x000000000069ECA0 in /usr/bin/python3 126: 46# _PyObject_MakeTpCall in /usr/bin/python3 126: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 48# 0x0000000000599C8E in /usr/bin/python3 126: 49# _PyObject_MakeTpCall in /usr/bin/python3 126: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 51# PyEval_EvalCode in /usr/bin/python3 126: 52# 0x000000000066DA21 in /usr/bin/python3 126: 53# 0x0000000000669A8C in /usr/bin/python3 126: 54# 0x0000000000682973 in /usr/bin/python3 126: 55# 0x0000000000682273 in /usr/bin/python3 126: 56# 0x00000000006820AE in /usr/bin/python3 126: 57# Py_RunMain in /usr/bin/python3 126: 58# Py_BytesMain in /usr/bin/python3 126: 59# 0x00007F7289F69CA8 in /lib/x86_64-linux-gnu/libc.so.6 126: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 126: 61# _start in /usr/bin/python3 126: ---------- 126: **** 126: 126: ...Warning: Atom Count for residue GLU5A does not match expected count 126: Warning: Atom Count for residue ASN39A does not match expected count 126: Warning: Atom Count for residue GLU53A does not match expected count 126: Warning: Atom Count for residue ARG64A does not match expected count 126: Warning: Atom Count for residue LYS80A does not match expected count 126: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN157A does not match expected count 126: Warning: Atom Count for residue GLU5A does not match expected count 122: =>start test GETAWAY 122: [09:35:10] test on : 365 molecules done 121/236 Test #122: testGETAWAY ............................ Passed 1.21 sec test 127 Start 127: pyMolDescriptors3D 127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/test3D.py" 127: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap 127: Test timeout computed to be: 1500 125: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN39A does not match expected count 125: Warning: Atom Count for residue ASN157A does not match expected count 126: Warning: Atom Count for residue GLU53A does not match expected count 126: Warning: Atom Count for residue ARG64A does not match expected count 127: ........ 127: ---------------------------------------------------------------------- 127: Ran 8 tests in 0.203s 127: 127: OK 122/236 Test #127: pyMolDescriptors3D ..................... Passed 0.61 sec test 128 Start 128: testFingerprints 128: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints 128: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 128: Test timeout computed to be: 1500 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: Atoms: 128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: 1 conj?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: 1 conj?: 1 128: 9 8->10 order: a conj?: 1 aromatic?: 1 128: 10 10->1 order: a conj?: 1 aromatic?: 1 128: 11 7->3 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: SMI: Oc1cc2[nH]cnc2c(O)n1 128: Atoms: 128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: 1 conj?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: 1 conj?: 1 128: 9 8->10 order: a conj?: 1 aromatic?: 1 128: 10 10->1 order: a conj?: 1 aromatic?: 1 128: 11 7->3 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: c1(O)cc2[nH]cnc2c(O)n1 128: Atoms: 128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: 1 conj?: 1 128: 1 0->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: 1 conj?: 1 128: 9 8->10 order: a conj?: 1 aromatic?: 1 128: 10 10->0 order: a conj?: 1 aromatic?: 1 128: 11 7->3 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: c1c(O)nc(O)c2c1[nH]cn2 128: Atoms: 128: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 3 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: 1 conj?: 1 128: 2 1->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: 1 conj?: 1 128: 5 4->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 7->0 order: a conj?: 1 aromatic?: 1 128: 11 10->6 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: c12cc(O)nc(O)c1nc[nH]2 128: Atoms: 128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 3 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: 1 conj?: 1 128: 3 2->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: 1 conj?: 1 128: 6 5->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 7->0 order: a conj?: 1 aromatic?: 1 128: 11 10->0 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: [nH]1c2cc(O)nc(O)c2nc1 128: Atoms: 128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 10 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: 1 conj?: 1 128: 4 3->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: 1 conj?: 1 128: 7 6->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 10->0 order: a conj?: 1 aromatic?: 1 128: 11 8->1 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: c1[nH]c2cc(O)nc(O)c2n1 128: Atoms: 128: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: 1 conj?: 1 128: 5 4->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: 1 conj?: 1 128: 8 7->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 10->0 order: a conj?: 1 aromatic?: 1 128: 11 9->2 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: n1c[nH]c2cc(O)nc(O)c21 128: Atoms: 128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 10 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: 1 conj?: 1 128: 6 5->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: 1 conj?: 1 128: 9 8->10 order: a conj?: 1 aromatic?: 1 128: 10 10->0 order: a conj?: 1 aromatic?: 1 128: 11 10->3 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: c12c(cc(O)nc1O)[nH]cn2 128: Atoms: 128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: 1 conj?: 1 128: 4 3->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: 1 conj?: 1 128: 7 1->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 6->0 order: a conj?: 1 aromatic?: 1 128: 11 10->0 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: c1(O)c2c(cc(O)n1)[nH]cn2 128: Atoms: 128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: 1 conj?: 1 128: 1 0->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: 1 conj?: 1 128: 6 5->7 order: a conj?: 1 aromatic?: 1 128: 7 3->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 7->0 order: a conj?: 1 aromatic?: 1 128: 11 10->2 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: Oc1c2c(cc(O)n1)[nH]cn2 128: Atoms: 128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: 1 conj?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: 1 conj?: 1 128: 6 5->7 order: a conj?: 1 aromatic?: 1 128: 7 3->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 7->1 order: a conj?: 1 aromatic?: 1 128: 11 10->2 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: n1c(O)cc2[nH]cnc2c1O 128: Atoms: 128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 6 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 10 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: 1 conj?: 1 128: 2 1->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: 1 conj?: 1 128: 10 9->0 order: a conj?: 1 aromatic?: 1 128: 11 8->4 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Morgan Fingerprints. 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Morgan Fingerprints using fromAtoms argument. 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Morgan Fingerprints as bit vects. 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Morgan Fingerprints with feature invariants. 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test additional Morgan fingerprints options. 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Atom Codes. 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Atom Pairs. 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Atom Pairs part 2. 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Topological Torsions. 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Bulk Topological Torsions. 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: Warning: Atom Count for residue LYS80A does not match expected count 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Hashed Atom Pairs. 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Hashed torsions. 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Rooted Atom Pairs. 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test ignoring atoms in Atom Pairs. 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Rooted Topological Torsions. 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test ignoring atoms in Topological Torsions. 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test atom info from morgan fingerprints. 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test atom info from morgan fingerprints including Info Redundant Environments. 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] ------------------------------------- 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] ------------------------------------- 128: [09:35:11] ------------------------------------- 128: [09:35:11] ------------------------------------- 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Atom Pairs including info about chirality. 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test Topological Torsions including info about chirality. 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test GitHub Issue 25: fingerprint backwards compatibility. 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test GitHub Issue 151: PatternFingerprint problems 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test 3D atom pairs. 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule 128: [09:35:11] done 128: [09:35:11] ------------------------------------- 128: [09:35:11] Test multithreading with the pattern FP 128: reading molecules 128: pass 1 128: launch :0 128: launch :1 128: launch :2 128: launch :3 95: 0,0 0 95: 0,1 0 95: 1,0 0 95: 1,1 0 95: 2,0 0 95: 2,1 0 123/236 Test #95: testEnumeration ........................ Passed 8.77 sec test 129 Start 129: testMHFPFingerprint 129: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 129: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 129: Test timeout computed to be: 1500 129: [09:35:11] ------------------------------------- 129: [09:35:11] Test MHFP fingerprint encoder initialization 129: [09:35:11] done 129: [09:35:11] ------------------------------------- 129: [09:35:11] Test MHFP shingling creation 129: [09:35:11] done 129: [09:35:11] ------------------------------------- 129: [09:35:11] Test MHFP hashing of string and uint arrays 129: [09:35:11] done 129: [09:35:11] ------------------------------------- 129: [09:35:11] Test SECFP fingerprint functionality 129: [09:35:11] done 124/236 Test #129: testMHFPFingerprint .................... Passed 0.10 sec test 130 Start 130: testFingerprintGenerators 130: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 130: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 130: Test timeout computed to be: 1500 128: pass 2 128: launch :0 128: launch :1 128: launch :2 128: launch :3 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test atom-pair fp generator 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test atom-pair fp generator with different arguments 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation 130: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 130: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 130: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 130: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 130: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 130: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 130: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 130: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 130: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 130: [09:35:11] DEPRECATION WARNING: please use AtomPairGenerator 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test atom-pair additional output 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test Folded Atom Pairs. 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test Rooted Atom Pairs. 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test ignoring atoms in Atom Pairs. 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test Atom Pairs including info about chirality. 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test Morgan Fingerprints. 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test morgan fp generator 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test Morgan Fingerprints using fromAtoms argument. 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test Morgan Fingerprints as bit vects. 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test Morgan Fingerprints with feature invariants. 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test additional Morgan fingerprints options. 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Single atoms setting radius 1 bits in Morgan fingerprints 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test different invariant generator combinations 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test invariant overriding 130: [09:35:11] done 130: [09:35:11] ------------------------------------- 130: [09:35:11] Test RDKit fp generator 117: =>start test GETAWAY custom 117: [09:35:11] test on : 365 molecules done 125/236 Test #117: testRDFcustom .......................... Passed 3.68 sec test 131 Start 131: fpTestCatch 131: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 131: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 131: Test timeout computed to be: 1500 131: Randomness seeded to: 1954320937 131: =============================================================================== 131: All tests passed (188 assertions in 16 test cases) 131: 126/236 Test #131: fpTestCatch ............................ Passed 0.02 sec test 132 Start 132: fpGenTestCatch 132: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 132: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 132: Test timeout computed to be: 1500 132: Randomness seeded to: 3261346054 132: =============================================================================== 132: All tests passed (2737 assertions in 7 test cases) 132: 127/236 Test #132: fpGenTestCatch ......................... Passed 0.19 sec test 133 Start 133: pyTestGenerator 133: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 133: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 133: Test timeout computed to be: 1500 130: [09:35:12] done 130: [09:35:12] ------------------------------------- 130: [09:35:12] Test unfolded version of RDKFP 130: [09:35:12] ------------------------------------- 130: [09:35:12] Test topological torsion fp generator 130: [09:35:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [09:35:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [09:35:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [09:35:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [09:35:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [09:35:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [09:35:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [09:35:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [09:35:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [09:35:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [09:35:12] done 130: [09:35:12] ------------------------------------- 130: [09:35:12] Test Topological Torsions. 130: [09:35:12] done 130: [09:35:12] ------------------------------------- 130: [09:35:12] Test Folded torsions. 130: [09:35:12] done 130: [09:35:12] ------------------------------------- 130: [09:35:12] Test Bulk Topological Torsions. 130: [09:35:12] done 130: [09:35:12] ------------------------------------- 130: [09:35:12] Test Rooted Topological Torsions. 130: [09:35:12] done 130: [09:35:12] ------------------------------------- 130: [09:35:12] Test ignoring atoms in Topological Torsions. 130: [09:35:12] done 130: [09:35:12] ------------------------------------- 130: [09:35:12] ------------------------------------- 130: [09:35:12] Test Topological Torsions including info about chirality. 130: [09:35:12] done 130: [09:35:12] ------------------------------------- 130: [09:35:12] Test GitHub Issue 25: fingerprint backwards compatibility. 130: [09:35:12] done 130: [09:35:12] ------------------------------------- 130: [09:35:12] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. 130: [09:35:12] done 130: [09:35:12] ------------------------------------- 130: [09:35:12] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 130: [09:35:12] done 130: [09:35:12] ------------------------------------- 130: [09:35:12] Test convenience and bulk fp calculation functions 126: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN157A does not match expected count 130: [09:35:12] done 130: [09:35:12] ------------------------------------- 130: [09:35:12] Test GitHub Issue #6958 130: [09:35:12] DEPRECATION WARNING: please use AtomPairGenerator 128/236 Test #130: testFingerprintGenerators .............. Passed 0.97 sec test 134 Start 134: pyTestMHFP 134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 134: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 134: Test timeout computed to be: 1500 133: .............. 133: ---------------------------------------------------------------------- 133: Ran 14 tests in 0.192s 133: 133: OK 129/236 Test #133: pyTestGenerator ........................ Passed 0.69 sec test 135 Start 135: testPartialCharges 135: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 135: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges 135: Test timeout computed to be: 1500 130/236 Test #135: testPartialCharges ..................... Passed 0.02 sec test 136 Start 136: pyPartialCharges 136: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 136: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 136: Test timeout computed to be: 1500 134: .. 134: ---------------------------------------------------------------------- 134: Ran 2 tests in 0.015s 134: 134: OK 131/236 Test #134: pyTestMHFP ............................. Passed 0.41 sec test 137 Start 137: testMolTransforms 137: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 137: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms 137: Test timeout computed to be: 1500 137: *********************************************************** 137: Testing MolTransforms 137: --------------------------------- 137: test1Canonicalization 137: 137: --------------------------------- 137: testGetSetBondLength 137: 137: --------------------------------- 137: testGetSetAngle 137: 137: --------------------------------- 137: testGetSetDihedral 137: 137: --------------------------------- 137: testGetSetDihedralThroughTripleBond 137: 137: --------------------------------- 137: testGithub1262: PMI descriptors incorrect 137: 137: --------------------------------- 137: testGithub1908: CanonicalizeMol() distorting bond lengths 137: 137: --------------------------------- 137: testGithub4302: native computeCanonicalTransform() generates non-canonical coords 137: 137: --------------------------------- 137: testWeightedCentroid 137: 137: *********************************************************** 132/236 Test #137: testMolTransforms ...................... Passed 0.02 sec test 138 Start 138: molTransformsTestCatch 138: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch 138: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms 138: Test timeout computed to be: 1500 138: Randomness seeded to: 1180220416 138: =============================================================================== 138: All tests passed (4 assertions in 1 test case) 138: 133/236 Test #138: molTransformsTestCatch ................. Passed 0.08 sec test 139 Start 139: pyMolTransforms 139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 139: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap 139: Test timeout computed to be: 1500 136: ....... 136: ---------------------------------------------------------------------- 136: Ran 7 tests in 0.103s 136: 136: OK 134/236 Test #136: pyPartialCharges ....................... Passed 0.60 sec test 140 Start 140: forceFieldHelpersCatch 140: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch 140: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers 140: Test timeout computed to be: 1500 140: Randomness seeded to: 4176936967 140: =============================================================================== 140: All tests passed (17 assertions in 2 test cases) 140: 135/236 Test #140: forceFieldHelpersCatch ................. Passed 0.09 sec test 141 Start 141: testMMFFForceFieldHelpers 141: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 141: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 141: Test timeout computed to be: 1500 141: [09:35:13] ------------------------------------- 141: [09:35:13] Test MMFF atom types. 139: ........ 139: ---------------------------------------------------------------------- 139: Ran 8 tests in 0.014s 139: 139: OK 141: [09:35:13] done 141: [09:35:13] ------------------------------------- 141: [09:35:13] Testing MMFF builder tools. 141: [09:35:13] done 141: [09:35:13] ------------------------------------- 141: [09:35:13] Testing MMFF builder+minimization. 136/236 Test #139: pyMolTransforms ........................ Passed 0.40 sec test 142 Start 142: testMMFFForceFieldHelpersMultiThread 142: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 142: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 142: Test timeout computed to be: 1500 142: [09:35:13] ------------------------------------- 142: [09:35:13] Test MMFF multithreading 141: [09:35:13] done 141: [09:35:13] ------------------------------------- 141: [09:35:13] Testing Issue239. 141: [09:35:13] done 141: [09:35:13] ------------------------------------- 141: [09:35:13] Testing calcEnergy with passed coords. 142: processing 142: launch :0 142: launch :1 142: launch :2 142: launch :3 142: launch :4 142: launch :5 142: launch :6 142: launch :7 142: launch :8 142: launch :9 142: launch :10 142: launch :11 142: launch :12 142: launch :13 142: launch :14 142: launch :15 142: launch :16 142: launch :17 142: launch :18 142: launch :19 142: launch :20 142: launch :21 142: launch :22 142: launch :23 141: [09:35:13] done 141: [09:35:13] ------------------------------------- 141: [09:35:13] Testing calcGrad. 141: [09:35:13] done 141: [09:35:13] ------------------------------------- 141: [09:35:13] Testing Issue242. 141: [09:35:13] done 141: [09:35:13] ------------------------------------- 141: [09:35:13] Testing github 308: crash during MMFF parameterization . 141: [09:35:13] ------------------------------------- 141: [09:35:13] Testing SFIssue1653802. 141: [09:35:13] done 141: [09:35:13] ------------------------------------- 141: [09:35:13] Testing SFIssue2378119. 141: [09:35:13] done 141: [09:35:13] ------------------------------------- 141: [09:35:13] Test MMFF force-field parameter getters. 141: [09:35:13] ------------------------------------- 141: [09:35:13] Test MMFF multithreading 141: generating reference data 142: done 142: [09:35:13] done 137/236 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.30 sec test 143 Start 143: testUFFForceFieldHelpers 143: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 143: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF 143: Test timeout computed to be: 1500 143: [09:35:13] ------------------------------------- 143: [09:35:13] Test UFF atom labels. 143: [09:35:13] done 143: [09:35:13] ------------------------------------- 143: [09:35:13] Test UFF atom typer. 143: [09:35:13] done 143: [09:35:13] ------------------------------------- 143: [09:35:13] Testing UFF builder tools. 143: [09:35:13] done 143: [09:35:13] ------------------------------------- 143: [09:35:13] Testing UFF builder+minimization. 143: [09:35:13] done 143: [09:35:13] ------------------------------------- 143: [09:35:13] Testing UFF special cases. 143: [09:35:13] UFFTYPER: Unrecognized charge state for atom: 0 143: [09:35:13] done 143: [09:35:13] ------------------------------------- 143: [09:35:13] Testing Issue239. 143: [09:35:13] done 143: [09:35:13] ------------------------------------- 143: [09:35:13] Testing calcEnergy with passed coords. 143: [09:35:13] done 143: [09:35:13] ------------------------------------- 143: [09:35:13] Testing calcGrad. 143: [09:35:13] done 143: [09:35:13] ------------------------------------- 143: [09:35:13] Testing SFIssue1653802. 143: [09:35:13] done 143: [09:35:13] ------------------------------------- 143: [09:35:13] Testing SFIssue2378119. 143: [09:35:13] done 143: [09:35:13] ------------------------------------- 143: [09:35:13] Test UFF force-field parameter getters. 143: [09:35:13] ------------------------------------- 143: [09:35:13] Testing handling missing parameters. 143: [09:35:13] UFFTYPER: Unrecognized hybridization for atom: 0 143: [09:35:13] UFFTYPER: Unrecognized atom type: Cu+1 (0) 143: [09:35:13] UFFTYPER: Unrecognized hybridization for atom: 0 143: [09:35:13] UFFTYPER: Unrecognized atom type: Cu+1 (0) 143: [09:35:13] done 143: [09:35:13] ------------------------------------- 143: [09:35:13] Testing SFIssue3009337. 143: [09:35:13] done 143: [09:35:13] ------------------------------------- 143: [09:35:13] Test UFF multithreading 143: generating reference data 141: processing 141: launch :0 141: launch :1 141: [09:35:14] Rep: 0 Mol:0 141: launch :2 141: [09:35:14] Rep: 0 Mol:1 141: launch :3 141: [09:35:14] Rep: 0 Mol:2 141: [09:35:14] Rep: 0 Mol:3 141: [09:35:14] Rep: 0 Mol:5 141: [09:35:14] Rep: 0 Mol:9 141: [09:35:14] Rep: 0 Mol:4 141: [09:35:14] Rep: 0 Mol:13 141: [09:35:14] Rep: 0 Mol:17 141: [09:35:14] Rep: 0 Mol:6 141: [09:35:14] Rep: 0 Mol:8 141: [09:35:14] Rep: 0 Mol:10 141: [09:35:14] Rep: 0 Mol:12 141: [09:35:14] Rep: 0 Mol:7 141: [09:35:14] Rep: 0 Mol:16 141: [09:35:14] Rep: 0 Mol:11 141: [09:35:14] Rep: 0 Mol:15 141: [09:35:14] Rep: 0 Mol:19 141: [09:35:14] Rep: 0 Mol:21 141: [09:35:14] Rep: 0 Mol:23 141: [09:35:14] Rep: 0 Mol:27 141: [09:35:14] Rep: 0 Mol:20 141: [09:35:14] Rep: 0 Mol:25 141: [09:35:14] Rep: 0 Mol:31 141: [09:35:14] Rep: 0 Mol:24 141: [09:35:14] Rep: 0 Mol:29 141: [09:35:14] Rep: 0 Mol:28 141: [09:35:14] Rep: 0 Mol:14 141: [09:35:14] Rep: 0 Mol:18 141: [09:35:14] Rep: 0 Mol:22 141: [09:35:14] Rep: 0 Mol:26 141: [09:35:14] Rep: 0 Mol:30 143: processing 143: launch :0 143: launch :1 143: [09:35:14] Rep: 0 Mol:0 launch :2 143: 143: [09:35:14] Rep: 0 Mol:1 143: launch :3 143: [09:35:14] Rep: 0 Mol:2 143: [09:35:14] Rep: 0 Mol:3 143: [09:35:14] Rep: 0 Mol:5 143: [09:35:14] Rep: 0 Mol:9 143: [09:35:14] Rep: 0 Mol:4 143: [09:35:14] Rep: 0 Mol:13 143: [09:35:14] Rep: 0 Mol:6 143: [09:35:14] Rep: 0 Mol:10 143: [09:35:14] Rep: 0 Mol:17 143: [09:35:14] Rep: 0 Mol:7 143: [09:35:14] Rep: 0 Mol:8 143: [09:35:14] Rep: 0 Mol:11 143: [09:35:14] Rep: 0 Mol:12 143: [09:35:14] Rep: 0 Mol:15 143: [09:35:14] Rep: 0 Mol:16 143: [09:35:14] Rep: 0 Mol:19 141: [09:35:14] Rep: 20 Mol:0 141: [09:35:14] Rep: 20 Mol:4 141: [09:35:14] Rep: 20 Mol:3 141: [09:35:14] Rep: 20 Mol:8 143: [09:35:14] Rep: 0 Mol:23 143: [09:35:14] Rep: 0 Mol:27 143: [09:35:14] Rep: 0 Mol:20 143: [09:35:14] Rep: 0 Mol:21 143: [09:35:14] Rep: 0 Mol:14 143: [09:35:14] Rep: 0 Mol:31 141: [09:35:14] Rep: 20 Mol:12 141: [09:35:14] Rep: 20 Mol:16 141: [09:35:14] Rep: 20 Mol:7 141: [09:35:14] Rep: 20 Mol:20 141: [09:35:14] Rep: 20 Mol:11 141: [09:35:14] Rep: 20 Mol:24 141: [09:35:14] Rep: 20 Mol:15 141: [09:35:14] Rep: 20 Mol:19 141: [09:35:14] Rep: 20 Mol:28 141: [09:35:14] Rep: 20 Mol:23 141: [09:35:14] Rep: 20 Mol:27 141: [09:35:14] Rep: 20 Mol:31 143: [09:35:14] Rep: 0 Mol:24 143: [09:35:14] Rep: 0 Mol:25 143: [09:35:14] Rep: 0 Mol:28 143: [09:35:14] Rep: 0 Mol:18 143: [09:35:14] Rep: 0 Mol:29 143: [09:35:14] Rep: 0 Mol:22 143: [09:35:14] Rep: 0 Mol:26 141: [09:35:14] Rep: 20 Mol:1 141: [09:35:14] Rep: 20 Mol:5 141: [09:35:14] Rep: 20 Mol:9 141: [09:35:14] Rep: 20 Mol:13 141: [09:35:14] Rep: 20 Mol:17 141: [09:35:14] Rep: 20 Mol:21 141: [09:35:14] Rep: 20 Mol:25 141: [09:35:14] Rep: 20 Mol:29 143: [09:35:14] Rep: 0 Mol:30 141: [09:35:14] Rep: 20 Mol:2 141: [09:35:14] Rep: 20 Mol:6 141: [09:35:14] Rep: 20 Mol:10 141: [09:35:14] Rep: 40 Mol:3 141: [09:35:14] Rep: 20 Mol:14 141: [09:35:14] Rep: 20 Mol:18 141: [09:35:14] Rep: 40 Mol:7 141: [09:35:14] Rep: 20 Mol:22 141: [09:35:14] Rep: 40 Mol:11 141: [09:35:14] Rep: 20 Mol:26 141: [09:35:14] Rep: 40 Mol:15 141: [09:35:14] Rep: 40 Mol:19 141: [09:35:14] Rep: 40 Mol:23 141: [09:35:14] Rep: 20 Mol:30 141: [09:35:14] Rep: 40 Mol:27 141: [09:35:14] Rep: 40 Mol:31 141: [09:35:14] Rep: 40 Mol:0 141: [09:35:14] Rep: 40 Mol:4 141: [09:35:14] Rep: 40 Mol:8 141: [09:35:14] Rep: 40 Mol:12 141: [09:35:14] Rep: 40 Mol:16 141: [09:35:14] Rep: 40 Mol:20 141: [09:35:14] Rep: 40 Mol:24 141: [09:35:14] Rep: 40 Mol:28 141: [09:35:14] Rep: 40 Mol:1 141: [09:35:14] Rep: 40 Mol:5 141: [09:35:14] Rep: 40 Mol:9 141: [09:35:14] Rep: 40 Mol:13 141: [09:35:14] Rep: 40 Mol:17 141: [09:35:14] Rep: 40 Mol:21 141: [09:35:14] Rep: 40 Mol:25 141: [09:35:14] Rep: 40 Mol:29 141: [09:35:14] Rep: 60 Mol:3 141: [09:35:14] Rep: 60 Mol:7 141: [09:35:14] Rep: 60 Mol:11 141: [09:35:14] Rep: 60 Mol:15 141: [09:35:14] Rep: 60 Mol:19 141: [09:35:14] Rep: 60 Mol:23 141: [09:35:14] Rep: 60 Mol:27 141: [09:35:14] Rep: 60 Mol:31 141: [09:35:14] Rep: 40 Mol:2 141: [09:35:14] Rep: 40 Mol:6 141: [09:35:14] Rep: 40 Mol:10 141: [09:35:14] Rep: 40 Mol:14 141: [09:35:14] Rep: 40 Mol:18 141: [09:35:14] Rep: 60 Mol:0 141: [09:35:14] Rep: 40 Mol:22 141: [09:35:14] Rep: 60 Mol:4 141: [09:35:14] Rep: 40 Mol:26 141: [09:35:14] Rep: 60 Mol:8 141: [09:35:14] Rep: 40 Mol:30 141: [09:35:14] Rep: 60 Mol:12 141: [09:35:14] Rep: 60 Mol:16 141: [09:35:14] Rep: 60 Mol:20 141: [09:35:14] Rep: 60 Mol:24 141: [09:35:14] Rep: 60 Mol:28 143: [09:35:14] Rep: 100 Mol:3 143: [09:35:14] Rep: 100 Mol:7 143: [09:35:14] Rep: 100 Mol:11 141: [09:35:14] Rep: 60 Mol:1 143: [09:35:14] Rep: 100 Mol:15 141: [09:35:14] Rep: 60 Mol:5 143: [09:35:14] Rep: 100 Mol:19 141: [09:35:14] Rep: 60 Mol:9 143: [09:35:14] Rep: 100 Mol:23 143: [09:35:14] Rep: 100 Mol:27 141: [09:35:14] Rep: 60 Mol:13 143: [09:35:14] Rep: 100 Mol:31 141: [09:35:14] Rep: 60 Mol:17 141: [09:35:14] Rep: 60 Mol:21 141: [09:35:14] Rep: 60 Mol:25 141: [09:35:14] Rep: 60 Mol:29 141: [09:35:14] Rep: 80 Mol:3 141: [09:35:14] Rep: 80 Mol:7 141: [09:35:14] Rep: 80 Mol:11 141: [09:35:14] Rep: 80 Mol:15 141: [09:35:14] Rep: 80 Mol:19 141: [09:35:14] Rep: 80 Mol:23 141: [09:35:14] Rep: 80 Mol:27 141: [09:35:14] Rep: 80 Mol:31 143: [09:35:14] Rep: 100 Mol:0 143: [09:35:14] Rep: 100 Mol:4 143: [09:35:14] Rep: 100 Mol:8 143: [09:35:14] Rep: 100 Mol:12 143: [09:35:14] Rep: 100 Mol:16 143: [09:35:14] Rep: 100 Mol:20 143: [09:35:14] Rep: 100 Mol:24 143: [09:35:14] Rep: 100 Mol:28 141: [09:35:14] Rep: 80 Mol:0 141: [09:35:14] Rep: 80 Mol:4 141: [09:35:14] Rep: 80 Mol:8 128: [09:35:14] done 128: [09:35:14] ------------------------------------- 128: [09:35:14] Test GitHub Issue 258: Bad pattern fingerprint for query molecule 141: [09:35:14] Rep: 80 Mol:12 141: [09:35:14] Rep: 80 Mol:16 141: [09:35:14] Rep: 80 Mol:20 141: [09:35:14] Rep: 80 Mol:24 141: [09:35:14] Rep: 80 Mol:28 128: [09:35:14] done 128: [09:35:14] ------------------------------------- 128: [09:35:14] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] done 128: [09:35:14] ------------------------------------- 128: [09:35:14] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints 128: [09:35:14] done 128: [09:35:14] ------------------------------------- 128: [09:35:14] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] done 128: [09:35:14] ------------------------------------- 128: [09:35:14] Test unfolded version of RDKFP 128: [09:35:14] ------------------------------------- 128: [09:35:14] Test bitinfo of RDKFP 128: 562: [ 2 ], 128: 709: [ 0 1 ], 128: 1118: [ 0 1 2 ], 128: 1183: [ 1 2 ], 128: 1233: [ 0 1 2 ], 128: 1308: [ 0 ], [ 1 ], 128: 1339: [ 2 ], 128: 1728: [ 1 2 ], 128: 1772: [ 0 ], [ 1 ], 128: 1813: [ 0 1 ], 128: ------------ 128: [09:35:14] ------------------------------------- 128: [09:35:14] Single atoms setting radius 1 bits in Morgan fingerprints 128: [09:35:14] done 128: [09:35:14] ------------------------------------- 128: [09:35:14] Github #879: Pattern fingerprint should set bits for single-atom fragments. 128: [09:35:14] done 128: [09:35:14] ------------------------------------- 128: [09:35:14] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms 128: [09:35:14] done 128: [09:35:14] ------------------------------------- 128: [09:35:14] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False 128: [09:35:14] done 128: [09:35:14] ------------------------------------- 128: [09:35:14] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:35:14] done 128: [09:35:14] ------------------------------------- 128: [09:35:14] Github #2115: BitInfo not complete for RDKFingerprint 128: [09:35:14] done 128: [09:35:14] ------------------------------------- 128: [09:35:14] Github #3723: Fingerprint crash for mols with Zero order bonds 128: [09:35:14] done 141: [09:35:14] Rep: 60 Mol:2 141: [09:35:14] Rep: 60 Mol:6 141: [09:35:14] Rep: 60 Mol:10 141: [09:35:14] Rep: 60 Mol:14 141: [09:35:14] Rep: 60 Mol:18 141: [09:35:14] Rep: 60 Mol:22 138/236 Test #128: testFingerprints ....................... Passed 3.61 sec 141: [09:35:14] Rep: 60 Mol:26 test 144 Start 144: testCrystalForceField 144: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField 144: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 144: Test timeout computed to be: 1500 141: [09:35:14] Rep: 60 Mol:30 144: ------------------------------------- 144: Test CrystalFF torsional term. 143: [09:35:14] Rep: 100 Mol:1 143: [09:35:14] Rep: 100 Mol:5 143: [09:35:14] Rep: 100 Mol:9 143: [09:35:14] Rep: 100 Mol:13 143: [09:35:14] Rep: 100 Mol:17 143: [09:35:14] Rep: 100 Mol:21 143: [09:35:14] Rep: 100 Mol:25 143: [09:35:14] Rep: 100 Mol:29 141: [09:35:14] Rep: 80 Mol:1 141: [09:35:14] Rep: 80 Mol:5 141: [09:35:14] Rep: 80 Mol:9 141: [09:35:14] Rep: 80 Mol:13 141: [09:35:14] Rep: 80 Mol:17 141: [09:35:14] Rep: 80 Mol:21 141: [09:35:14] Rep: 80 Mol:25 141: [09:35:14] Rep: 80 Mol:29 143: [09:35:14] Rep: 100 Mol:2 139/236 Test #144: testCrystalForceField .................. Passed 0.11 sec 143: [09:35:14] Rep: 100 Mol:6 143: [09:35:14] Rep: 100 Mol:10 test 145 Start 145: pyForceFieldHelpers 145: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 145: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 145: Test timeout computed to be: 1500 143: [09:35:14] Rep: 100 Mol:14 143: [09:35:14] Rep: 100 Mol:18 143: [09:35:14] Rep: 100 Mol:22 143: [09:35:14] Rep: 100 Mol:26 143: [09:35:14] Rep: 100 Mol:30 141: [09:35:14] Rep: 80 Mol:2 141: [09:35:14] Rep: 80 Mol:6 141: [09:35:14] Rep: 80 Mol:10 141: [09:35:14] Rep: 80 Mol:14 141: [09:35:14] Rep: 80 Mol:18 141: [09:35:14] Rep: 80 Mol:22 141: [09:35:14] Rep: 80 Mol:26 141: [09:35:14] Rep: 80 Mol:30 141: [09:35:14] done 141: [09:35:14] ------------------------------------- 141: [09:35:14] Test MMFF multithreading2 145: [09:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:14] Molecule does not have explicit Hs. Consider calling AddHs() 145: [09:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:14] Molecule does not have explicit Hs. Consider calling AddHs() 145: [09:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:14] Molecule does not have explicit Hs. Consider calling AddHs() 145: [09:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:14] Molecule does not have explicit Hs. Consider calling AddHs() 145: [09:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:14] Molecule does not have explicit Hs. Consider calling AddHs() 145: ..[09:35:14] Molecule does not have explicit Hs. Consider calling AddHs() 145: [09:35:14] Molecule does not have explicit Hs. Consider calling AddHs() 145: .[09:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:14] Molecule does not have explicit Hs. Consider calling AddHs() 145: .[09:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:14] Molecule does not have explicit Hs. Consider calling AddHs() 145: .[09:35:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145: .[09:35:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 125: Warning: Atom Count for residue GLU5A does not match expected count 143: [09:35:15] done 143: [09:35:15] ------------------------------------- 143: [09:35:15] Test UFF multithreading2 125: Warning: Atom Count for residue ASN39A does not match expected count 125: Warning: Atom Count for residue GLU53A does not match expected count 125: Warning: Atom Count for residue ARG64A does not match expected count 145: .[09:35:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 125: Warning: Atom Count for residue LYS80A does not match expected count 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145: .[09:35:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145: .[09:35:15] UFFTYPER: Unrecognized hybridization for atom: 0 145: [09:35:15] UFFTYPER: Unrecognized atom type: Cu+1 (0) 145: .[09:35:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145: [09:35:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145: [09:35:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145: [09:35:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145: [09:35:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145: .[09:35:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145: .[09:35:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145: .[09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145: ...[09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 125: Warning: Atom Count for residue GLU150A does not match expected count 125: Warning: Atom Count for residue ASN157A does not match expected count 126: Warning: Atom Count for residue GLU5A does not match expected count 126: Warning: Atom Count for residue ASN39A does not match expected count 141: [09:35:15] done 141: [09:35:15] ------------------------------------- 141: [09:35:15] Test MMFF multithreading3 126: Warning: Atom Count for residue GLU53A does not match expected count 126: Warning: Atom Count for residue ARG64A does not match expected count 126: Warning: Atom Count for residue LYS80A does not match expected count 126: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN157A does not match expected count 126: .[09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: .[09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: ..[09:35:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:15] DEPRECATION WARNING: please use AtomPairGenerator 126: .[09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ...[09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 125: =============================================================================== 125: All tests passed (515 assertions in 10 test cases) 125: 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 126: [09:35:15] DEPRECATION WARNING: please use MorganGenerator 140/236 Test #125: descriptorsTestCatch ................... Passed 5.80 sec test 146 Start 146: testDistGeomHelpers 146: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 146: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 146: Test timeout computed to be: 1500 126: ....[09:35:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:15] DEPRECATION WARNING: please use AtomPairGenerator 126: ....[09:35:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:35:15] DEPRECATION WARNING: please use AtomPairGenerator 126: .[09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 145: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 126: ..[09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: .[09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:35:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ... 126: ---------------------------------------------------------------------- 126: Ran 31 tests in 5.289s 126: 126: OK 126: exactmw 78.046950192 126: amw 78.11399999999999 126: lipinskiHBA 0.0 126: lipinskiHBD 0.0 126: NumRotatableBonds 0.0 126: NumHBD 0.0 126: NumHBA 0.0 126: NumHeavyAtoms 6.0 126: NumAtoms 12.0 126: NumHeteroatoms 0.0 126: NumAmideBonds 0.0 126: FractionCSP3 0.0 126: NumRings 1.0 126: NumAromaticRings 1.0 126: NumAliphaticRings 0.0 126: NumSaturatedRings 0.0 126: NumHeterocycles 0.0 126: NumAromaticHeterocycles 0.0 126: NumSaturatedHeterocycles 0.0 126: NumAliphaticHeterocycles 0.0 126: NumSpiroAtoms 0.0 126: NumBridgeheadAtoms 0.0 126: NumAtomStereoCenters 0.0 126: NumUnspecifiedAtomStereoCenters 0.0 126: labuteASA 37.43140311949697 126: tpsa 0.0 126: CrippenClogP 1.6866 126: CrippenMR 26.441999999999993 126: chi0v 3.464101615137755 126: chi1v 2.0000000000000004 126: chi2v 0.6666666666666671 126: chi3v 0.6666666666666671 126: chi4v 0.38490017945975075 126: chi0n 3.464101615137755 126: chi1n 2.0000000000000004 126: chi2n 0.6666666666666671 126: chi3n 0.6666666666666671 126: chi4n 0.38490017945975075 126: hallKierAlpha -0.78 126: kappa1 3.4115708812260532 126: kappa2 1.6057694396735218 126: kappa3 0.5823992601400448 126: Phi 0.9130327103921437 126: CustomNumAtoms 6.0 126: exactmw 78.046950192 126: lipinskiHBA 0.0 145: ... 145: ---------------------------------------------------------------------- 145: Ran 19 tests in 0.295s 145: 145: OK 146: [09:35:15] ******************************************************** 146: [09:35:15] Testing DistGeomHelpers 146: [09:35:15] --------------------------------- 146: [09:35:15] test2 146: 146: go 146: ------------------------------------- 146: 141/236 Test #126: pyMolDescriptors ....................... Passed 5.77 sec test 147 Start 147: distGeomHelpersCatch 147: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 147: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 147: Test timeout computed to be: 1500 142/236 Test #145: pyForceFieldHelpers .................... Passed 0.67 sec test 148 Start 148: pyDistGeomHelpers 148: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 148: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 148: Test timeout computed to be: 1500 147: Randomness seeded to: 2097922129 147: [09:35:15] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] 147: [09:35:15] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [09:35:15] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] 147: [09:35:15] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 147: [09:35:15] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [09:35:15] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [09:35:15] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: ----------- 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [09:35:15] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [09:35:15] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 147: ----------- 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [09:35:15] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 147: ----------- 147: ----------- 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [09:35:15] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [09:35:15] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [09:35:15] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [09:35:15] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [09:35:15] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [09:35:15] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 141: [09:35:15] done 141: [09:35:15] ------------------------------------- 141: [09:35:15] Testing github 162: Incorrect SMILES after MMFF parameterization . 141: [09:35:15] done 141: [09:35:15] ------------------------------------- 141: [09:35:15] Testing github 224: crash during MMFF parameterization . 141: [09:35:15] done 141: [09:35:15] ------------------------------------- 141: [09:35:15] Testing github6728: crash due to missing stretch-bend params. 143/236 Test #141: testMMFFForceFieldHelpers .............. Passed 2.12 sec test 149 Start 149: testMolAlign 149: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 149: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 149: Test timeout computed to be: 1500 143: [09:35:15] done 143: [09:35:15] ------------------------------------- 143: [09:35:15] Test UFF multithreading3 147: [09:35:15] UFFTYPER: Unrecognized atom type: Pt5+2 (1) 147: [09:35:15] UFFTYPER: Unrecognized charge state for atom: 1 147: [09:35:15] UFFTYPER: Unrecognized charge state for atom: 1 147: [09:35:15] UFFTYPER: Unrecognized charge state for atom: 1 147: [09:35:15] UFFTYPER: Unrecognized charge state for atom: 5 147: [09:35:15] UFFTYPER: Unrecognized charge state for atom: 5 147: [09:35:15] UFFTYPER: Unrecognized charge state for atom: 5 147: [09:35:15] UFFTYPER: Unrecognized charge state for atom: 6 147: [09:35:15] UFFTYPER: Unrecognized charge state for atom: 6 147: [09:35:15] UFFTYPER: Unrecognized charge state for atom: 6 149: *********************************************************** 149: Testing MolAlign 149: --------------------------------- 149: test1MolAlign 149: 149: --------------------------------- 149: test1GetBestRMS 149: 149: --------------------------------- 149: test1MolWithQueryAlign 149: 149: --------------------------------- 149: test2AtomMap 149: 149: --------------------------------- 149: test3Weights 149: 149: --------------------------------- 149: testIssue241 149: 149: *********************************************************** 144/236 Test #149: testMolAlign ........................... Passed 0.29 sec test 150 Start 150: testO3AAlign 150: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 150: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 150: Test timeout computed to be: 1500 143: [09:35:15] done 143: [09:35:15] ------------------------------------- 143: [09:35:15] Testing GitHubIssue62. 143: [09:35:15] beta-lactam 39.6387 143: [09:35:15] cyclopropanone 174.698 143: [09:35:15] aziridine 337.986 143: [09:35:15] aziridinone 115.248 143: [09:35:15] isobutene 2.48217 143: [09:35:15] acetone 1.91788 143: [09:35:15] cyclopentanone 10.1648 143: [09:35:15] cyclopropene 99.4921 143: [09:35:15] cyclobutene 41.0156 143: [09:35:15] cyclopropane 267.236 143: [09:35:15] gamma-lactam 15.7471 148: .[09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:35:15] trans-2,3-diphenylcyclopropan-1-one 203.398 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: ..[09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:35:15] cis-2,3-diphenylcyclopropan-1-one 206.852 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: ..[09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: .[09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:35:15] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:35:15] cyclopropylidencyclobutane 218.879 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:35:15] diphenylmethylidencyclobutane 79.6139 143: [09:35:15] done 143: [09:35:15] ------------------------------------- 143: [09:35:15] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. 143: [09:35:15] done 143: [09:35:15] ------------------------------------- 143: [09:35:15] Test square planar complexes 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:35:15] done 143: [09:35:15] ------------------------------------- 143: [09:35:15] Test octahedral complexes 143: [09:35:15] done 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 145/236 Test #143: testUFFForceFieldHelpers ............... Passed 2.13 sec test 151 Start 151: molAlignCatchTest 151: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 151: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 151: Test timeout computed to be: 1500 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 151: Randomness seeded to: 1645740143 151: 48922218 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 151: 13472609 148: [09:35:15] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: .[09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 147: [09:35:16] UFFTYPER: Warning: hybridization set to SP3 for atom 6 147: [09:35:16] UFFTYPER: Warning: hybridization set to SP3 for atom 6 147: [09:35:16] UFFTYPER: Warning: hybridization set to SP3 for atom 6 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 147: [09:35:16] UFFTYPER: Warning: hybridization set to SP3 for atom 11 147: [09:35:16] UFFTYPER: Warning: hybridization set to SP3 for atom 11 147: [09:35:16] UFFTYPER: Warning: hybridization set to SP3 for atom 11 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:35:15] --------------------------------- 146: [09:35:15] test3 146: 146: [09:35:15] --------------------------------- 146: [09:35:15] test4 146: 146: [09:35:15] --------------------------------- 146: [09:35:15] test5 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] test6 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] test15Dists 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] test Issue 215 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] testMultipleConfs 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] testMultipleConfsExpTors 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] testIssue227 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] testIssue236 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] testOrdering 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] testIssue244 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] testIssue251 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] testIssue276 146: [09:35:16] --------------------------------- 146: [09:35:16] testIssue284 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] testIssue285 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] testIssue355 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] testRandomCoords 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] test sf.net issue 1989539 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] test sf.net issue 2091864 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] test constrained embedding 146: 146: [09:35:16] ssd: 0.0752641 146: [09:35:16] ssd: 0.0659363 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 151: 738453861 146: [09:35:16] --------------------------------- 146: [09:35:16] test sf.net issue 2091974 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] test sf.net issue 2835784 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] test sf.net issue 3019283 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] test sf.net issue 3238580 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] test sf.net issue 3483968 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] test github issue 55 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] test1 146: 146: [09:35:16] --------------------------------- 146: [09:35:16] test multi-threading 146: 146: building molecules 146: generating reference data 148: [09:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 151: 301395657 151: =============================================================================== 151: All tests passed (73 assertions in 3 test cases) 151: 146/236 Test #151: molAlignCatchTest ...................... Passed 1.17 sec test 152 Start 152: pyMolAlign 152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 152: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap 152: Test timeout computed to be: 1500 148: [09:35:17] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:17] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:17] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:17] Molecule does not have explicit Hs. Consider calling AddHs() 150: *********************************************************** 150: Testing O3AAlign 150: --------------------------------- 150: testMMFFO3A 150: 150: --------------------------------- 150: testMMFFO3A with pre-computed dmat and MolHistogram 150: 150: --------------------------------- 150: testMMFFO3A with constraints 150: 150: --------------------------------- 150: testMMFFO3A with variable weight constraints followed by local-only optimization 150: 150: --------------------------------- 150: testCrippenO3A 150: 150: --------------------------------- 150: testCrippenO3A with pre-computed dmat and MolHistogram 150: 150: --------------------------------- 150: testCrippenO3A with constraints 150: 150: --------------------------------- 150: testCrippenO3A with variable weight constraints followed by local-only optimization 150: 150: --------------------------------- 150: testMMFFO3A multithreading 150: 150: generating reference data 148: [09:35:17] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:17] Molecule does not have explicit Hs. Consider calling AddHs() 146: validating reference data 150: processing 150: launch :0 150: launch :1 150: launch :2 150: launch :3 148: .[09:35:18] Molecule does not have explicit Hs. Consider calling AddHs() 146: processing 146: launch :0 146: launch :1 146: launch :2 146: launch :3 152: .............[09:35:28] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:28] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:28] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:28] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:28] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:28] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:28] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:28] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:28] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:28] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:28] Molecule does not have explicit Hs. Consider calling AddHs() 152: ...[09:35:30] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:30] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:30] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:30] Molecule does not have explicit Hs. Consider calling AddHs() 152: [09:35:30] Molecule does not have explicit Hs. Consider calling AddHs() 150: --------------------------------- 150: test O3A multithreading bug 150: 150: --------------------------------- 150: testCrippenO3A multithreading 150: 150: generating reference data 152: ... 152: ---------------------------------------------------------------------- 152: Ran 19 tests in 13.008s 152: 152: OK 152: Testing MolAlign Wrappers 147/236 Test #152: pyMolAlign ............................. Passed 13.29 sec test 153 Start 153: testFeatures 153: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures 153: Test timeout computed to be: 1500 153: [09:35:30] ------------------------------------- 153: [09:35:30] AtomType parser testing. 153: [09:35:30] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] 153: [09:35:30] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' 153: [09:35:30] done 153: [09:35:30] ------------------------------------- 153: [09:35:30] FeatureDefinition parser testing. 153: [09:35:30] done 153: [09:35:30] ------------------------------------- 153: [09:35:30] Test pulling feat defs from a string. 153: [09:35:30] done 153: [09:35:30] ------------------------------------- 153: [09:35:30] FeatureDef functionality testing. 153: [09:35:30] done 153: [09:35:30] ------------------------------------- 153: [09:35:30] FeatureFactory testing. 153: [09:35:30] 1 153: [09:35:30] 2 153: [09:35:30] 3 153: [09:35:30] 4 153: [09:35:30] 5 153: [09:35:30] 6 153: [09:35:30] done 153: [09:35:30] ------------------------------------- 153: [09:35:30] Feature Location testing. 153: [09:35:30] done 153: [09:35:30] ------------------------------------- 153: [09:35:30] Test building a FeatureFactory from a file 153: [09:35:30] done 153: [09:35:30] ------------------------------------- 153: [09:35:30] Testing Issue 224. 153: [09:35:30] done 153: [09:35:30] ------------------------------------- 153: [09:35:30] Testing Issue 225. 153: [09:35:30] done 153: [09:35:30] ------------------------------------- 153: [09:35:30] Test Issue346 153: [09:35:30] done 153: [09:35:30] ------------------------------------- 153: [09:35:30] Test Issue347 153: [09:35:30] done 153: [09:35:30] ------------------------------------- 153: [09:35:30] Testing Issue 348. 153: [09:35:30] SMARTS Parse Error: syntax error while parsing: [C[C] 153: [09:35:30] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' 153: [09:35:30] ------------------------------------- 153: [09:35:30] Testing Nested AtomType definitions. 153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] 153: [09:35:30] ------------------------------------- 153: [09:35:30] Testing Github Issue #252: crash when calling getPos() with no conformer. 153: [09:35:30] expect a precondition failure message below 153: [09:35:30] 153: 153: **** 153: Pre-condition Violation 153: molecule has no conformers 153: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp 153: Failed Expression: dp_mol->getNumConformers() 153: ---------- 153: Stacktrace: 153: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 153: 4# 0x000055B7CDDBBE50 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: 5# 0x000055B7CDDB0743 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: 6# 0x00007F6FB3433CA8 in /lib/x86_64-linux-gnu/libc.so.6 153: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 153: 8# 0x000055B7CDDB0841 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: ---------- 153: **** 153: 153: [09:35:30] Done 153: [09:35:30] ------------------------------------- 153: [09:35:30] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() 153: [09:35:30] done 148/236 Test #153: testFeatures ........................... Passed 0.01 sec test 154 Start 154: pyChemicalFeatures 154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 154: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 154: Test timeout computed to be: 1500 150: processing 150: launch :0 150: launch :1 150: launch :2 150: launch :3 154: .[09:35:30] Molecule does not have explicit Hs. Consider calling AddHs() 154: .[09:35:30] Molecule does not have explicit Hs. Consider calling AddHs() 154: ..[09:35:30] Molecule does not have explicit Hs. Consider calling AddHs() 154: .[09:35:30] Molecule does not have explicit Hs. Consider calling AddHs() 154: .[09:35:30] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] 154: [09:35:30] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' 154: ... 154: ---------------------------------------------------------------------- 154: Ran 9 tests in 0.086s 154: 154: OK 149/236 Test #154: pyChemicalFeatures ..................... Passed 0.32 sec test 155 Start 155: testShapeHelpers 155: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 155: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers 155: Test timeout computed to be: 1500 155: *********************************************************** 155: Testing ShapeHelpers 155: --------------------------------- 155: test1Encode 155: 155: --------------------------------- 155: test2Compare 155: 155: --------------------------------- 155: testGithub4364 155: 155: *********************************************************** 150/236 Test #155: testShapeHelpers ....................... Passed 0.07 sec test 156 Start 156: pyShapeHelpers 156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" 156: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 156: Test timeout computed to be: 1500 156: . 156: ---------------------------------------------------------------------- 156: Ran 1 test in 0.081s 156: 156: OK 156: Testing Shape Helpers wrapper 151/236 Test #156: pyShapeHelpers ......................... Passed 0.32 sec test 157 Start 157: testMolCatalog 157: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 157: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog 157: Test timeout computed to be: 1500 152/236 Test #157: testMolCatalog ......................... Passed 0.01 sec test 158 Start 158: pyMolCatalog 158: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 158: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 158: Test timeout computed to be: 1500 158: . 158: ---------------------------------------------------------------------- 158: Ran 1 test in 0.005s 158: 158: OK 153/236 Test #158: pyMolCatalog ........................... Passed 0.28 sec test 159 Start 159: moldraw2DTest1 159: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 159: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 159: Test timeout computed to be: 1500 159: ----------------- Test 1 159: file test1_5.svg gave hash 2383324771U not the expected 2811480876U 159: Done 159: ----------------- Test 2 159: file test2_1.png gave hash 240594419U not the expected 638584804U 159: file test2_2.png gave hash 278647755U not the expected 610424244U 159: Done 159: ----------------- Test 4 159: file test4_1.png gave hash 509333604U not the expected 3993974247U 159: Done 159: ----------------- Test 5 159: file test5_1.png gave hash 650561118U not the expected 571291290U 159: file test5_2.png gave hash 2649140411U not the expected 97265124U 159: file test5_3.png gave hash 2951986966U not the expected 606188176U 159: Done 159: ----------------- Test 6 (atom labels) 159: Done 159: ----------------- Test 7 (backgrounds) 159: file test7_1.png gave hash 2406197059U not the expected 1322246680U 159: file test7_2.png gave hash 4033628357U not the expected 1499012715U 159: Done 159: ----------------- Test8: PrepareMolDrawing 159: Done 159: ----------------- Test multi-threaded drawing 159: reading molecules 159: generating reference drawings 159: processing 159: launch :0 159: launch :1 159: launch :2 159: launch :3 5: [09:35:32] Finished: testMultipleTimes() 5: [09:35:32] 5: ----------------------------------------- 154/236 Test #5: testConcurrentQueue .................... Passed 36.37 sec test 160 Start 160: moldraw2DTestCatch 160: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 160: Test timeout computed to be: 1500 160: Randomness seeded to: 1750475450 160: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U 160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U 160: file contourMol_2.svg gave hash 4241964660U not the expected 1815941817U 160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U 160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U 160: file contourMol_5.svg gave hash 3954963517U not the expected 3792684719U 160: file testGithub3226_1.png gave hash 2093087177U not the expected 3165135374U 160: file testGithub3226_2.png gave hash 228776032U not the expected 643975155U 160: file testGithub3226_3.png gave hash 1938488947U not the expected 3119571946U 160: file testPNGMetadata_1.png gave hash 3033029091U not the expected 997629701U 160: file testPNGMetadata_2.png gave hash 2637596984U not the expected 1797853056U 160: [09:35:32] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [09:35:32] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U 160: [09:35:32] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [09:35:32] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-1.png gave hash 70252907U not the expected 3894611804U 160: [09:35:32] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [09:35:32] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-2.svg gave hash 1534109833U not the expected 794717511U 160: [09:35:32] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [09:35:32] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-2.png gave hash 4273438430U not the expected 1443443188U 160: [09:35:32] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [09:35:32] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U 160: [09:35:32] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [09:35:32] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-3.png gave hash 258221924U not the expected 865629432U 160: [09:35:32] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [09:35:32] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U 160: [09:35:32] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [09:35:32] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-4.png gave hash 2602629668U not the expected 3919767093U 160: file testHandDrawn-5a.svg gave hash 3327818543U not the expected 1567781555U 160: [09:35:33] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [09:35:33] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-5b.svg gave hash 2125846125U not the expected 66354106U 160: [09:35:33] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [09:35:33] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-5.png gave hash 2441005674U not the expected 828378555U 160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U 160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U 160: [09:35:33] unrecognized bond typefile testGithub4238_1.png gave hash 2704600159U not the expected 2623427676U 160: file testGithub4323_1.png gave hash 1936109620U not the expected 3075787867U 160: file testGithub4323_3.png gave hash 1732257634U not the expected 381907253U 160: [09:35:33] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 160: file testFlexiCanvas.2a.png gave hash 1389326866U not the expected 2609920321U 160: file testFlexiCanvas.2b.png gave hash 614693993U not the expected 3615599154U 160: file testFlexiCanvas.3.svg gave hash 236661785U not the expected 3544316588U 160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U 160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U 160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U 160: file testGithub4764.sz1.png gave hash 517897906U not the expected 2179222277U 160: file testGithub4764.sz2.png gave hash 2568067924U not the expected 444262090U 160: file testGithub4764.sz3.png gave hash 2910755141U not the expected 3567162200U 160: file github5383_1.svg gave hash 4241964660U not the expected 1815941817U 160: file github5383_2.svg gave hash 2560846108U not the expected 0U 160: file github5383_1.png gave hash 1118153320U not the expected 2893520928U 160: file acs1996_1.png gave hash 1014030062U not the expected 2329725800U 160: file acs1996_2.png gave hash 1604110899U not the expected 2996350718U 160: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U 160: [09:35:34] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. 160: file bond_highlights_8.svg gave hash 3610726614U not the expected 3119784980U 160: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U 160: file AtropManyChiralsEnhanced.svg gave hash 3443464321U not the expected 2256768013U 160: file testGithub_7739_1.svg gave hash 3358510977U not the expected 2615562225U 160: file testGithub_7739_3.svg gave hash 176211825U not the expected 1037942338U 160: file testGithub_7739_4.svg gave hash 3309264286U not the expected 3549083171U 160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U 148: .........[09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: .[09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: .[09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 148: [09:35:34] Molecule does not have explicit Hs. Consider calling AddHs() 160: =============================================================================== 160: All tests passed (6857 assertions in 116 test cases) 160: 155/236 Test #160: moldraw2DTestCatch ..................... Passed 2.68 sec test 161 Start 161: moldraw2DRxnTest1 161: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 161: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 161: Test timeout computed to be: 1500 161: ----------------- Test 1 161: file rxn_test1_1.png gave hash 760679292U not the expected 801892091U 161: file rxn_test1_2.png gave hash 3312211595U not the expected 507435337U 161: file rxn_test1_3.png gave hash 288594716U not the expected 1590809137U 161: file rxn_test1_4.png gave hash 1996676260U not the expected 1766700542U 161: file rxn_test1_5.png gave hash 1068409486U not the expected 2552100594U 161: file rxn_test1_6.png gave hash 1112775934U not the expected 3791582903U 161: file rxn_test1_7.png gave hash 1360101162U not the expected 1461397406U 161: file rxn_test1_7.svg gave hash 2324077060U not the expected 1831465890U 161: Done 161: ----------------- Test 2: some examples that caused problems in testing 161: file rxn_test2_1.png gave hash 3339775168U not the expected 3551633840U 161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C 161: file rxn_test2_2_1.png gave hash 457778262U not the expected 1268122583U 161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl 161: file rxn_test2_2_2.png gave hash 4285088210U not the expected 82821108U 161: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C 161: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl 161: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C 161: file rxn_test2_2_3.png gave hash 660865433U not the expected 3828365604U 161: 3 [CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC 161: file rxn_test2_2_4.png gave hash 1904681261U not the expected 1230108677U 161: Done 161: ----------------- Test 3: test reactant highlighting 161: file rxn_test3_1.png gave hash 786828249U not the expected 4189980366U 161: Done 161: ----------------- Test 4: some examples from SMARTS in testing 161: draw! 161: file rxn_test4_1.png gave hash 1704194173U not the expected 2745201873U 161: done 161: file rxn_test4_2.png gave hash 30753303U not the expected 3094925886U 161: Done 156/236 Test #161: moldraw2DRxnTest1 ...................... Passed 0.34 sec test 162 Start 162: pyMolDraw2D 162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" 162: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 162: Test timeout computed to be: 1500 159: Done 159: ----------------- Test Github #781: Rendering single-atom molecules 159: Done 159: ----------------- Test 3 159: file test3_1.png gave hash 123800385U not the expected 675908852U 159: file test3_2.png gave hash 1032419673U not the expected 2452584093U 159: file test3_3.png gave hash 4020047355U not the expected 1907006999U 159: file test3_4.png gave hash 3725504342U not the expected 2305641511U 159: file test3_5.png gave hash 3317652686U not the expected 3842605920U 162: ...[09:35:35] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. 162: [09:35:35] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 159: file test3_6.png gave hash 513359294U not the expected 662622011U 159: file test3_7.png gave hash 98439579U not the expected 469729412U 159: Done 159: ----------------- Test Github774: upside-down drawings 162: ..........[09:35:35] 162: 162: **** 159: file test774_1.png gave hash 2947517748U not the expected 428322245U 162: Pre-condition Violation 162: molecule must not be None 162: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp 162: Failed Expression: m 162: ---------- 162: Stacktrace: 162: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 162: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 162: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 162: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector7 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 162: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 162: 5# 0x00007F053EA9162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 162: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 162: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 162: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 162: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 162: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 162: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 162: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 162: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 162: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 162: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 162: 16# 0x00007F053D1B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 162: 17# 0x00007F053D1B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 162: 18# 0x00007F053D1B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 162: 19# 0x00007F053D1B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 162: 20# 0x00007F053D1B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 162: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 162: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 162: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 162: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 162: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 162: 26# 0x00007F053EA8E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 162: 27# _PyObject_MakeTpCall in /usr/bin/python3 162: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 29# 0x00000000005C30D9 in /usr/bin/python3 162: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 31# 0x000000000064B89F in /usr/bin/python3 162: 32# 0x000000000069ECA0 in /usr/bin/python3 162: 33# _PyObject_MakeTpCall in /usr/bin/python3 162: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 35# 0x00000000005C30D9 in /usr/bin/python3 162: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 37# 0x000000000064B89F in /usr/bin/python3 162: 38# 0x000000000069ECA0 in /usr/bin/python3 162: 39# _PyObject_MakeTpCall in /usr/bin/python3 162: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 41# 0x00000000005C30D9 in /usr/bin/python3 162: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 43# 0x000000000064B89F in /usr/bin/python3 162: 44# 0x000000000069ECA0 in /usr/bin/python3 162: 45# _PyObject_MakeTpCall in /usr/bin/python3 162: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 47# 0x0000000000599C8E in /usr/bin/python3 162: 48# _PyObject_MakeTpCall in /usr/bin/python3 162: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 50# PyEval_EvalCode in /usr/bin/python3 162: 51# 0x000000000066DA21 in /usr/bin/python3 162: 52# 0x0000000000669A8C in /usr/bin/python3 162: 53# 0x0000000000682973 in /usr/bin/python3 162: 54# 0x0000000000682273 in /usr/bin/python3 162: 55# 0x00000000006820AE in /usr/bin/python3 162: 56# Py_RunMain in /usr/bin/python3 162: 57# Py_BytesMain in /usr/bin/python3 162: 58# 0x00007F053FD0DCA8 in /lib/x86_64-linux-gnu/libc.so.6 162: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 162: 60# _start in /usr/bin/python3 162: ---------- 162: **** 162: 159: file test774_2.png gave hash 3968995771U not the expected 4095288521U 159: Done 159: ----------------- Test 9 (molecule legends) 159: file test9_1.svg gave hash 923579170U not the expected 1484349178U 159: Done 159: ----------------- Test Github852: Lines used to wedge bonds are too thick 159: file test852_1.png gave hash 1401513420U not the expected 271517011U 159: file test852_2.png gave hash 1268186246U not the expected 967452082U 159: ---------------- 159: ---------------- 159: ---------------- 159: ---------------- 159: Done 159: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right 159: file test860_1.png gave hash 2465667142U not the expected 2835587240U 159: file test860_2.png gave hash 3702727304U not the expected 1116015475U 159: file test860_3.png gave hash 524479710U not the expected 1872467868U 159: Done 159: ----------------- Test Github #910: ugly coordinates generated for peptide chains 159: Done 159: ----------------- Test Github #932: mistake in SVG for wedged bonds 159: Done 159: ----------------- Test Github #953: default color should not be cyan 159: Done 159: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly 159: Done 159: ----------------- Test Deuterium, Tritium 159: Done 159: ----------------- Test crossed bonds 159: Done 159: ----------------- Testing drawing a second molecule 159: Done 159: ----------------- Testing drawing a grid of molecules 159: Done 159: ----------------- Testing drawMolecules 159: file test12_1.svg gave hash 76786371U not the expected 826649652U 162: ...................... 162: ---------------------------------------------------------------------- 162: Ran 35 tests in 0.159s 162: 162: OK 162: json lasso 157/236 Test #162: pyMolDraw2D ............................ Passed 0.37 sec test 163 Start 163: testFMCS 163: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/testFMCS 163: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS 163: Test timeout computed to be: 1500 159: Done 159: ----------------- Test JSON Configuration 159: Done 159: ----------------- Testing github 1090: escape html characters in SVG output 159: Done 159: ----------------- Testing github 1035: overflow bug in SVG color generation 159: Done 159: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes 159: Done 159: ----------------- Testing github 1322: add custom atom labels 159: Done 159: ----------------- Testing use of a black & white palette 159: Done 159: ----------------- Testing use of continuous highlighting with drawMolecules 159: Done 159: ----------------- Test 17 - Testing maximum font size 159: Done 159: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list 159: Done 159: ----------------- Testing use of fixed scales for drawing. 159: Done 159: ----------------- Testing rotation of 2D drawing. 159: Done 159: ----------------- Testing inclusion of molecule metadata 159: Done 159: ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default 159: Done 159: ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions 159: file testGithub2151_1.svg gave hash 3620378781U not the expected 4119581143U 159: file testGithub2151_2.svg gave hash 3896781930U not the expected 425960913U 159: Done 159: ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn 159: Done 159: ----------------- Testing testGithub2931: multi-coloured molecule highlights. 159: file testGithub2931_1.svg gave hash 811930351U not the expected 3635831631U 159: file testGithub2931_3.svg gave hash 1986517899U not the expected 2885834646U 159: Done 159: ----------------- Testing annotation of 2D Drawing. 159: file test20_1.png gave hash 1197378089U not the expected 200877868U 159: file test20_2.png gave hash 717262667U not the expected 1651164846U 159: file test20_3.png gave hash 1844565424U not the expected 1463603076U 159: file test20_4.png gave hash 284908271U not the expected 1714613205U 159: Done 159: ----------------- Test 21 - different font 159: [09:35:35] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/No_Such_Font_File.ttf not found. 159: [09:35:35] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 159: Done 159: ----------------- Test 22 - draw explicit methyls. 159: Done 159: ----------------- Testing drawing of legends. 159: Done 159: ----------------- Test Github 3305 - change and scale line widths. 159: file testGithub3305_1.png gave hash 3066881557U not the expected 3303791649U 159: file testGithub3305_2.png gave hash 3473051322U not the expected 4003267433U 159: file testGithub3305_3.png gave hash 748608900U not the expected 273338209U 159: file testGithub3305_4.png gave hash 3317652686U not the expected 3842605920U 159: file testGithub3305_5.png gave hash 2008868897U not the expected 151279576U 159: file testGithub3305_5.svg gave hash 3310590632U not the expected 1335449325U 159: file testGithub3305_6.png gave hash 1479310253U not the expected 613418460U 159: file testGithub3305_7.png gave hash 526001191U not the expected 2835747678U 159: Done 159: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules. 159: Done 159: ----------------- Test Github 4156 - bad scale for radicals in grid 159: Done 159: ----------------- Test JSON atomColourPalette 159: Done 159: ----------------- Test draw aromatic OR queries 159: Done 159: ----------------- Test AND queries 159: Done 158/236 Test #159: moldraw2DTest1 ......................... Passed 4.34 sec test 164 Start 164: pyFMCS 164: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Wrap/testFMCS.py" 164: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap 164: Test timeout computed to be: 1500 163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 163: Time elapsed 0.000 seconds 163: 163: test32() 163: MCS: [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]=[#6]-[#6](-[#7]-[#6]1:[#6]:[#6](-[#16](-[#7]2-[#6]-[#6]-[#8]-[#6]-[#6]-2)(=[#8])=[#8]):[#6]:[#6]:[#6]:1-[#7](-[#6]-[#6])-[#6]-[#6])=[#8] 31 atoms, 33 bonds 163: Time elapsed 0.046 seconds 163: 163: test190() 163: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds 163: Time elapsed 0.004 seconds 163: 163: test3() 163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds 163: Time elapsed 0.006 seconds 163: 163: testSimpleFast() 163: MCS: [#6]-[#8]-[#6]-[#6]1:[#6]:[#7]:[#6]:[#6](:[#6]:1):[#7]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#8]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17] 24 atoms, 26 bonds 163: Time elapsed 0.042 seconds 163: 163: testSimple() 163: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 163: Time elapsed 0.069 seconds 163: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 163: Time elapsed 0.046 seconds 163: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 163: Time elapsed 0.067 seconds 163: 163: testSegFault() 163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds 163: Time elapsed 0.006 seconds 163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds 163: Time elapsed 0.007 seconds 163: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds 163: Time elapsed 0.005 seconds 163: 163: testThreshold() 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: Time elapsed 0.000 seconds 163: 163: testRing1() 163: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds 163: Time elapsed 0.172 seconds 163: MCS MatchFusedRings: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds 163: Time elapsed 0.173 seconds 163: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#7;r6,!R1]:&@[#6;r6,!R1](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds 163: Time elapsed 0.157 seconds 163: 163: testAtomCompareIsotopes() 163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds 163: Time elapsed 0.000 seconds 163: 163: testAtomCompareAnyAtom() 163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds 163: Time elapsed 0.000 seconds 163: 163: testAtomCompareAnyAtom() 163: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds 163: Time elapsed 0.000 seconds 163: 163: testAtomCompareAnyAtom() 163: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds 163: Time elapsed 0.000 seconds 163: 163: testAtomCompareAnyAtom() 163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds 163: Time elapsed 0.000 seconds 163: 163: testJnk1LigandsDistance() 163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds 163: Time elapsed 0.004 seconds 163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds 163: Time elapsed 0.001 seconds 163: 163: test18() 163: Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1 163: MCS: [#6](:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#7]:[#6]:[#6]:[#6]:[#6]:1)-[#6]-[#6]-[#6]-[#6]-[#7]):[#6]:[#6]:[#6] 21 atoms, 21 bonds 163: Time elapsed 0.003 seconds 163: 163: test504() 163: Query +MAP [CH2:0]([CH2:1][CH2:2][NH:3][C:4]([CH:5]1[CH2:6][CH:7]1[c:8]1[c:9][c:10]([Cl:11])[c:12]([Cl:13])[cH:14][c:15]1)=[O:16])[CH2:17][CH2:18][N:19]1[CH2:20][CH2:21][CH:22]([NH:23][C:24]([NH:25][c:26]2[cH:27][cH:28][c:29]([Cl:30])[cH:31][cH:32]2)=[O:33])[CH2:34]1 163: MCS: [#6](-[#6]-[#6]-[#7]-[#6](-[#6]1-[#6]-[#6]-1-[#6]1:[#6]:[#6](-[#17]):[#6](:[#6]:[#6]:1)-[#17])=[#8])-[#6]-[#6]-[#7](-[#6]-[#6]-[#6]-[#7]-[#6](-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)=[#8])-[#6] 34 atoms, 36 bonds 163: Time elapsed 0.035 seconds 163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 163: Time elapsed 0.000 seconds 163: MCS: [#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])-[#6] 25 atoms, 28 bonds 163: Time elapsed 0.010 seconds 163: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds 163: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0003 seconds. bond[0]=6 163: STATISTICS: 163: Total Growing Steps = 1, MCS found on 1 step, for 0.0003 seconds 163: Initial Seeds = 1, Mismatched 0 163: Inspected Seeds = 2 163: Rejected by BestSize = 0 163: IndividualBondExcluded = 0 163: MatchCheck Seeds = 2 163: MatchCalls = 2 163: MatchFound = 1 163: fastMatchCalls = 1 163: fastMatchFound = 0 163: slowMatchCalls = 2 163: slowMatchFound = 1 163: DupCacheFound = 0 0 matched, 0 mismatched 163: HashCache size = 1 keys 163: HashCache size = 1 entries 163: FindHashInCache = 2 163: HashFoundInCache= 0 163: ExactMatchCalls = 0 163: ExactMatchFound = 0 163: Time elapsed 0.000 seconds 163: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 163: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 163: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 163: res sub = 1 size=3 163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 163: res sub = 1 size=3 163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds 163: test target = CC[C@H](F)Cl query = CCC useChirality = 0 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = CC[C@H](F)Cl query = CCC useChirality = 1 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = CCC(F)Cl query = CC useChirality = 0 163: res sub = 1 size=2 163: MCS: [#6]-[#6] 2 atoms, 1 bonds 163: test target = CCC(F)Cl query = CC useChirality = 1 163: res sub = 1 size=2 163: MCS: [#6]-[#6] 2 atoms, 1 bonds 163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 163: res sub = 1 size=4 163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 163: res sub = 1 size=4 163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 163: res sub = 0 size=0 163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 163: res sub = 0 size=0 163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 163: res sub = 0 size=0 163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = OC(F)CCl query = OC(F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = OC(F)CCl query = OC(F)C useChirality = 1 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 163: res sub = 0 size=0 163: MCS: [#9] 1 atoms, 0 bonds 163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 163: res sub = 0 size=0 163: MCS: [#9] 1 atoms, 0 bonds 163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 163: res sub = 1 size=3 163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 163: res sub = 1 size=3 163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 163: res sub = 1 size=3 163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 163: res sub = 1 size=3 163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 163: 163: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> 163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: done 150: --------------------------------- 150: test getO3AForProbeConfs 150: 150: *********************************************************** 159/236 Test #150: testO3AAlign ........................... Passed 20.80 sec test 165 Start 165: FMCStest 165: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 165: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test 165: Test timeout computed to be: 1500 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_15113.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_16613.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_30745.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_30861.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_31495.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_34869.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_36158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_36559.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_37434.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_39147.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_43754.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_44011.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_44158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_48076.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_48961.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_49648.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_49703.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_51128.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_51343.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_51842.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_54554.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_55749.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_17256.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20244.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20245.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30149.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30499.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_36186.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_39262.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_43966.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_45279.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_48029.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49064.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49801.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_50681.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_54039.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58265.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58358.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58866.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_60810.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21358.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21597.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30111.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31746.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31822.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_35220.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37603.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37964.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_39508.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42164.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42577.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_44072.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_45522.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46700.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46719.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46744.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_48517.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_49087.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_50034.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_51475.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53483.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53506.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_54598.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55614.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55737.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57090.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57705.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57785.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_58463.txt 165: 165: testChEMBfopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: L_Txt() chembl_II_sets/Target_no_10193_58700.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61003.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10260_38526.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10260_50778.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10260_52179.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10260_54285.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_30224.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_31222.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37369.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37465.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37541.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_38371.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44314.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44578.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_45765.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_46281.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_47928.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_50624.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51341.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51662.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51767.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53081.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53396.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53407.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_58823.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_59190.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_60672.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_61176.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_20905.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30074.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30175.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30423.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_31555.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_34878.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_35926.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_42168.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_20859.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_30060.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_30061.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_30606.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_30866.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_31249.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_34921.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_35188.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_36636.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_37466.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_39202.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_43952.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_49345.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_49591.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_49854.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_51416.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_53537.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_58879.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_60679.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_61269.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_20600.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_20859.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_30060.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_30606.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_30866.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_31558.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_35188.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_37466.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_43875.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_48911.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_49591.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_49854.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: no_108_57887.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_60679.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_6857.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_15478.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_20853.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30840.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30862.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30918.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30994.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31014.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31508.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31623.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35003.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35004.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35281.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35957.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36520.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36641.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_38586.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_44431.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_45093.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_51302.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5247.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_52937.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_57198.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5739.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_6535.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20205.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20986.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_30091.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34698.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34705.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37038.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37272.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37447.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38909.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38953.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_39472.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_45825.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_47179.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49028.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49860.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_51984.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53395.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53826.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54121.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54530.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_55738.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_57725.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_58590.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_20432.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_30331.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_37956.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_48114.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_58566.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34731.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34818.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37318.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37339.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37564.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39504.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39561.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46082.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46089.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47757.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_51593.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_54754.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58262.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58958.txt 165: 165: testChEMBL_Txt(fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: ) chembl_II_sets/Target_no_114_16827.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_20503.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_20724.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_30254.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_30321.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_30572.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_31116.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_31281.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_31443.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_34747.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_34920.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_35040.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_36623.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_37136.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_37208.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_38298.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_38554.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_39088.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_39543.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_44049.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_44562.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_45180.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_45867.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_46087.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_46829.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_47546.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_48395.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_50461.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_50765.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_51669.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_52381.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_57231.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_58246.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_30999.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31021.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31650.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_35011.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_37014.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_44598.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_48446.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50614.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50615.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50618.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_51950.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_31616.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_38381.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_45757.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_46816.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_50701.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_54049.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_57890.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_61045.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_30194.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_31421.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_35538.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_55727.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_60676.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_61130.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_6444.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_15623.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_20096.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_21591.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_30184.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_30380.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_30745.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_30861.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_31619.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_34869.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_35284.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_36158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_36915.txt 165: 165: testChEMBL_Txfopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: t() chembl_II_sets/Target_no_121_37434.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_37541.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_37677.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_38837.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_39530.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_43793.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44164.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44579.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44593.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44692.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44914.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_45878.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_48050.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_48706.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_48944.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_48961.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_49880.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_50055.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_50512.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_51064.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_53537.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_55749.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_58879.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_6876.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_44664.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_46451.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_50640.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_56102.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_58015.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59089.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59092.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_61340.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_31458.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_38481.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_42104.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49475.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49933.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_50558.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_37249.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_39117.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_48227.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_48229.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_53969.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_54262.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_55353.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_61212.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20250.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20506.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20626.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20689.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_21358.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_34843.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_35220.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36318.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36800.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_39349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45385.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45676.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46700.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46719.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_48517.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_52690.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_53483.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_55435.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_56102.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58015.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58375.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_1295fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: 2_58700.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_16724.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_2710.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_30128.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_31250.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_35519.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_36905.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_46788.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_4737.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_55736.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_57473.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_16146.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_30313.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_30539.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_30653.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_30988.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_31179.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_31339.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_3525.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_36886.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_37020.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_38128.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_43952.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_45210.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_45899.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_47889.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_51800.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_53158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_5330.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_55648.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_56096.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_57287.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_57399.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_57606.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_58470.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_60894.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_15010.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_20304.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_20542.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_20788.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_21358.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_30349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_31103.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_31764.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_31822.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_35220.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_37964.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_42164.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_44072.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_45522.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_46719.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_46744.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_48416.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_49740.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_50034.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_50640.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_53483.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_53506.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_53814.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_55435.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_56074.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_56107.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_57090.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_57705.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_57785.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_57861.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_58583.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_59089.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_59092.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_20600.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_30764.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_34876.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_37427.tfopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: xt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_38266.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_45283.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_46990.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_47123.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_47900.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_48050.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_48062.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_48076.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_50718.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_50972.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_51372.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_51830.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_53049.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_53505.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_54021.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_54565.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_54570.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_57666.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_57890.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_58072.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_58634.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_58643.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_59080.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_59202.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_59346.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_60379.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_60385.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_61098.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_31154.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_35648.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_48914.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_51975.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_52435.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_55790.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_58958.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_61146.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20191.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20562.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20606.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20607.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30003.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30402.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30726.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30924.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31457.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31460.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31600.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31620.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31640.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31782.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31797.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31829.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31856.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34690.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34691.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34694.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_35712.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37497.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37539.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48070.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48219.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48824.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48902.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_52867.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_53534.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_54570.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_58727.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60159.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60661.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_30037.txt 165: 165: testChEMBL_Txt() chefopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: mbl_II_sets/Target_no_259_34734.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_35365.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_35787.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_36793.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_37845.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_38328.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_39374.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_43936.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_44059.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_44405.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_44424.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_45166.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_46158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_46425.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_47187.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48435.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48817.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48849.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48957.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48965.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_49519.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_49921.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_50392.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_50972.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_52405.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_52442.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_53169.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_54640.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_57207.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_58537.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_58920.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_60358.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_25_16077.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_25_34943.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_25_36391.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_25_36574.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_25_52906.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_25_54642.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_16385.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_20333.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_20774.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_35825.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_37637.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_47741.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_48567.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_48841.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_49589.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_50564.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_51201.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_53150.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_55747.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_58276.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_20813.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_2331.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_2391.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_30374.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_30512.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_30796.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_31058.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_31450.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_36609.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_36636.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_38266.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_43800.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_47621.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_49433.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_49550.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_49865.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_51005.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_52373.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_53878.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_54554.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_57508.txtfopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_57618.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_59484.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_6563.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_16845.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_37106.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_37272.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_47947.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_50754.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_55800.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_57380.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_65_35328.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_65_36137.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_65_38826.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_65_44596.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_65_51275.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_65_55671.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_20155.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_30616.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_30653.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_30988.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_31339.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_31527.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_31631.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_36047.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_36568.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_36636.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_37020.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_38128.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_43952.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_45210.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_47889.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_51064.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_51800.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_5330.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_57508.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_58470.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_60894.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_20730.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_20753.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_30097.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_30663.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_35365.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_35375.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_35918.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_36010.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_36780.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_36793.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_37845.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_39110.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_39546.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_43936.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_44405.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_44424.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_44683.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_45166.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_46648.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_46986.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_47070.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_47187.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_48435.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_48817.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49138.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49460.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49519.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49532.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49829.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_50608.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_54640.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_61082.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_90_15727.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_90_20155.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_90_30407.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_90_3525.txt 165: 165: testChEMBfopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: L_Txt() chembl_II_sets/Target_no_93_12377.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_1308.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_34759.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_35447.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_42214.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_45877.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_47082.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_57082.txt 165: 165: testFileSDF_RandomSet(): benchmark/chembl13-10000-random-pairs.sdf 165: ERROR: RDKit could not load input file 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_pairs.smi 165: ERROR: RDKit could not load input file 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_knearest_2.smi 165: ERROR: RDKit could not load input file 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_knearest_10.smi 165: ERROR: RDKit could not load input file 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_knearest_100.smi 165: ERROR: RDKit could not load input file 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_80.smi 165: ERROR: RDKit could not load input file 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 165: ERROR: RDKit could not load input file 160/236 Test #165: FMCStest ............................... Passed 0.01 sec test 166 Start 166: molHashCatchTest 166: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 166: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash 166: Test timeout computed to be: 1500 166: Randomness seeded to: 3821028840 166: =============================================================================== 166: All tests passed (363 assertions in 14 test cases) 166: 161/236 Test #166: molHashCatchTest ....................... Passed 0.03 sec test 167 Start 167: pyMolHash 167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/Wrap/testMolHash.py" 167: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap 167: Test timeout computed to be: 1500 167: .... 167: ---------------------------------------------------------------------- 167: Ran 4 tests in 0.009s 167: 167: OK 162/236 Test #167: pyMolHash .............................. Passed 0.18 sec test 168 Start 168: testMMPA 168: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/testMMPA 168: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA 168: Test timeout computed to be: 1500 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 168: Time elapsed 0.002098 seconds 168: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 168: 1: NOREF. Reference data NOT LISTED in test case. 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 168: 2: NOREF. Reference data NOT LISTED in test case. 168: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 168: 4: NOREF. Reference data NOT LISTED in test case. 168: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 168: 5: NOREF. Reference data NOT LISTED in test case. 168: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 6: NOREF. Reference data NOT LISTED in test case. 168: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 168: 9: NOREF. Reference data NOT LISTED in test case. 168: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 168: 11: NOREF. Reference data NOT LISTED in test case. 168: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 168: 12: NOREF. Reference data NOT LISTED in test case. 168: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 13: NOREF. Reference data NOT LISTED in test case. 168: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 14: NOREF. Reference data NOT LISTED in test case. 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 168: 15: NOREF. Reference data NOT LISTED in test case. 168: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. 168: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- 168: Time elapsed 0.001687 seconds 168: 168: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 168: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 168: 1: PASSED. matchedRefRes = 4 168: 2: O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21, C[*:1].O=C(NCCO)[*:2] 168: 2: PASSED. matchedRefRes = 1 168: 3: O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OCC[*:2] 168: 3: PASSED. matchedRefRes = 6 168: 4: O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OC[*:2] 168: 4: PASSED. matchedRefRes = 13 168: 5: O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].O[*:2] 168: 5: PASSED. matchedRefRes = 12 168: 6: NULL, Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 168: 6: PASSED. matchedRefRes = 10 168: 7: O=C(N[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case.O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 8: O=C(NC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 8: NOREF. Reference data NOT LISTED in test case.O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 9: O=C(NCC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 168: 11: C([*:1])[*:2], Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 12: PASSED. matchedRefRes = 8 168: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 13: PASSED. matchedRefRes = 9 168: 14: C([*:1])[*:2], Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 14: PASSED. matchedRefRes = 11 168: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 168: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2] 168: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 168: ----------------------------------- 168: 168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 168: Time elapsed 0.001700 seconds 168: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 168: 1: PASSED. matchedRefRes = 4 168: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] 168: 2: PASSED. matchedRefRes = 1 168: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] 168: 3: PASSED. matchedRefRes = 6 168: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] 168: 4: PASSED. matchedRefRes = 13 168: 5: res= O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2] 168: 5: PASSED. matchedRefRes = 12 168: 6: res= NULL,Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 168: 6: PASSED. matchedRefRes = 10 168: 7: res= O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 9: NOREF. Reference data NOT LISTED in test case. 168: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 168: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 11: NOREF. Reference data NOT LISTED in test case. 168: 12: res= C(C[*:2])[*:1],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 12: PASSED. matchedRefRes = 8 168: 13: res= NULL,Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 13: PASSED. matchedRefRes = 9 168: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 14: PASSED. matchedRefRes = 11 168: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 168: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2] 168: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 168: ----------------------------------- 168: 168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE 168: Time elapsed 0.000489 seconds 168: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 168: 1: PASSED. matchedRefRes = 2 168: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] 168: 2: PASSED. matchedRefRes = 3 168: 3: res= C([*:1])([*:2])[*:3],C1CN1[*:3].C[*:1].O=C[*:2] 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= C1CN1C([*:1])[*:2],C[*:1].O=C[*:2] 168: 4: PASSED. matchedRefRes = 4 168: 5: res= NULL,C1CN1[*:1].CC(C=O)[*:1] 168: 5: PASSED. matchedRefRes = 5 168: 6: res= CC([*:1])[*:2],C1CN1[*:2].O=C[*:1] 168: 6: NOREF. Reference data NOT LISTED in test case. 168: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1] 168: 7: PASSED. matchedRefRes = 7 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3] 168: 6: CC(N1CC1)C(=O),Case1-SIMPLE,CC([*:1])[*:2],C1CN1[*:1].O=C[*:2] 168: ----------------------------------- 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 168: Time elapsed 0.001855 seconds 168: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 168: 1: NOREF. Reference data NOT LISTED in test case. 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 168: 2: NOREF. Reference data NOT LISTED in test case. 168: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 168: 4: NOREF. Reference data NOT LISTED in test case. 168: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 168: 5: NOREF. Reference data NOT LISTED in test case. 168: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 6: NOREF. Reference data NOT LISTED in test case. 168: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 168: 9: NOREF. Reference data NOT LISTED in test case. 168: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 168: 11: NOREF. Reference data NOT LISTED in test case. 168: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 168: 12: NOREF. Reference data NOT LISTED in test case. 168: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 13: NOREF. Reference data NOT LISTED in test case. 168: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 14: NOREF. Reference data NOT LISTED in test case. 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 168: 15: NOREF. Reference data NOT LISTED in test case. 168: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. 168: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- 168: 168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 168: Time elapsed 0.002010 seconds 168: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 168: 1: NOREF. Reference data NOT LISTED in test case. 168: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 168: 2: NOREF. Reference data NOT LISTED in test case. 168: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 168: 4: NOREF. Reference data NOT LISTED in test case. 168: 5: res= O=C(O[*:1])C([*:2])[*:3],O[*:2].c1ccc(C[*:1])cc1.c1ccc([*:3])cc1 168: 5: NOREF. Reference data NOT LISTED in test case. 168: 6: res= O=C(O[*:1])C(O)[*:2],c1ccc(C[*:1])cc1.c1ccc([*:2])cc1 168: 6: NOREF. Reference data NOT LISTED in test case. 168: 7: res= NULL,O=C(OC[*:1])C(O)c1ccccc1.c1ccc([*:1])cc1 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(OC[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc([*:2])cc1 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1 168: 9: NOREF. Reference data NOT LISTED in test case. 168: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 168: 11: NOREF. Reference data NOT LISTED in test case. 168: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] 168: 12: NOREF. Reference data NOT LISTED in test case. 168: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] 168: 13: NOREF. Reference data NOT LISTED in test case. 168: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1 168: 14: PASSED. matchedRefRes = 1 168: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1 168: 15: NOREF. Reference data NOT LISTED in test case. 168: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. 168: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 168: 18: NOREF. Reference data NOT LISTED in test case. 168: 168: --- ALL PASSED --- 168: ----------------------------------- 168: 5 TEST CASES FAILED 163/236 Test #168: testMMPA ............................... Passed 0.07 sec test 169 Start 169: pyMMPA 169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/Wrap/testMMPA.py" 169: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap 169: Test timeout computed to be: 1500 163: [09:35:36] The provided InitialSeed is not an MCS and will be ignored 148: ... 148: ---------------------------------------------------------------------- 148: Ran 22 tests in 21.176s 148: 148: OK 164/236 Test #148: pyDistGeomHelpers ...................... Passed 21.64 sec test 170 Start 170: testRascalMCES 170: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES 170: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES 170: Test timeout computed to be: 1500 164: ........................................[09:35:37] The provided InitialSeed is not an MCS and will be ignored 164: [09:35:37] The provided InitialSeed is not an MCS and will be ignored 164: [09:35:37] The provided InitialSeed is not an MCS and will be ignored 164: .[09:35:37] The provided InitialSeed is not an MCS and will be ignored 164: [09:35:37] The provided InitialSeed is not an MCS and will be ignored 164: [09:35:37] The provided InitialSeed is not an MCS and will be ignored 164: .[09:35:37] The provided InitialSeed is not an MCS and will be ignored 164: [09:35:37] The provided InitialSeed is not an MCS and will be ignored 164: [09:35:37] The provided InitialSeed is not an MCS and will be ignored 164: .[09:35:37] The provided InitialSeed is not an MCS and will be ignored 164: [09:35:37] The provided InitialSeed is not an MCS and will be ignored 164: [09:35:37] The provided InitialSeed is not an MCS and will be ignored 164: ................. 164: ---------------------------------------------------------------------- 164: Ran 60 tests in 1.698s 164: 164: OK 165/236 Test #164: pyFMCS ................................. Passed 1.92 sec test 171 Start 171: testRascalCluster 171: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster 171: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES 171: Test timeout computed to be: 1500 169: ......... 169: ---------------------------------------------------------------------- 169: Ran 9 tests in 0.693s 169: 169: OK 166/236 Test #169: pyMMPA ................................. Passed 0.84 sec test 172 Start 172: pyRascalMCES 172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" 172: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap 172: Test timeout computed to be: 1500 172: ..........[09:35:38] Too many matching bond pairs (1032) so can't continue. 172: .... 172: ---------------------------------------------------------------------- 172: Ran 14 tests in 0.906s 172: 172: OK 167/236 Test #172: pyRascalMCES ........................... Passed 1.19 sec test 173 Start 173: testSynthonSpaceSubstructureSearch 173: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch 173: Test timeout computed to be: 1500 171: Randomness seeded to: 1522069503 171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi 173: Randomness seeded to: 2385079698 173: [09:35:39] Writing the enumerated file may take quite some time and result in a large file. 173: [09:35:42] Building the fingerprints may take some time. 173: [09:35:42] 173: 173: **** 173: Invariant Violation 173: molzip: bond info not properly setup for bgn atom with label:1 173: Violation occurred on line 1090 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 173: Failed Expression: bond.a 173: ---------- 173: Stacktrace: 173: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 173: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 173: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 173: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 173: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 173: 5# RDKit::SynthonSpaceSearch::SynthonSet::makeSynthonSearchMols() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 173: 6# RDKit::SynthonSpaceSearch::SynthonSpace::readTextFile(std::__cxx11::basic_string, std::allocator > const&, bool&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 173: 7# 0x000055C54DEC556A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: 8# 0x000055C54DF0FD78 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: 9# 0x000055C54DF10898 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: 10# 0x000055C54DF10D10 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: 11# 0x000055C54DEE22C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: 12# 0x000055C54DEE262C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: 13# 0x000055C54DEC478E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: 14# 0x00007F8645A33CA8 in /lib/x86_64-linux-gnu/libc.so.6 173: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 173: 16# 0x000055C54DEC47D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: ---------- 173: **** 173: 173: [09:35:42] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) 173: molzip: bond info not properly setup for bgn atom with label:1 173: [09:35:42] Explicit valence for atom # 4 C, 5, is greater than permitted 173: [09:35:42] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) 173: Explicit valence for atom # 4 C, 5, is greater than permitted 173: [09:35:42] Complex queries can be slow. 173: [09:35:42] Complex queries can be slow. 173: [09:35:42] Complex queries can be slow. 173: [09:35:42] Complex queries can be slow. 173: [09:35:42] Complex queries can be slow. 173: [09:35:42] Complex queries can be slow. 173: [09:35:42] Complex queries can be slow. 173: [09:35:42] Complex queries can be slow. 173: [09:35:42] Complex queries can be slow. 173: [09:35:43] Complex queries can be slow. 173: [09:35:43] Complex queries can be slow. 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: TOTAL Time elapsed 8.66 seconds 168/236 Test #163: testFMCS ............................... Passed 8.69 sec test 174 Start 174: testSynthonSpaceRascalSearch 174: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceRascalSearch 174: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch 174: Test timeout computed to be: 1500 147: [09:35:45] UFFTYPER: Unrecognized atom type: S_6+6 (0) 147: [09:35:45] UFFTYPER: Warning: hybridization set to SP3 for atom 0 147: [09:35:45] UFFTYPER: Unrecognized charge state for atom: 0 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:46] Complex queries can be slow. 173: [09:35:47] Complex queries can be slow. 173: [09:35:47] Complex queries can be slow. 173: =============================================================================== 173: All tests passed (121 assertions in 17 test cases) 173: 169/236 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 8.27 sec test 175 Start 175: testCIPLabeler 175: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 175: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler 175: Test timeout computed to be: 1500 175: Randomness seeded to: 2321071578 175: [09:35:47] non kekulizable aromatic bond being treated as bond order 1 175: [09:35:47] non kekulizable aromatic bond being treated as bond order 1 175: [09:35:47] non kekulizable aromatic bond being treated as bond order 1 175: [09:35:47] non kekulizable aromatic bond being treated as bond order 1 175: [09:35:47] non kekulizable aromatic bond being treated as bond order 1 175: [09:35:47] non kekulizable aromatic bond being treated as bond order 1 175: [09:35:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 175: [09:35:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 175: =============================================================================== 175: All tests passed (6577 assertions in 19 test cases) 175: 170/236 Test #175: testCIPLabeler ......................... Passed 0.10 sec test 176 Start 176: pyCIPLabelsWrapTest 176: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" 176: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 176: Test timeout computed to be: 1500 176: .... 176: ---------------------------------------------------------------------- 176: Ran 4 tests in 0.007s 176: 176: OK 171/236 Test #176: pyCIPLabelsWrapTest .................... Passed 0.14 sec test 177 Start 177: pyCIPLabelsValidation 177: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 177: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 177: Test timeout computed to be: 1500 170: Randomness seeded to: 1398482966 170: [09:35:48] Timed out after 11 seconds. 177: VS001: PASSED 177: VS002: PASSED 177: VS003: PASSED 177: VS004: PASSED 177: VS005: PASSED 177: VS006: PASSED 177: VS007: PASSED 177: VS008: PASSED 177: VS009: PASSED 177: VS010: PASSED 177: VS011: PASSED 177: VS012: PASSED 177: VS013: PASSED 177: VS014: PASSED 177: VS015: PASSED 177: VS016: PASSED 177: VS017: PASSED 177: VS018: PASSED 177: VS019: PASSED 177: VS020: PASSED 177: VS021: PASSED 177: VS022: PASSED 177: VS023: PASSED 177: VS024: PASSED 177: VS025: PASSED 177: VS026: PASSED 177: VS027: PASSED 177: VS028: PASSED 177: VS029: PASSED 177: VS030: PASSED 177: VS031: PASSED 177: VS032: PASSED 177: VS033: PASSED 177: VS034: PASSED 177: VS035: PASSED 177: VS036: PASSED 177: VS037: PASSED 177: VS038: PASSED 177: VS039: PASSED 177: VS040: PASSED 177: VS041: PASSED 177: VS042: PASSED 177: VS043: PASSED 177: VS044: PASSED 177: VS045: PASSED 177: VS046: PASSED 177: VS047: PASSED 177: VS048: PASSED 177: VS049: PASSED 177: VS050: PASSED 177: VS051: PASSED 177: VS052: PASSED 177: VS053: PASSED 177: VS054: PASSED 177: VS055: PASSED 177: VS056: PASSED 177: VS057: PASSED 177: VS058: PASSED 177: VS059: PASSED 177: VS060: PASSED 177: VS061: PASSED 177: VS062: PASSED 177: VS063: PASSED 177: VS064: PASSED 177: VS065: PASSED 177: VS066: PASSED 177: VS067: PASSED 177: VS068: PASSED 177: VS069: PASSED 177: VS070: PASSED 177: VS071: PASSED 177: VS072: PASSED 177: VS073: PASSED 177: VS074: PASSED 177: VS075: PASSED 177: VS076: PASSED 177: VS077: PASSED 177: VS078: PASSED 177: VS079: PASSED 177: VS080: PASSED 177: VS081: PASSED 177: VS082: PASSED 177: VS083: PASSED 177: VS084: PASSED 177: VS085: PASSED 177: VS086: PASSED 177: VS087: PASSED 177: VS088: PASSED 177: VS089: PASSED 177: VS090: PASSED 177: VS091: PASSED 177: VS092: PASSED 177: VS093: PASSED 177: VS094: PASSED 177: VS095: PASSED 177: VS096: PASSED 177: VS097: PASSED 177: VS098: PASSED 177: VS099: PASSED 177: VS100: PASSED 177: VS101: PASSED 177: VS102: PASSED 177: VS103: PASSED 177: VS104: PASSED 177: VS105: PASSED 177: VS106: PASSED 177: VS107: PASSED 177: VS108: PASSED 177: VS109: PASSED 177: VS110: PASSED 177: VS111: PASSED 177: VS112: PASSED 177: VS113: PASSED 177: VS114: PASSED 177: VS115: PASSED 177: VS116: PASSED 177: VS117: PASSED 177: VS118: PASSED 177: VS119: PASSED 177: VS120: PASSED 177: VS121: PASSED 177: VS122: PASSED 177: VS123: PASSED 177: VS124: PASSED 177: VS125: PASSED 177: VS126: PASSED 177: VS127: PASSED 177: VS128: PASSED 177: VS129: PASSED 177: VS130: PASSED 177: VS131: PASSED 177: VS132: PASSED 177: VS133: PASSED 177: VS134: PASSED 177: VS135: PASSED 177: VS136: PASSED 177: VS137: PASSED 177: VS138: PASSED 177: VS139: PASSED 177: VS140: PASSED 177: VS141: PASSED 177: VS142: PASSED 177: VS143: PASSED 177: VS144: PASSED 177: VS145: PASSED 177: VS146: PASSED 177: VS147: PASSED 177: VS148: PASSED 177: VS149: PASSED 177: VS150: PASSED 177: VS151: PASSED 177: VS152: PASSED 177: VS153: PASSED 177: VS154: PASSED 177: VS155: PASSED 177: VS156: PASSED 177: VS157: PASSED 177: VS158: PASSED 177: VS159: PASSED 177: VS160: PASSED 177: VS161: PASSED 177: VS162: PASSED 177: VS163: PASSED 177: VS164: PASSED 177: VS165: PASSED 177: VS166: PASSED 177: VS167: PASSED 177: VS168: PASSED 177: VS169: PASSED 177: VS170: PASSED 177: VS171: PASSED 177: VS172: PASSED 177: VS173: PASSED 177: VS174: PASSED 177: VS175: PASSED 177: VS176: PASSED 177: VS177: PASSED 177: VS178: PASSED 177: VS179: PASSED 177: VS180: PASSED 177: VS181: PASSED 177: VS182: PASSED 177: VS183: PASSED 177: VS184: PASSED 177: VS185: PASSED 177: VS186: PASSED 177: VS187: PASSED 177: VS188: PASSED 177: VS189: PASSED 177: VS190: PASSED 177: VS191: PASSED 177: VS192: PASSED 177: VS193: PASSED 177: VS194: PASSED 177: VS195: PASSED 177: VS196: PASSED 177: VS197: PASSED 177: VS198: PASSED 177: VS199: PASSED 177: VS200: PASSED 177: VS201: PASSED 177: VS202: PASSED 177: VS203: PASSED 177: VS204: PASSED 177: VS205: PASSED 177: VS206: PASSED 177: VS207: PASSED 177: VS208: PASSED 177: VS209: PASSED 177: VS210: PASSED 177: VS211: PASSED 177: VS212: PASSED 177: VS213: PASSED 177: VS214: PASSED 177: VS215: PASSED 177: VS216: PASSED 177: VS217: PASSED 177: VS218: PASSED 177: VS219: PASSED 177: VS220: PASSED 177: VS221: PASSED 177: VS222: PASSED 177: VS223: PASSED 177: VS224: PASSED 177: VS225: PASSED 177: VS226: PASSED 177: VS227: PASSED 177: VS228: PASSED 177: VS229: PASSED 177: VS230: PASSED 177: VS231: PASSED 177: VS232: PASSED 177: VS233: PASSED 177: VS234: PASSED 177: VS235: PASSED 177: VS236: PASSED 177: VS237: PASSED 177: VS238: PASSED 177: VS239: PASSED 177: VS240: PASSED 177: VS241: PASSED 177: VS242: PASSED 177: VS243: PASSED 177: VS244: PASSED 177: VS245: PASSED 177: VS246: PASSED 177: VS247: PASSED 177: VS248: PASSED 177: VS249: PASSED 177: VS250: PASSED 177: VS251: PASSED 177: VS252: PASSED 177: VS253: PASSED 177: VS254: PASSED 177: VS255: PASSED 177: VS256: PASSED 177: VS257: PASSED 177: VS258: PASSED 177: VS259: PASSED 177: VS260: PASSED 177: VS261: PASSED 177: VS262: PASSED 177: VS263: PASSED 177: VS264: PASSED 177: VS265: PASSED 177: VS266: PASSED 177: VS267: PASSED 177: VS268: PASSED 177: VS269: PASSED 177: VS270: PASSED 177: VS271: PASSED 177: VS272: PASSED 177: VS273: PASSED 177: VS274: PASSED 177: VS275: PASSED 177: VS276: PASSED 177: VS277: PASSED 177: VS278: PASSED 177: VS279: PASSED 177: VS280: PASSED 177: VS281: PASSED 177: VS282: PASSED 177: VS283: PASSED 177: VS284: PASSED 177: VS285: PASSED 177: VS286: PASSED 177: VS287: PASSED 177: VS288: PASSED 177: VS289: PASSED 177: VS290: PASSED 177: VS291: PASSED 177: VS292: PASSED 177: VS293: PASSED 177: VS294: PASSED 177: VS295: PASSED 177: VS296: PASSED 177: VS297: PASSED 177: VS298: PASSED 177: VS299: PASSED 177: VS300: PASSED 177: Check finished: 0 molecules failed. 177: Failed: 172/236 Test #177: pyCIPLabelsValidation .................. Passed 2.60 sec test 178 Start 178: deprotectTest 178: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 178: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect 178: Test timeout computed to be: 1500 178: Randomness seeded to: 3243329858 178: =============================================================================== 178: All tests passed (111 assertions in 3 test cases) 178: 173/236 Test #178: deprotectTest .......................... Passed 0.04 sec test 179 Start 179: pyDeprotect 179: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Wrap/rough_test.py" 179: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap 179: Test timeout computed to be: 1500 179: ..... 179: ---------------------------------------------------------------------- 179: Ran 5 tests in 0.018s 179: 179: OK 179: Testing tert-butyldimethylsilyl 179: Testing methoxytrityl 179: Testing tetrahydropyranyl 179: Testing methoxymethyl_ether 179: Testing beta-Methoxyethoxymethyl_ether 179: Testing benzyl 179: Testing trimethylsilyl 179: Testing benzoyl 179: Testing pivaloyl 179: Testing triisopropylsilyl 179: Testing acetyl 179: Testing para-methoxybenzyl_ether 179: Testing triphenylmethyl 179: Testing phthaloyl 179: Testing trimethylsilylethoxymethyl 179: Testing para-methoxyphenyl 179: Testing tosyl 179: Testing tert-butyloxycarbonyl 179: Testing trifluoroacetyl 179: Testing benzoyl 179: Testing 9-fluorenylmethyloxycarbonyl 179: Testing benzylamine 179: Testing acetamide 179: Testing carbobenzyloxy 179: Testing Acetal/Ketal 179: Testing tert-butyldimethylsilyl 179: Testing methoxytrityl 179: Testing tetrahydropyranyl 179: Testing methoxymethyl_ether 179: Testing beta-Methoxyethoxymethyl_ether 179: Testing benzyl 179: Testing trimethylsilyl 179: Testing benzoyl 179: Testing pivaloyl 179: Testing triisopropylsilyl 179: Testing acetyl 179: Testing para-methoxybenzyl_ether 179: Testing triphenylmethyl 179: Testing phthaloyl 179: Testing trimethylsilylethoxymethyl 179: Testing para-methoxyphenyl 179: Testing tosyl 179: Testing tert-butyloxycarbonyl 179: Testing trifluoroacetyl 179: Testing benzoyl 179: Testing 9-fluorenylmethyloxycarbonyl 179: Testing benzylamine 179: Testing acetamide 179: Testing carbobenzyloxy 179: Testing Acetal/Ketal 174/236 Test #179: pyDeprotect ............................ Passed 0.15 sec test 180 Start 180: testReducedGraphs 180: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs 180: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs 180: Test timeout computed to be: 1500 180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 180: 180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 180: 180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 180: 175/236 Test #180: testReducedGraphs ...................... Passed 0.02 sec test 181 Start 181: pyReducedGraphs 181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" 181: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap 181: Test timeout computed to be: 1500 181: ..... 181: ---------------------------------------------------------------------- 181: Ran 5 tests in 0.007s 181: 181: OK 176/236 Test #181: pyReducedGraphs ........................ Passed 0.14 sec test 182 Start 182: trajectoryTest 182: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 182: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory 182: Test timeout computed to be: 1500 177/236 Test #182: trajectoryTest ......................... Passed 0.13 sec test 183 Start 183: substructLibraryTest 183: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 183: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary 183: Test timeout computed to be: 1500 183: [09:35:50] ------------------------------------- 183: [09:35:50] Test1 183: [09:35:50] done 183: [09:35:50] ------------------------------------- 183: [09:35:50] Test2 183: [09:35:50] done 183: [09:35:50] ------------------------------------- 183: [09:35:50] Test3 (stereo options) 183: [09:35:50] Done (stereo options) 183: [09:35:50] ------------------------------------- 183: [09:35:50] Test4 (trusted smiles) 183: [09:35:50] Done (trusted smiles) 183: [09:35:50] ------------------------------------- 183: [09:35:50] Testing C++ docs 183: [09:35:50] Done (C++ doc tests) 183: [09:35:50] ------------------------------------- 183: [09:35:50] Testing C++ ring query: PatternHolder 183: [09:35:50] Done (C++ ring query tests) 183: [09:35:50] ------------------------------------- 183: [09:35:50] Testing C++ ring query: TautomerPatternHolder 183: [09:35:50] Done (C++ ring query tests) 183: [09:35:50] ------------------------------------- 183: [09:35:50] Add Patterns 146: [09:35:50] done 183: [09:35:51] ------------------------------------- 183: [09:35:51] testing PatternHolder 183: [09:35:51] ------------------------------------- 183: [09:35:51] testing TautomerPatternHolder 183: [09:35:51] ------------------------------------- 183: [09:35:51] testSegFaultInHolder 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf[09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf[09:35:51] 183: 183: [09:35:51] [09:35:51] SMILES Parse Error: check for mistakes around position [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position [09:35:51] 1: 183: [09:35:51] dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position [09:35:51] SMILES Parse Error: [09:35:51] 1SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdfsyntax error 183: [09:35:51] [09:35:51] SMILES Parse Error: SMILES Parse Error: check for mistakes around position syntax error[09:35:51] 1 while parsing: ^[09:35:51] SMILES Parse Error: syntax error while parsing: while parsing: :dsafsdfdsafsdf[09:35:51] 183: [09:35:51] 183: 1[09:35:51] syntax error[09:35:51] SMILES Parse Error: dsafsdfsyntax error 183: while parsing: :dsafsdf 183: dsafsdf 183: SMILES Parse Error: 183: [09:35:51] [09:35:51] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: [09:35:51] :[09:35:51] while parsing: :syntax errorsyntax error[09:35:51] while parsing: dsafsdfdsafsdf 183: 183: [09:35:51] [09:35:51] SMILES Parse Error: syntax error while parsing: 183: dsafsdf 183: 183: SMILES Parse Error: [09:35:51] [09:35:51] SMILES Parse Error: check for mistakes around position 1 while parsing: [09:35:51] SMILES Parse Error: dsafsdf[09:35:51] SMILES Parse Error: SMILESSMILES Parse Error: Parse Error: syntax errorFailed parsing SMILES 'dsafsdf'^ 183: SMILES Parse Error: [09:35:51] dsafsdf 183: [09:35:51] SMILES Parse Error: SMILES Parse Error: check for mistakes around position syntax error while parsing: 183: dsafsdf[09:35:51] 183: [09:35:51] SMILES Parse Error: check for mistakes around position 183: [09:35:51] [09:35:51] SMILES:[09:35:51] Parse Error: dsafsdf 183: SMILES Parse Error: [09:35:51] SMILES Parse Error: check for mistakes around position [09:35:51] [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: SMILES Parse Error: [09:35:51] SMILES Parse Error: 183: [09:35:51] 1:1[09:35:51] dsafsdf 183: syntax error[09:35:51] while parsing: SMILES Parse Error: [09:35:51] while parsing: SMILES Parse Error: syntax errordsafsdf for input: ' while parsing: syntax errordsafsdf 183: while parsing: dsafsdf[09:35:51] SMILES Parse Error: check for mistakes around position 1 183: [09:35:51] SMILES Parse Error: check for mistakes around position [09:35:51] 1[09:35:51] SMILES Parse Error: [09:35:51] :SMILES Parse Error: dsafsdfsyntax error while parsing: dsafsdf[09:35:51] :SMILES Parse Error: check for mistakes around position 1[09:35:51] 183: [09:35:51] dsafsdf 183: ^[09:35:51] 183: ^ 183: syntax errordsafsdf while parsing: dsafsdf[09:35:51] Failed parsing SMILES 'dsafsdf'dsafsdf 183: syntax error for input: 'syntax errorsyntax error1SMILES Parse Error: syntax error 183: [09:35:51] [09:35:51] dsafsdf[09:35:51] SMILES Parse Error: check for mistakes around position syntax error 183: while parsing: dsafsdf[09:35:51] ^[09:35:51] [09:35:51] dsafsdf while parsing: : 183: 183: while parsing: [09:35:51] ' 183: SMILES Parse Error: syntax error 183: syntax error while parsing: SMILES Parse Error: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 183: dsafsdf[09:35:51] [09:35:51] SMILES Parse Error: check for mistakes around position while parsing: [09:35:51] dsafsdf 183: 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: 183: 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: while parsing: SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] [09:35:51] dsafsdf 183: [09:35:51] dsafsdfSMILES Parse Error: check for mistakes around position 183: dsafsdf:[09:35:51] SMILESdsafsdf 183: Parse Error: 183: Failed parsing SMILES 'dsafsdf'syntax error 183: syntax error[09:35:51] while parsing: while parsing: [09:35:51] dsafsdf 183: 183: [09:35:51] ^^ 183: while parsing: [09:35:51] SMILES Parse Error: check for mistakes around position for input: 'dsafsdf1SMILESdsafsdf 183: :[09:35:51] 183: [09:35:51] [09:35:51] [09:35:51] SMILES Parse Error: check for mistakes around position 1[09:35:51] : 183: dsafsdf[09:35:51] ' 183: SMILES Parse Error: check for mistakes around position dsafsdf Parse Error: 183: 183: Failed parsing SMILES 'dsafsdf'[09:35:51] [09:35:51] 1[09:35:51] SMILESSMILES 183: [09:35:51] [09:35:51] 183: SMILES Parse Error: check for mistakes around position 1[09:35:51] SMILES1SMILES Parse Error: check for mistakes around position SMILES1^dsafsdf[09:35:51] ^ 183: dsafsdf[09:35:51] 183: [09:35:51] [09:35:51] SMILES Parse Error: check for mistakes around position ^SMILES Parse Error: check for mistakes around position 183: for input: '1 Parse Error: :SMILES 183: Parse Error: :: 183: 183: 183: :^dsafsdf 183: : 183: 183: Parse Error: SMILESFailed parsing SMILES 'dsafsdf' Parse Error: 'Failed parsing SMILES 'dsafsdf'1Failed parsing SMILES 'dsafsdf'^ 183: ^ 183: [09:35:51] [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[09:35:51] SMILES[09:35:51] Parse Error: Failed parsing SMILES 'dsafsdf'^ 183: [09:35:51] 183: SMILES Parse Error: check for mistakes around position 183: [09:35:51] for input: ' Parse Error: [09:35:51] Failed parsing SMILES 'dsafsdf'dsafsdf for input: ''[09:35:51] [09:35:51] dsafsdf 183: 1 Parse Error: for input: '[09:35:51] :dsafsdf'Failed parsing SMILES 'dsafsdf' 183: for input: 'dsafsdfdsafsdf' for input: ' 183: 1SMILES Parse Error: check for mistakes around position : 183: 1[09:35:51] :dsafsdf 183: [09:35:51] ^ 183: : 183: [09:35:51] dsafsdf[09:35:51] 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: 183: dsafsdf' 183: 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] [09:35:51] SMILES Parse Error: syntax errorSMILES Parse Error: check for mistakes around position 1:1: 183: 183: Failed parsing SMILES 'dsafsdf'[09:35:51] ^dsafsdf[09:35:51] 183: SMILES Parse Error: dsafsdfsyntax error 183: while parsing: [09:35:51] [09:35:51] ^ 183: SMILES Parse Error: SMILES Parse Error: check for mistakes around position while parsing: 1SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[09:35:51] 183: SMILES Parse Error: SMILESFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf[09:35:51] dsafsdf' 183: ^[09:35:51] 183: [09:35:51] [09:35:51] dsafsdfdsafsdf[09:35:51] 183: :' 183: 183: [09:35:51] SMILES for input: 'dsafsdfdsafsdf' 183: ' 183: SMILES Parse Error: syntax error 183: dsafsdf while parsing: 183: dsafsdfSMILES[09:35:51] Parse Error: ^[09:35:51] dsafsdf Parse Error: SMILES Parse Error: check for mistakes around position Failed parsing SMILES 'dsafsdf' 183: dsafsdf[09:35:51] 183: [09:35:51] [09:35:51] [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' 183: [09:35:51] :Failed parsing SMILES 'dsafsdf'dsafsdf for input: ' 183: dsafsdf[09:35:51] [09:35:51] 183: SMILES Parse Error: syntax error[09:35:51] while parsing: [09:35:51] dsafsdf 183: 183: SMILES Parse Error: for input: 'syntax error' Parse Error: 183: Failed parsing SMILES 'dsafsdf'[09:35:51] for input: 'SMILES Parse Error: for input: 'dsafsdf 183: SMILES Parse Error: check for mistakes around position 183: [09:35:51] ^[09:35:51] 'SMILES Parse Error: check for mistakes around position 183: [09:35:51] [09:35:51] dsafsdfdsafsdf 183: 183: [09:35:51] 183: ^[09:35:51] dsafsdf 183: [09:35:51] dsafsdfdsafsdf' while parsing: syntax errordsafsdf1[09:35:51] ^ 183: [09:35:51] ^SMILES 183: [09:35:51] dsafsdfdsafsdfSMILES 183: Parse Error: while parsing: [09:35:51] dsafsdf[09:35:51] SMILES Parse Error: check for mistakes around position for input: '[09:35:51] ' 183: [09:35:51] SMILES Parse Error: 183: Failed parsing SMILES 'dsafsdf'[09:35:51] 'SMILES: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: 183: ^ 183: dsafsdfsyntax error 183: 1 183: 183: ^[09:35:51] 183: [09:35:51] SMILESdsafsdf' 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: 183: [09:35:51] ^ 183: 183: [09:35:51] [09:35:51] SMILESSMILES Parse Error: check for mistakes around position Parse Error: Parse Error: 1 183: Parse Error: [09:35:51] 183: Failed parsing SMILES 'dsafsdf'1::Failed parsing SMILES 'dsafsdf' 183: for input: 'SMILES Parse Error: syntax error:Failed parsing SMILES 'dsafsdf'[09:35:51] 183: for input: 'SMILES Parse Error: [09:35:51] dsafsdfdsafsdf 183: [09:35:51] ' 183: 183: ^ while parsing: 183: ^[09:35:51] for input: 'Failed parsing SMILES 'dsafsdf'[09:35:51] dsafsdfSMILESdsafsdf[09:35:51] [09:35:51] syntax errorSMILES Parse Error: check for mistakes around position 1: 183: dsafsdf 183: Parse Error: Failed parsing SMILES 'dsafsdf' 183: 183: [09:35:51] for input: ''[09:35:51] ^SMILES[09:35:51] while parsing: Parse Error: [09:35:51] dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position dsafsdf 183: ^' 183: 1 183: : 183: 183: [09:35:51] SMILES[09:35:51] [09:35:51] [09:35:51] dsafsdf 183: for input: '[09:35:51] SMILES Parse Error: 183: syntax error[09:35:51] SMILES Parse Error: check for mistakes around position [09:35:51] while parsing: Parse Error: dsafsdfdsafsdf^ 183: 183: [09:35:51] 183: for input: '[09:35:51] 1dsafsdfdsafsdf[09:35:51] 183: SMILES Parse Error: check for mistakes around position ^Failed parsing SMILES 'dsafsdf' 183: for input: 'dsafsdfFailed parsing SMILES 'dsafsdf'dsafsdf[09:35:51] 'SMILES 183: ^ 183: while parsing: 1[09:35:51] ^: 183: 183: SMILES[09:35:51] dsafsdfdsafsdf:dsafsdf' 183: [09:35:51] ^ 183: [09:35:51] Parse Error: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'syntax error for input: ' for input: ' while parsing: dsafsdfdsafsdfSMILES'dsafsdf 183: 183: 183: [09:35:51] Parse Error: 183: ' 183: SMILES Parse Error: check for mistakes around position [09:35:51] '[09:35:51] [09:35:51] SMILES Parse Error: [09:35:51] Failed parsing SMILES 'dsafsdf'SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '^[09:35:51] dsafsdfSMILESSMILES1 Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: 183: dsafsdf[09:35:51] SMILES 183: Parse Error: [09:35:51] Parse Error: 183: for input: 'dsafsdf'[09:35:51] SMILES Parse Error: check for mistakes around position [09:35:51] '[09:35:51] Failed parsing SMILES 'dsafsdf' for input: '1dsafsdfFailed parsing SMILES 'dsafsdf'' for input: '[09:35:51] [09:35:51] 183: SMILES Parse Error: syntax error while parsing: SMILES Parse Error: [09:35:51] dsafsdf[09:35:51] SMILES Parse Error: check for mistakes around position 183: 1[09:35:51] SMILES Parse Error: SMILES Parse Error: ::syntax errordsafsdf' 183: ^SMILES Parse Error: Failed parsing SMILES 'dsafsdf':Failed parsing SMILES 'dsafsdf' 183: for input: '' Parse Error: 183: 183: 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1dsafsdf 183: 1 183: syntax error[09:35:51] while parsing: Failed parsing SMILES 'dsafsdf': for input: 'dsafsdf: 183: for input: 'Failed parsing SMILES 'dsafsdf'[09:35:51] [09:35:51] dsafsdfSMILES Parse Error: 183: dsafsdf' 183: dsafsdf'' 183: for input: ' 183: dsafsdf' 183: 183: dsafsdf[09:35:51] 183: ^[09:35:51] 183: 183: [09:35:51] dsafsdfsyntax error 183: [09:35:51] [09:35:51] SMILESdsafsdfSMILES Parse Error: check for mistakes around position 183: [09:35:51] [09:35:51] SMILES Parse Error: Parse Error: 183: Failed parsing SMILES 'dsafsdf' for input: ' 183: while parsing: dsafsdf 183: '[09:35:51] 183: 1syntax errorSMILES while parsing: dsafsdf: 183: Parse Error: ^[09:35:51] [09:35:51] [09:35:51] 183: dsafsdf 183: 183: dsafsdf^ 183: 183: [09:35:51] SMILES Parse Error: check for mistakes around position [09:35:51] dsafsdfSMILES[09:35:51] Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfFailed parsing SMILES 'dsafsdf'' 183: SMILES[09:35:51] 183: ^ 183: [09:35:51] ^ 183: SMILES Parse Error: check for mistakes around position [09:35:51] 1 for input: ': 183: 1[09:35:51] [09:35:51] ^ 183: dsafsdf: 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'SMILES[09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfdsafsdf'' 183: dsafsdf 183: [09:35:51] [09:35:51] ^ Parse Error: 183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf''dsafsdf 183: [09:35:51] ^ 183: 183: Parse Error: [09:35:51] 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] [09:35:51] [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf[09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: syntax error while parsing: dsafsdf[09:35:51] [09:35:51] SMILES Parse Error: 183: SMILES Parse Error: SMILES Parse Error: 183: syntax error 183: syntax error[09:35:51] while parsing: dsafsdfSMILES Parse Error: check for mistakes around position 1 183: :[09:35:51] SMILES Parse Error: [09:35:51] syntax error while parsing: dsafsdf[09:35:51] 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: [09:35:51] syntax errorSMILES Parse Error: check for mistakes around position SMILES Parse Error: syntax error1 183: while parsing: syntax error[09:35:51] while parsing: dsafsdf 183: : 183: SMILES Parse Error: [09:35:51] [09:35:51] syntax error[09:35:51] dsafsdf:SMILES Parse Error: dsafsdfSMILES Parse Error: syntax errorsyntax error 183: SMILES Parse Error: [09:35:51] while parsing: syntax error 183: while parsing: while parsing: while parsing: [09:35:51] [09:35:51] ^[09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: dsafsdf while parsing: 183: dsafsdf[09:35:51] SMILES Parse Error: check for mistakes around position 183: 1:dsafsdfSMILES Parse Error: 183: syntax error[09:35:51] 183: while parsing: [09:35:51] syntax errordsafsdf 183: while parsing: dsafsdf 183: [09:35:51] [09:35:51] [09:35:51] [09:35:51] 183: SMILES Parse Error: [09:35:51] dsafsdfSMILES Parse Error: [09:35:51] dsafsdfdsafsdf 183: dsafsdf[09:35:51] syntax error 183: 183: SMILES Parse Error: [09:35:51] syntax error[09:35:51] SMILES Parse Error: check for mistakes around position while parsing: SMILES Parse Error: check for mistakes around position [09:35:51] dsafsdf[09:35:51] syntax error 183: while parsing: [09:35:51] 1:SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1:[09:35:51] 1 183: [09:35:51] 183: SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] [09:35:51] [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] while parsing: dsafsdf 183: 183: [09:35:51] SMILES Parse Error: dsafsdfsyntax error while parsing: dsafsdf^[09:35:51] SMILES Parse Error: SMILES Parse Error: dsafsdf[09:35:51] SMILES Parse Error: check for mistakes around position [09:35:51] 1:[09:35:51] SMILES Parse Error: check for mistakes around position 183: SMILES Parse Error: 183: syntax error 183: [09:35:51] 183: SMILES Parse Error: check for mistakes around position [09:35:51] while parsing: SMILES Parse Error: SMILES Parse Error: syntax error[09:35:51] [09:35:51] [09:35:51] while parsing: [09:35:51] SMILES Parse Error: check for mistakes around position 1[09:35:51] [09:35:51] 1syntax error^dsafsdf while parsing: syntax error[09:35:51] [09:35:51] dsafsdf[09:35:51] SMILES Parse Error: check for mistakes around position 183: syntax error[09:35:51] ^:1SMILES Parse Error: check for mistakes around position while parsing: SMILESSMILES Parse Error: check for mistakes around position [09:35:51] dsafsdfdsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1::[09:35:51] SMILES Parse Error: check for mistakes around position ^ 183: 1:[09:35:51] SMILES Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf' 183: for input: ' while parsing: dsafsdf 183: 183: '[09:35:51] 183: SMILES 183: SMILES Parse Error: 1 183: :1[09:35:51] 183: :SMILES Parse Error: check for mistakes around position SMILES Parse Error: 1: 183: 183: [09:35:51] 1:: 183: [09:35:51] while parsing: SMILES Parse Error: 1syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position syntax errorSMILES while parsing: Parse Error: [09:35:51] dsafsdf 183: dsafsdfdsafsdfSMILES Parse Error: check for mistakes around position syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position syntax error[09:35:51] 1dsafsdf: 183: 183: 183: [09:35:51] dsafsdf 183: dsafsdf:SMILES[09:35:51] 183: Parse Error: [09:35:51] [09:35:51] SMILES Parse Error: check for mistakes around position [09:35:51] 1Failed parsing SMILES 'dsafsdf'SMILES Parse Error: check for mistakes around position 183: [09:35:51] 183: 183: [09:35:51] dsafsdf[09:35:51] ^ 183: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: Failed parsing SMILES 'dsafsdf'SMILES 183: : 183: while parsing: dsafsdf 183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: SMILES Parse Error: check for mistakes around position 1:: 183: 183: [09:35:51] 1dsafsdf 183: : 183: [09:35:51] [09:35:51] 183: [09:35:51] [09:35:51] dsafsdf 183: for input: 'dsafsdfdsafsdf1:[09:35:51] SMILES Parse Error: Parse Error: 183: Failed parsing SMILES 'dsafsdf'[09:35:51] [09:35:51] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1[09:35:51] [09:35:51] dsafsdfdsafsdf 183: 183: 1 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] [09:35:51] [09:35:51] SMILES Parse Error: 183: dsafsdf[09:35:51] ^ 183: syntax errorSMILES Parse Error: Failed parsing SMILES 'dsafsdf' 183: 183: [09:35:51] 11: 183: [09:35:51] ^ 183: [09:35:51] dsafsdf 183: [09:35:51] [09:35:51] dsafsdfsyntax errordsafsdf for input: ' for input: 'dsafsdf' for input: ':dsafsdf[09:35:51] [09:35:51] 183: :[09:35:51] 183: while parsing: [09:35:51] ^dsafsdf^ 183: 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1[09:35:51] SMILES 183: :[09:35:51] [09:35:51] 183: dsafsdfSMILES^ Parse Error: 183: dsafsdfFailed parsing SMILES 'dsafsdf''dsafsdf[09:35:51] for input: ' 183: [09:35:51] while parsing: 183: ^ 183: dsafsdfdsafsdf 183: 183: Parse Error: 183: [09:35:51] dsafsdf'[09:35:51] 183: [09:35:51] dsafsdf^' 183: 183: ^ 183: SMILES 183: 183: Parse Error: 183: [09:35:51] Failed parsing SMILES 'dsafsdf':SMILES 183: dsafsdf[09:35:51] ^[09:35:51] ' 183: [09:35:51] 183: [09:35:51] 183: 183: [09:35:51] 183: [09:35:51] [09:35:51] SMILESFailed parsing SMILES 'dsafsdf'[09:35:51] ^ 183: ^SMILES Parse Error: dsafsdf^ 183: ^ 183: [09:35:51] [09:35:51] [09:35:51] SMILES Parse Error: syntax error while parsing: ^[09:35:51] [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES[09:35:51] Parse Error: 183: [09:35:51] 183: [09:35:51] [09:35:51] SMILESSMILES Parse Error: Parse Error: dsafsdf 183: for input: 'dsafsdfdsafsdf[09:35:51] ^Failed parsing SMILES 'dsafsdf' for input: ' Parse Error: for input: ' 183: dsafsdfdsafsdf 183: ' Parse Error: [09:35:51] Failed parsing SMILES 'dsafsdf'[09:35:51] [09:35:51] for input: 'dsafsdf^' 183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[09:35:51] 183: [09:35:51] SMILES Parse Error: syntax error while parsing: Failed parsing SMILES 'dsafsdf'dsafsdf for input: ' 183: [09:35:51] [09:35:51] [09:35:51] dsafsdf 183: SMILES Parse Error: syntax error 183: SMILES 183: Parse Error: [09:35:51] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1dsafsdf[09:35:51] SMILESSMILES 183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] ^ 183: 183: [09:35:51] ^ 183: [09:35:51] Failed parsing SMILES 'dsafsdf'[09:35:51] for input: 'dsafsdf'[09:35:51] Parse Error: SMILES Parse Error: check for mistakes around position Failed parsing SMILES 'dsafsdf'dsafsdf for input: 'dsafsdf'' 183: [09:35:51] 183: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: [09:35:51] ^SMILES[09:35:51] [09:35:51] dsafsdfSMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'SMILES Parse Error: check for mistakes around position 183: 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: while parsing: dsafsdf[09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[09:35:51] for input: '^dsafsdf'SMILES' 183: 183: 1:SMILESsyntax error 183: 1[09:35:51] :SMILES Parse Error: check for mistakes around position Parse Error: ^Failed parsing SMILES 'dsafsdf'SMILES 183: 183: [09:35:51] SMILES Parse Error: [09:35:51] ^ 183: [09:35:51] 183: 183: 183: 183: 1 Parse Error: :[09:35:51] 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: :' 183: [09:35:51] SMILES Parse Error: syntax errordsafsdf for input: '[09:35:51] Parse Error: [09:35:51] SMILESSMILESSMILES Parse Error: SMILESdsafsdfsyntax error while parsing: 'SMILESsyntax error 183: while parsing: '[09:35:51] dsafsdfFailed parsing SMILES 'dsafsdf'dsafsdf Parse Error: Parse Error: [09:35:51] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'Failed parsing SMILES 'dsafsdf' while parsing: for input: 'syntax errordsafsdf 183: SMILES Parse Error: syntax error while parsing: dsafsdf 183: SMILES[09:35:51] 183: 183: Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' 183: 'Failed parsing SMILES 'dsafsdf'dsafsdf while parsing: for input: ' Parse Error: dsafsdf for input: 'dsafsdf[09:35:51] SMILES Parse Error: check for mistakes around position 183: '1dsafsdf 183: [09:35:51] :Failed parsing SMILES 'dsafsdf''dsafsdf 183: 183: [09:35:51] 183: SMILES Parse Error: check for mistakes around position dsafsdf[09:35:51] 183: for input: 'dsafsdf' 183: 183: '[09:35:51] dsafsdf'Failed parsing SMILES 'dsafsdf'[09:35:51] dsafsdf for input: '' 183: '1 183: 183: [09:35:51] ^ 183: Parse Error: 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'SMILES Parse Error: while parsing: syntax errordsafsdfdsafsdf[09:35:51] 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1^[09:35:51] dsafsdf 183: 183: while parsing: SMILES Parse Error: check for mistakes around position SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[09:35:51] 183: [09:35:51] ^ 183: dsafsdf 183: [09:35:51] SMILES 183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'syntax error1SMILESdsafsdf Parse Error: [09:35:51] :SMILES Parse Error: check for mistakes around position 1dsafsdf' while parsing: [09:35:51] dsafsdf 183: dsafsdf[09:35:51] [09:35:51] 'SMILES 183: 183: SMILES Parse Error: : 183: syntax errorSMILES Parse Error: check for mistakes around position 183: 183: 1SMILES Parse Error: check for mistakes around position 183: 1Failed parsing SMILES 'dsafsdf' Parse Error: :Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf 183: [09:35:51] SMILES Parse Error: [09:35:51] : for input: 'dsafsdf 183: while parsing: :[09:35:51] 183: dsafsdf' 183: syntax error[09:35:51] while parsing: dsafsdf 183: SMILES Parse Error: check for mistakes around position [09:35:51] :1[09:35:51] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position [09:35:51] 183: dsafsdfdsafsdfdsafsdf' 183: 1:[09:35:51] 183: [09:35:51] dsafsdf 183: 183: 183: [09:35:51] '^:1 183: [09:35:51] [09:35:51] ^: 183: 183: 183: [09:35:51] 183: dsafsdfSMILES Parse Error: [09:35:51] 183: 183: ^[09:35:51] [09:35:51] syntax error 183: [09:35:51] 183: dsafsdf^ 183: [09:35:51] [09:35:51] [09:35:51] 183: dsafsdf 183: SMILES[09:35:51] [09:35:51] dsafsdfSMILES 183: [09:35:51] [09:35:51] ^^dsafsdf Parse Error: while parsing: ^dsafsdf 183: 183: 183: 183: ^ 183: Parse Error: 183: [09:35:51] ^Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' 183: [09:35:51] [09:35:51] SMILES for input: ' Parse Error: [09:35:51] SMILES 183: [09:35:51] for input: '[09:35:51] [09:35:51] Failed parsing SMILES 'dsafsdf'SMILES[09:35:51] dsafsdfSMILES' Parse Error: for input: 'SMILES Parse Error: [09:35:51] dsafsdf 183: '^SMILES 183: Parse Error: [09:35:51] Failed parsing SMILES 'dsafsdf'SMILES for input: 'Failed parsing SMILES 'dsafsdf'dsafsdf Parse Error: 183: Parse Error: SMILES Parse Error: check for mistakes around position 'Failed parsing SMILES 'dsafsdf'[09:35:51] dsafsdf' for input: ' Parse Error: 183: Failed parsing SMILES 'dsafsdf'SMILES for input: ' Parse Error: for input: 'Failed parsing SMILES 'dsafsdf' 183: Failed parsing SMILES 'dsafsdf'1 for input: ':dsafsdfdsafsdf' 183: dsafsdf' 183: for input: 'Failed parsing SMILES 'dsafsdf'dsafsdf' 183: [09:35:51] ' 183: dsafsdf for input: 'dsafsdf 183: ' 183: 183: [09:35:51] ^ 183: [09:35:51] SMILESdsafsdf' 183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] SMILES Parse Error: syntax error while parsing: dsafsdf 183: [09:35:51] SMILES Parse Error: check for mistakes around position 1: 183: [09:35:51] dsafsdf 183: [09:35:51] ^ 183: [09:35:51] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: [09:35:51] ------------------------------------- 183: [09:35:51] Results do not depend on numThreads 183: [09:35:52] ------------------------------------- 183: [09:35:52] Results do not depend on numThreads (all same) 183: [09:35:52] ------------------------------------- 183: [09:35:52] testTautomerQueries 183: [09:35:52] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... 183: [09:35:52] ------------------------------------- 183: [09:35:52] github3881 recursive smarts with rings 146: [09:35:50] --------------------------------- 146: [09:35:50] test github issue 256: handling of zero-atom molecules 146: 146: [09:35:50] --------------------------------- 146: [09:35:50] test embedder callback function 146: [09:35:50] --------------------------------- 146: [09:35:50] test multi-threaded multi-conf embedding 146: 146: [09:35:52] --------------------------------- 146: [09:35:52] test github issue 563: Incorrect ring stereochemistry after embedding 146: 146: CNC[C@H]1CC[C@H](C[NH3+])CC1 178/236 Test #183: substructLibraryTest ................... Passed 2.29 sec test 184 Start 184: substructLibraryCatchTest 184: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 184: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary 184: Test timeout computed to be: 1500 184: Randomness seeded to: 4246416239 184: =============================================================================== 184: All tests passed (171 assertions in 5 test cases) 184: 179/236 Test #184: substructLibraryCatchTest .............. Passed 0.07 sec test 185 Start 185: pySubstructLibrary 185: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 185: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 185: Test timeout computed to be: 1500 146: [09:35:53] --------------------------------- 146: [09:35:53] test github issue 568: Incorrect stereochemistry after embedding 146: 146: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 146: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 146: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 146: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 146: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O 185: ......[09:35:54] 185: 185: **** 185: Pre-condition Violation 185: RingInfo not initialized 185: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp 185: Failed Expression: df_init 185: ---------- 185: Stacktrace: 185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 185: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 185: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 185: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 185: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 12# 0x00007FCFF9E5D1D5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 14# 0x00007FCFFC2EE62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 185: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 185: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 185: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 20# 0x00007FCFF9DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 21# 0x00007FCFF9DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 22# 0x00007FCFF9DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 23# 0x00007FCFF9DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 24# 0x00007FCFF9DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 29# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 30# 0x00007FCFFC2EB3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 31# _PyObject_MakeTpCall in /usr/bin/python3 185: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 33# 0x00000000005C30D9 in /usr/bin/python3 185: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 35# 0x000000000064B89F in /usr/bin/python3 185: 36# 0x000000000069ECA0 in /usr/bin/python3 185: 37# _PyObject_MakeTpCall in /usr/bin/python3 185: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 39# 0x00000000005C30D9 in /usr/bin/python3 185: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 41# 0x000000000064B89F in /usr/bin/python3 185: 42# 0x000000000069ECA0 in /usr/bin/python3 185: 43# _PyObject_MakeTpCall in /usr/bin/python3 185: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 45# 0x00000000005C30D9 in /usr/bin/python3 185: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 47# 0x000000000064B89F in /usr/bin/python3 185: 48# 0x000000000069ECA0 in /usr/bin/python3 185: 49# _PyObject_MakeTpCall in /usr/bin/python3 185: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 51# 0x0000000000599C8E in /usr/bin/python3 185: 52# _PyObject_MakeTpCall in /usr/bin/python3 185: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 54# PyEval_EvalCode in /usr/bin/python3 185: 55# 0x000000000066DA21 in /usr/bin/python3 185: 56# 0x0000000000669A8C in /usr/bin/python3 185: 57# 0x0000000000682973 in /usr/bin/python3 185: 58# 0x0000000000682273 in /usr/bin/python3 185: 59# 0x00000000006820AE in /usr/bin/python3 185: 60# Py_RunMain in /usr/bin/python3 185: 61# Py_BytesMain in /usr/bin/python3 185: 62# 0x00007FCFFCC92CA8 in /lib/x86_64-linux-gnu/libc.so.6 185: 63# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 185: 64# _start in /usr/bin/python3 185: ---------- 185: **** 185: 185: [09:35:54] 185: 185: **** 185: Pre-condition Violation 185: RingInfo not initialized 185: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp 185: Failed Expression: df_init 185: ---------- 185: Stacktrace: 185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 185: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 185: 3# 0x00007FCFF98E6800 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 185: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 185: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 13# 0x00007FCFF9E5D1D5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 15# 0x00007FCFFC2EE62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 185: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 185: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 185: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 21# 0x00007FCFF9DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 22# 0x00007FCFF9DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 23# 0x00007FCFF9DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 24# 0x00007FCFF9DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 25# 0x00007FCFF9DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 30# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 31# 0x00007FCFFC2EB3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 32# _PyObject_MakeTpCall in /usr/bin/python3 185: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 34# 0x00000000005C30D9 in /usr/bin/python3 185: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 36# 0x000000000064B89F in /usr/bin/python3 185: 37# 0x000000000069ECA0 in /usr/bin/python3 185: 38# _PyObject_MakeTpCall in /usr/bin/python3 185: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 40# 0x00000000005C30D9 in /usr/bin/python3 185: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 42# 0x000000000064B89F in /usr/bin/python3 185: 43# 0x000000000069ECA0 in /usr/bin/python3 185: 44# _PyObject_MakeTpCall in /usr/bin/python3 185: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 46# 0x00000000005C30D9 in /usr/bin/python3 185: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 48# 0x000000000064B89F in /usr/bin/python3 185: 49# 0x000000000069ECA0 in /usr/bin/python3 185: 50# _PyObject_MakeTpCall in /usr/bin/python3 185: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 52# 0x0000000000599C8E in /usr/bin/python3 185: 53# _PyObject_MakeTpCall in /usr/bin/python3 185: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 55# PyEval_EvalCode in /usr/bin/python3 185: 56# 0x000000000066DA21 in /usr/bin/python3 185: 57# 0x0000000000669A8C in /usr/bin/python3 185: 58# 0x0000000000682973 in /usr/bin/python3 185: 59# 0x0000000000682273 in /usr/bin/python3 185: 60# 0x00000000006820AE in /usr/bin/python3 185: 61# Py_RunMain in /usr/bin/python3 185: 62# Py_BytesMain in /usr/bin/python3 185: 63# 0x00007FCFFCC92CA8 in /lib/x86_64-linux-gnu/libc.so.6 185: 64# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 185: 65# _start in /usr/bin/python3 185: ---------- 185: **** 185: 146: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC 146: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O 185: ............. 185: ---------------------------------------------------------------------- 185: Ran 19 tests in 3.002s 185: 185: OK 185: Testing atom rings 185: testing bond rings 185: searching atom rings 185: searching bond rings 185: done 180/236 Test #185: pySubstructLibrary ..................... Passed 3.16 sec test 186 Start 186: testRGroupDecomp 186: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 186: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 186: Test timeout computed to be: 1500 186: [09:35:56] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters 186: [09:35:56] WARNING: not removing hydrogen atom with dummy atom neighbors 146: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 146: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 146: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 146: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 186: iterative 186: bulk 146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 146: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O 146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 186: bulk, no symmetry 146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 186: [09:35:59] Relabelling existing label 186: Best mapping 181/236 Test #186: testRGroupDecomp ....................... Passed 3.61 sec test 187 Start 187: testRGroupDecompInternals 187: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 187: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 187: Test timeout computed to be: 1500 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 187: [09:35:59] WARNING: not removing hydrogen atom with dummy atom neighbors 182/236 Test #187: testRGroupDecompInternals .............. Passed 0.02 sec test 188 Start 188: rgroupCatchTests 188: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 188: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 188: Test timeout computed to be: 1500 188: Randomness seeded to: 1290934530 188: =============================================================================== 188: All tests passed (1475 assertions in 14 test cases) 188: 183/236 Test #188: rgroupCatchTests ....................... Passed 0.13 sec test 189 Start 189: pyRGroupDecomposition 189: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 189: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 189: Test timeout computed to be: 1500 146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 146: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 171: =============================================================================== 171: All tests passed (93 assertions in 5 test cases) 171: 184/236 Test #171: testRascalCluster ...................... Passed 22.92 sec test 190 Start 190: molInterchangeTest1 190: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 190: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 190: Test timeout computed to be: 1500 190: [09:36:00] test1: basics 190: [09:36:00] done 190: [09:36:00] test2: basic writing 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,0]}]}]} 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]} 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]} 190: [09:36:00] done 190: [09:36:00] test3: writing conformers 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1988,-0.0452],[-0.3332,0.4556],[0.166,1.322],[0.5332,-0.0438],[-2.0652,0.4542],[-0.834,1.3212]]},{"dim":3,"coords":[[0.9554,-0.3743,-0.4679],[-0.3616,-0.1311,-0.0795],[-0.5097,1.6256,0.1706],[-0.5779,-0.792,1.1042],[1.5277,0.1064,0.1628],[-1.0339,-0.4346,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} 190: [09:36:00] done 190: [09:36:00] test4: writing properties 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,0]}]}]} 190: [09:36:00] done 190: [09:36:00] test5: writing partial charges 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[0.5,-0.5]}]}]} 190: [09:36:00] testing parse options 190: [09:36:00] done 190: [09:36:00] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} 190: [09:36:00] done 190: [09:36:00] testing 'either' stereochemistry 190: [09:36:00] done 185/236 Test #190: molInterchangeTest1 .................... Passed 0.02 sec test 191 Start 191: molInterchangeCatchTest 191: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 191: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 191: Test timeout computed to be: 1500 191: Randomness seeded to: 2026879411 191: [09:36:00] unrecognized bond type 12 set to zero while writing 191: [09:36:00] unrecognized bond type 0 set to zero while writing 191: =============================================================================== 191: All tests passed (125 assertions in 7 test cases) 191: 186/236 Test #191: molInterchangeCatchTest ................ Passed 0.02 sec test 192 Start 192: pyMolInterchange 192: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 192: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 192: Test timeout computed to be: 1500 189: .................... 189: ---------------------------------------------------------------------- 189: Ran 20 tests in 0.671s 189: 189: OK 187/236 Test #189: pyRGroupDecomposition .................. Passed 0.83 sec test 193 Start 193: testSLNParse 193: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 193: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse 193: Test timeout computed to be: 1500 193: Atoms: 193: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb: 193: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 193: 2 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 193: 3 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 193: 4 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 193: 5 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 193: Bonds: 193: 0 0->1 order: 1 193: 1 0->2 order: 1 193: 2 0->3 order: 1 193: 3 0->4 order: 1 193: 4 0->5 order: 1 193: [09:36:00] SLN Parse Error: syntax error while parsing: CH4[I=13] 193: [09:36:00] Failed parsing SLN 'CH4[I=13]' 193: [09:36:00] SLN Parser error: Atom ID 1 appears *after* its ring closure. 193: [09:36:00] SLN Parser error: Ring closure 1 does not have a corresponding opener. 193: [09:36:00] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) 193: [09:36:00] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' 193: [09:36:00] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) 193: [09:36:00] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' 193: [09:36:00] SLN Parse Error: syntax error while parsing: CH4 fff 193: [09:36:00] Failed parsing SLN 'CH4 fff' 193: [09:36:00] SLN Parse Error: syntax error while parsing: C[charge=+1] foo 193: [09:36:00] Failed parsing SLN 'C[charge=+1] foo' 193: [09:36:00] Query property 'is' ignored on non-query atom 193: [09:36:00] Query property 'is' ignored on non-query atom 188/236 Test #193: testSLNParse ........................... Passed 0.02 sec test 194 Start 194: pySLNParse 194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/testSLN.py" 194: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap 194: Test timeout computed to be: 1500 192: .. 192: ---------------------------------------------------------------------- 192: Ran 2 tests in 0.006s 192: 192: OK 189/236 Test #192: pyMolInterchange ....................... Passed 0.14 sec test 195 Start 195: pyGraphMolWrap 195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rough_test.py" 195: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 195: Test timeout computed to be: 1500 146: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 194: .. 194: ---------------------------------------------------------------------- 194: Ran 2 tests in 0.005s 194: 194: OK 190/236 Test #194: pySLNParse ............................. Passed 0.13 sec test 196 Start 196: pyTestConformerWrap 196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testConformer.py" 196: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 196: Test timeout computed to be: 1500 146: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 196: ...... 196: ---------------------------------------------------------------------- 196: Ran 6 tests in 0.007s 196: 196: OK 195: ..............[09:36:00] SMARTS Parse Error: syntax error while parsing: fiib 195: [09:36:00] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' 195: ....[09:36:00] ERROR: Problems encountered parsing data fields 195: [09:36:00] ERROR: moving to the beginning of the next molecule 195: [09:36:00] ERROR: Problems encountered parsing data fields 195: [09:36:00] ERROR: moving to the beginning of the next molecule 195: [09:36:00] Spurious data before the first property will be ignored 195: [09:36:00] Property will be truncated after the first blank line 195: [09:36:00] Property will be truncated after the first blank line 195: [09:36:00] Property will be truncated after the first blank line 195: [09:36:00] ERROR: Problems encountered parsing data fields 195: [09:36:00] ERROR: moving to the beginning of the next molecule 195: [09:36:00] ERROR: Problems encountered parsing data fields 195: [09:36:00] ERROR: moving to the beginning of the next molecule 195: [09:36:00] Spurious data before the first property will be ignored 195: [09:36:00] Property will be truncated after the first blank line 195: [09:36:00] Property will be truncated after the first blank line 195: [09:36:00] Property will be truncated after the first blank line 195: [09:36:00] ERROR: Problems encountered parsing data fields 195: [09:36:00] ERROR: moving to the beginning of the next molecule 195: [09:36:00] Property will be truncated after the first blank line 195: [09:36:00] ERROR: Problems encountered parsing data fields 195: [09:36:00] ERROR: moving to the beginning of the next molecule 195: [09:36:00] Property will be truncated after the first blank line 195: .[09:36:00] SMILES Parse Error: syntax error while parsing: fail 195: [09:36:00] SMILES Parse Error: check for mistakes around position 1: 195: [09:36:00] fail 195: [09:36:00] ^ 195: [09:36:00] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' 195: [09:36:00] ERROR: Smiles parse error on line 2 195: [09:36:00] ERROR: Cannot create molecule from : 'fail' 195: >>> This may result in an infinite loop. It should finish almost instantly 195: <<< OK, it finished. 191/236 Test #196: pyTestConformerWrap .................... Passed 0.14 sec test 197 Start 197: pyTestTrajectory 197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testTrajectory.py" 197: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 197: Test timeout computed to be: 1500 195: ............[09:36:00] Explicit valence for atom # 1 C, 5, is greater than permitted 195: ......[09:36:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 195: [09:36:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 195: [09:36:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 195: [09:36:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 195: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| 195: ........[09:36:01] non-ring atom 0 marked aromatic 195: [09:36:01] non-ring atom 0 marked aromatic 195: [09:36:01] 195: 195: **** 195: Range Error 195: idx 195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 195: Failed Expression: 12 < 6 195: ---------- 195: Stacktrace: 195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 4# 0x00007F14F7084A70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# 0x00007F14F97D962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 17# 0x00007F14F6FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 18# 0x00007F14F6FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 19# 0x00007F14F6FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 20# 0x00007F14F6FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# 0x00007F14F6FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# 0x00007F14F97D63C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 28# _PyObject_MakeTpCall in /usr/bin/python3 195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 30# 0x00000000005C30D9 in /usr/bin/python3 195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 32# 0x000000000064B89F in /usr/bin/python3 195: 33# 0x000000000069ECA0 in /usr/bin/python3 195: 34# _PyObject_MakeTpCall in /usr/bin/python3 195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 36# 0x00000000005C30D9 in /usr/bin/python3 195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 38# 0x000000000064B89F in /usr/bin/python3 195: 39# 0x000000000069ECA0 in /usr/bin/python3 195: 40# _PyObject_MakeTpCall in /usr/bin/python3 195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 42# 0x00000000005C30D9 in /usr/bin/python3 195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 44# 0x000000000064B89F in /usr/bin/python3 195: 45# 0x000000000069ECA0 in /usr/bin/python3 195: 46# _PyObject_MakeTpCall in /usr/bin/python3 195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 48# 0x0000000000599C8E in /usr/bin/python3 195: 49# _PyObject_MakeTpCall in /usr/bin/python3 195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 51# PyEval_EvalCode in /usr/bin/python3 195: 52# 0x000000000066DA21 in /usr/bin/python3 195: 53# 0x0000000000669A8C in /usr/bin/python3 195: 54# 0x0000000000682973 in /usr/bin/python3 195: 55# 0x0000000000682273 in /usr/bin/python3 195: 56# 0x00000000006820AE in /usr/bin/python3 195: 57# Py_RunMain in /usr/bin/python3 195: 58# Py_BytesMain in /usr/bin/python3 195: 59# 0x00007F14FA014CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 61# _start in /usr/bin/python3 195: ---------- 195: **** 195: 195: [09:36:01] non-ring atom 0 marked aromatic 195: [09:36:01] non-ring atom 0 marked aromatic 195: [09:36:01] 195: 195: **** 195: Range Error 195: idx 195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 195: Failed Expression: 12 < 6 195: ---------- 195: Stacktrace: 195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 4# 0x00007F14F7084A70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# 0x00007F14F97D962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 17# 0x00007F14F6FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 18# 0x00007F14F6FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 19# 0x00007F14F6FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 20# 0x00007F14F6FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# 0x00007F14F6FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# 0x00007F14F97D63C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 28# _PyObject_MakeTpCall in /usr/bin/python3 195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 30# 0x00000000005C30D9 in /usr/bin/python3 195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 32# 0x000000000064B89F in /usr/bin/python3 195: 33# 0x000000000069ECA0 in /usr/bin/python3 195: 34# _PyObject_MakeTpCall in /usr/bin/python3 195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 36# 0x00000000005C30D9 in /usr/bin/python3 195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 38# 0x000000000064B89F in /usr/bin/python3 195: 39# 0x000000000069ECA0 in /usr/bin/python3 195: 40# _PyObject_MakeTpCall in /usr/bin/python3 195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 42# 0x00000000005C30D9 in /usr/bin/python3 195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 44# 0x000000000064B89F in /usr/bin/python3 195: 45# 0x000000000069ECA0 in /usr/bin/python3 195: 46# _PyObject_MakeTpCall in /usr/bin/python3 195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 48# 0x0000000000599C8E in /usr/bin/python3 195: 49# _PyObject_MakeTpCall in /usr/bin/python3 195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 51# PyEval_EvalCode in /usr/bin/python3 195: 52# 0x000000000066DA21 in /usr/bin/python3 195: 53# 0x0000000000669A8C in /usr/bin/python3 195: 54# 0x0000000000682973 in /usr/bin/python3 195: 55# 0x0000000000682273 in /usr/bin/python3 195: 56# 0x00000000006820AE in /usr/bin/python3 195: 57# Py_RunMain in /usr/bin/python3 195: 58# Py_BytesMain in /usr/bin/python3 195: 59# 0x00007F14FA014CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 61# _start in /usr/bin/python3 195: ---------- 195: **** 195: 195: ...............[09:36:01] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. 195: [09:36:01] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. 195: ..............[09:36:01] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 195: [09:36:01] Explicit valence for atom # 1 C, 5, is greater than permitted 197: [09:36:01] 197: 197: **** 197: Pre-condition Violation 197: from must be < size() 197: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 197: Failed Expression: from < static_cast(size()) 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 5# 0x00007F921687B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 11# 0x00007F92143B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 12# 0x00007F92143B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 13# 0x00007F92143B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 14# 0x00007F92143B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 15# 0x00007F92143B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 21# 0x00007F92168783C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 26# 0x000000000064B89F in /usr/bin/python3 197: 27# 0x000000000069ECA0 in /usr/bin/python3 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x00000000005C30D9 in /usr/bin/python3 197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 32# 0x000000000064B89F in /usr/bin/python3 197: 33# 0x000000000069ECA0 in /usr/bin/python3 197: 34# _PyObject_MakeTpCall in /usr/bin/python3 197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 36# 0x00000000005C30D9 in /usr/bin/python3 197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 38# 0x000000000064B89F in /usr/bin/python3 197: 39# 0x000000000069ECA0 in /usr/bin/python3 197: 40# _PyObject_MakeTpCall in /usr/bin/python3 197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 42# 0x0000000000599C8E in /usr/bin/python3 197: 43# _PyObject_MakeTpCall in /usr/bin/python3 197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 45# PyEval_EvalCode in /usr/bin/python3 197: 46# 0x000000000066DA21 in /usr/bin/python3 197: 47# 0x0000000000669A8C in /usr/bin/python3 197: 48# 0x0000000000682973 in /usr/bin/python3 197: 49# 0x0000000000682273 in /usr/bin/python3 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 197: 53# 0x00007F9217085CA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: 197: .[09:36:01] 197: 197: **** 197: Pre-condition Violation 197: from must be < size() 197: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 197: Failed Expression: from < static_cast(size()) 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 5# 0x00007F921687B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 11# 0x00007F92143B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 12# 0x00007F92143B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 13# 0x00007F92143B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 14# 0x00007F92143B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 15# 0x00007F92143B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 21# 0x00007F92168783C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 26# 0x000000000064B89F in /usr/bin/python3 197: 27# 0x000000000069ECA0 in /usr/bin/python3 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x00000000005C30D9 in /usr/bin/python3 197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 32# 0x000000000064B89F in /usr/bin/python3 197: 33# 0x000000000069ECA0 in /usr/bin/python3 197: 34# _PyObject_MakeTpCall in /usr/bin/python3 197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 36# 0x00000000005C30D9 in /usr/bin/python3 197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 38# 0x000000000064B89F in /usr/bin/python3 197: 39# 0x000000000069ECA0 in /usr/bin/python3 197: 40# _PyObject_MakeTpCall in /usr/bin/python3 197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 42# 0x0000000000599C8E in /usr/bin/python3 197: 43# _PyObject_MakeTpCall in /usr/bin/python3 197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 45# PyEval_EvalCode in /usr/bin/python3 197: 46# 0x000000000066DA21 in /usr/bin/python3 197: 47# 0x0000000000669A8C in /usr/bin/python3 197: 48# 0x0000000000682973 in /usr/bin/python3 197: 49# 0x0000000000682273 in /usr/bin/python3 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 197: 53# 0x00007F9217085CA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: 197: .[09:36:01] 197: 197: **** 197: Range Error 197: snapshotNum 197: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 197: Failed Expression: 0 < 0 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::Trajectory::getSnapshot(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# 0x00007F921687B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 12# 0x00007F92143B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 13# 0x00007F92143B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 14# 0x00007F92143B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 15# 0x00007F92143B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# 0x00007F92143B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# 0x00007F92168783C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x00000000005C30D9 in /usr/bin/python3 197: 26# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 27# 0x000000000064B89F in /usr/bin/python3 197: 28# 0x000000000069ECA0 in /usr/bin/python3 197: 29# _PyObject_MakeTpCall in /usr/bin/python3 197: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 31# 0x00000000005C30D9 in /usr/bin/python3 197: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 33# 0x000000000064B89F in /usr/bin/python3 197: 34# 0x000000000069ECA0 in /usr/bin/python3 197: 35# _PyObject_MakeTpCall in /usr/bin/python3 197: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 37# 0x00000000005C30D9 in /usr/bin/python3 197: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 39# 0x000000000064B89F in /usr/bin/python3 197: 40# 0x000000000069ECA0 in /usr/bin/python3 197: 41# _PyObject_MakeTpCall in /usr/bin/python3 197: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 43# 0x0000000000599C8E in /usr/bin/python3 197: 44# _PyObject_MakeTpCall in /usr/bin/python3 197: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 46# PyEval_EvalCode in /usr/bin/python3 197: 47# 0x000000000066DA21 in /usr/bin/python3 197: 48# 0x0000000000669A8C in /usr/bin/python3 197: 49# 0x0000000000682973 in /usr/bin/python3 197: 50# 0x0000000000682273 in /usr/bin/python3 197: 51# 0x00000000006820AE in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 197: 54# 0x00007F9217085CA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: 197: .[09:36:01] 197: 197: **** 195: ............................[09:36:01] unable to set wavy bonds for double bonds: 3 197: Pre-condition Violation 197: The trajectory must have dimension == 3 197: Violation occurred on line 113 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 197: Failed Expression: traj.dimension() == 3 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 5# 0x00007F921687B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 11# 0x00007F92143B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 12# 0x00007F92143B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 13# 0x00007F92143B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 14# 0x00007F92143B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 15# 0x00007F92143B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 21# 0x00007F92168783C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 26# 0x000000000064B89F in /usr/bin/python3 197: 27# 0x000000000069ECA0 in /usr/bin/python3 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x00000000005C30D9 in /usr/bin/python3 197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 32# 0x000000000064B89F in /usr/bin/python3 197: 33# 0x000000000069ECA0 in /usr/bin/python3 197: 34# _PyObject_MakeTpCall in /usr/bin/python3 197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 36# 0x00000000005C30D9 in /usr/bin/python3 197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 38# 0x000000000064B89F in /usr/bin/python3 197: 39# 0x000000000069ECA0 in /usr/bin/python3 197: 40# _PyObject_MakeTpCall in /usr/bin/python3 197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 42# 0x0000000000599C8E in /usr/bin/python3 197: 43# _PyObject_MakeTpCall in /usr/bin/python3 197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 45# PyEval_EvalCode in /usr/bin/python3 197: 46# 0x000000000066DA21 in /usr/bin/python3 197: 47# 0x0000000000669A8C in /usr/bin/python3 197: 48# 0x0000000000682973 in /usr/bin/python3 197: 49# 0x0000000000682273 in /usr/bin/python3 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 197: 53# 0x00007F9217085CA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: 197: ..[09:36:01] 197: 197: **** 197: Pre-condition Violation 197: The trajectory must have dimension == 3 197: Violation occurred on line 154 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 197: Failed Expression: traj.dimension() == 3 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 5# 0x00007F921687B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 11# 0x00007F92143B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 12# 0x00007F92143B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 13# 0x00007F92143B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 14# 0x00007F92143B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 15# 0x00007F92143B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 21# 0x00007F92168783C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 26# 0x000000000064B89F in /usr/bin/python3 197: 27# 0x000000000069ECA0 in /usr/bin/python3 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x00000000005C30D9 in /usr/bin/python3 197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 32# 0x000000000064B89F in /usr/bin/python3 197: 33# 0x000000000069ECA0 in /usr/bin/python3 197: 34# _PyObject_MakeTpCall in /usr/bin/python3 197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 36# 0x00000000005C30D9 in /usr/bin/python3 197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 38# 0x000000000064B89F in /usr/bin/python3 197: 39# 0x000000000069ECA0 in /usr/bin/python3 197: 40# _PyObject_MakeTpCall in /usr/bin/python3 197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 42# 0x0000000000599C8E in /usr/bin/python3 197: 43# _PyObject_MakeTpCall in /usr/bin/python3 197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 45# PyEval_EvalCode in /usr/bin/python3 197: 46# 0x000000000066DA21 in /usr/bin/python3 197: 47# 0x0000000000669A8C in /usr/bin/python3 197: 48# 0x0000000000682973 in /usr/bin/python3 197: 49# 0x0000000000682273 in /usr/bin/python3 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 197: 53# 0x00007F9217085CA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: 197: .[09:36:01] 197: 197: **** 197: Pre-condition Violation 197: d_pos must not be NULL 197: Violation occurred on line 23 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 197: Failed Expression: d_pos 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 5# 0x00007F921687B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 11# 0x00007F92143B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 12# 0x00007F92143B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 13# 0x00007F92143B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 14# 0x00007F92143B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 15# 0x00007F92143B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 21# 0x00007F92168783C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 26# 0x000000000064B89F in /usr/bin/python3 197: 27# 0x000000000069ECA0 in /usr/bin/python3 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x00000000005C30D9 in /usr/bin/python3 197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 32# 0x000000000064B89F in /usr/bin/python3 197: 33# 0x000000000069ECA0 in /usr/bin/python3 197: 34# _PyObject_MakeTpCall in /usr/bin/python3 197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 36# 0x00000000005C30D9 in /usr/bin/python3 197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 38# 0x000000000064B89F in /usr/bin/python3 197: 39# 0x000000000069ECA0 in /usr/bin/python3 197: 40# _PyObject_MakeTpCall in /usr/bin/python3 197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 42# 0x0000000000599C8E in /usr/bin/python3 197: 43# _PyObject_MakeTpCall in /usr/bin/python3 197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 45# PyEval_EvalCode in /usr/bin/python3 197: 46# 0x000000000066DA21 in /usr/bin/python3 197: 47# 0x0000000000669A8C in /usr/bin/python3 197: 48# 0x0000000000682973 in /usr/bin/python3 197: 49# 0x0000000000682273 in /usr/bin/python3 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 197: 53# 0x00007F9217085CA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: 197: [09:36:01] 197: 197: **** 197: Pre-condition Violation 197: d_trajectory must not be NULL 197: Violation occurred on line 24 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 197: Failed Expression: d_trajectory 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 5# 0x00007F921687B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 11# 0x00007F92143B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 12# 0x00007F92143B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 13# 0x00007F92143B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 14# 0x00007F92143B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 15# 0x00007F92143B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 21# 0x00007F92168783C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 26# 0x000000000064B89F in /usr/bin/python3 197: 27# 0x000000000069ECA0 in /usr/bin/python3 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x00000000005C30D9 in /usr/bin/python3 197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 32# 0x000000000064B89F in /usr/bin/python3 197: 33# 0x000000000069ECA0 in /usr/bin/python3 197: 34# _PyObject_MakeTpCall in /usr/bin/python3 197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 36# 0x00000000005C30D9 in /usr/bin/python3 197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 38# 0x000000000064B89F in /usr/bin/python3 197: 39# 0x000000000069ECA0 in /usr/bin/python3 197: 40# _PyObject_MakeTpCall in /usr/bin/python3 197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 42# 0x0000000000599C8E in /usr/bin/python3 197: 43# _PyObject_MakeTpCall in /usr/bin/python3 197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 45# PyEval_EvalCode in /usr/bin/python3 197: 46# 0x000000000066DA21 in /usr/bin/python3 197: 47# 0x0000000000669A8C in /usr/bin/python3 197: 48# 0x0000000000682973 in /usr/bin/python3 197: 49# 0x0000000000682273 in /usr/bin/python3 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 197: 53# 0x00007F9217085CA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: 197: .[09:36:01] 197: 197: **** 197: Range Error 197: snapshotNum 197: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 197: Failed Expression: 5 < 5 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::Trajectory::getSnapshot(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# 0x00007F921687B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 12# 0x00007F92143B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 13# 0x00007F92143B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 14# 0x00007F92143B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 15# 0x00007F92143B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# 0x00007F92143B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# 0x00007F92168783C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x00000000005C30D9 in /usr/bin/python3 197: 26# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 27# 0x000000000064B89F in /usr/bin/python3 197: 28# 0x000000000069ECA0 in /usr/bin/python3 197: 29# _PyObject_MakeTpCall in /usr/bin/python3 197: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 31# 0x00000000005C30D9 in /usr/bin/python3 197: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 33# 0x000000000064B89F in /usr/bin/python3 197: 34# 0x000000000069ECA0 in /usr/bin/python3 197: 35# _PyObject_MakeTpCall in /usr/bin/python3 197: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 37# 0x00000000005C30D9 in /usr/bin/python3 197: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 39# 0x000000000064B89F in /usr/bin/python3 197: 40# 0x000000000069ECA0 in /usr/bin/python3 197: 41# _PyObject_MakeTpCall in /usr/bin/python3 197: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 43# 0x0000000000599C8E in /usr/bin/python3 197: 44# _PyObject_MakeTpCall in /usr/bin/python3 197: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 46# PyEval_EvalCode in /usr/bin/python3 197: 47# 0x000000000066DA21 in /usr/bin/python3 197: 48# 0x0000000000669A8C in /usr/bin/python3 197: 49# 0x0000000000682973 in /usr/bin/python3 197: 50# 0x0000000000682273 in /usr/bin/python3 197: 51# 0x00000000006820AE in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 197: 54# 0x00007F9217085CA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: 197: [09:36:01] 197: 197: **** 197: Range Error 197: pointNum 197: Violation occurred on line 27 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 197: Failed Expression: 10 < 10 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 5# 0x00007F921687B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 11# 0x00007F92143B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 12# 0x00007F92143B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 13# 0x00007F92143B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 14# 0x00007F92143B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 15# 0x00007F92143B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 21# 0x00007F92168783C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 26# 0x000000000064B89F in /usr/bin/python3 197: 27# 0x000000000069ECA0 in /usr/bin/python3 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x00000000005C30D9 in /usr/bin/python3 197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 32# 0x000000000064B89F in /usr/bin/python3 197: 33# 0x000000000069ECA0 in /usr/bin/python3 197: 34# _PyObject_MakeTpCall in /usr/bin/python3 197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 36# 0x00000000005C30D9 in /usr/bin/python3 197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 38# 0x000000000064B89F in /usr/bin/python3 197: 39# 0x000000000069ECA0 in /usr/bin/python3 197: 40# _PyObject_MakeTpCall in /usr/bin/python3 197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 42# 0x0000000000599C8E in /usr/bin/python3 197: 43# _PyObject_MakeTpCall in /usr/bin/python3 197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 45# PyEval_EvalCode in /usr/bin/python3 197: 46# 0x000000000066DA21 in /usr/bin/python3 197: 47# 0x0000000000669A8C in /usr/bin/python3 197: 48# 0x0000000000682973 in /usr/bin/python3 197: 49# 0x0000000000682273 in /usr/bin/python3 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 197: 53# 0x00007F9217085CA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: 197: .[09:36:01] 197: 197: **** 197: Range Error 197: snapshotNum 197: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 197: Failed Expression: 5 < 5 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::Trajectory::getSnapshot(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# 0x00007F921687B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 12# 0x00007F92143B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 13# 0x00007F92143B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 14# 0x00007F92143B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 15# 0x00007F92143B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# 0x00007F92143B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# 0x00007F92168783C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x00000000005C30D9 in /usr/bin/python3 197: 26# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 27# 0x000000000064B89F in /usr/bin/python3 197: 28# 0x000000000069ECA0 in /usr/bin/python3 197: 29# _PyObject_MakeTpCall in /usr/bin/python3 197: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 31# 0x00000000005C30D9 in /usr/bin/python3 197: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 33# 0x000000000064B89F in /usr/bin/python3 197: 34# 0x000000000069ECA0 in /usr/bin/python3 197: 35# _PyObject_MakeTpCall in /usr/bin/python3 197: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 37# 0x00000000005C30D9 in /usr/bin/python3 197: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 39# 0x000000000064B89F in /usr/bin/python3 197: 40# 0x000000000069ECA0 in /usr/bin/python3 197: 41# _PyObject_MakeTpCall in /usr/bin/python3 197: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 43# 0x0000000000599C8E in /usr/bin/python3 197: 44# _PyObject_MakeTpCall in /usr/bin/python3 197: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 46# PyEval_EvalCode in /usr/bin/python3 197: 47# 0x000000000066DA21 in /usr/bin/python3 197: 48# 0x0000000000669A8C in /usr/bin/python3 197: 49# 0x0000000000682973 in /usr/bin/python3 197: 50# 0x0000000000682273 in /usr/bin/python3 197: 51# 0x00000000006820AE in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 197: 54# 0x00007F9217085CA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: 197: [09:36:01] 197: 197: **** 197: Pre-condition Violation 197: d_dimension must be == 2 197: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 197: Failed Expression: d_trajectory->dimension() == 2 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 5# 0x00007F921687B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 11# 0x00007F92143B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 12# 0x00007F92143B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 13# 0x00007F92143B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 14# 0x00007F92143B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 15# 0x00007F92143B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 21# 0x00007F92168783C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 26# 0x000000000064B89F in /usr/bin/python3 197: 27# 0x000000000069ECA0 in /usr/bin/python3 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x00000000005C30D9 in /usr/bin/python3 197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 32# 0x000000000064B89F in /usr/bin/python3 197: 33# 0x000000000069ECA0 in /usr/bin/python3 197: 34# _PyObject_MakeTpCall in /usr/bin/python3 197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 36# 0x00000000005C30D9 in /usr/bin/python3 197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 38# 0x000000000064B89F in /usr/bin/python3 197: 39# 0x000000000069ECA0 in /usr/bin/python3 197: 40# _PyObject_MakeTpCall in /usr/bin/python3 197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 42# 0x0000000000599C8E in /usr/bin/python3 197: 43# _PyObject_MakeTpCall in /usr/bin/python3 197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 45# PyEval_EvalCode in /usr/bin/python3 197: 46# 0x000000000066DA21 in /usr/bin/python3 197: 47# 0x0000000000669A8C in /usr/bin/python3 197: 48# 0x0000000000682973 in /usr/bin/python3 197: 49# 0x0000000000682273 in /usr/bin/python3 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 197: 53# 0x00007F9217085CA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: 197: [09:36:01] 197: 197: **** 195: .............[09:36:01] 195: 195: **** 197: Pre-condition Violation 197: d_dimension must be == 2 197: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 197: Failed Expression: d_trajectory->dimension() == 2 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 5# 0x00007F921687B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 11# 0x00007F92143B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 12# 0x00007F92143B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 13# 0x00007F92143B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 14# 0x00007F92143B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 15# 0x00007F92143B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 21# 0x00007F92168783C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 26# 0x000000000064B89F in /usr/bin/python3 197: 27# 0x000000000069ECA0 in /usr/bin/python3 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x00000000005C30D9 in /usr/bin/python3 197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 32# 0x000000000064B89F in /usr/bin/python3 197: 33# 0x000000000069ECA0 in /usr/bin/python3 197: 34# _PyObject_MakeTpCall in /usr/bin/python3 197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 36# 0x00000000005C30D9 in /usr/bin/python3 197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 38# 0x000000000064B89F in /usr/bin/python3 197: 39# 0x000000000069ECA0 in /usr/bin/python3 197: 40# _PyObject_MakeTpCall in /usr/bin/python3 197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 42# 0x0000000000599C8E in /usr/bin/python3 197: 43# _PyObject_MakeTpCall in /usr/bin/python3 197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 45# PyEval_EvalCode in /usr/bin/python3 197: 46# 0x000000000066DA21 in /usr/bin/python3 197: 47# 0x0000000000669A8C in /usr/bin/python3 197: 48# 0x0000000000682973 in /usr/bin/python3 197: 49# 0x0000000000682273 in /usr/bin/python3 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 197: 53# 0x00007F9217085CA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: 197: . 197: ---------------------------------------------------------------------- 197: Ran 9 tests in 0.173s 197: 197: OK 197: Testing Trajectory wrapper 195: Range Error 195: idx 195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 195: Failed Expression: 6 < 5 195: ---------- 195: Stacktrace: 195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# 0x00007F14F97D962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 17# 0x00007F14F6FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 18# 0x00007F14F6FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 19# 0x00007F14F6FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 20# 0x00007F14F6FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# 0x00007F14F6FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# 0x00007F14F97D63C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 28# _PyObject_MakeTpCall in /usr/bin/python3 195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 30# 0x00000000005C30D9 in /usr/bin/python3 195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 32# 0x000000000064B89F in /usr/bin/python3 195: 33# 0x000000000069ECA0 in /usr/bin/python3 195: 34# _PyObject_MakeTpCall in /usr/bin/python3 195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 36# 0x00000000005C30D9 in /usr/bin/python3 195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 38# 0x000000000064B89F in /usr/bin/python3 195: 39# 0x000000000069ECA0 in /usr/bin/python3 195: 40# _PyObject_MakeTpCall in /usr/bin/python3 195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 42# 0x00000000005C30D9 in /usr/bin/python3 195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 44# 0x000000000064B89F in /usr/bin/python3 195: 45# 0x000000000069ECA0 in /usr/bin/python3 195: 46# _PyObject_MakeTpCall in /usr/bin/python3 195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 48# 0x0000000000599C8E in /usr/bin/python3 195: 49# _PyObject_MakeTpCall in /usr/bin/python3 195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 51# PyEval_EvalCode in /usr/bin/python3 195: 52# 0x000000000066DA21 in /usr/bin/python3 195: 53# 0x0000000000669A8C in /usr/bin/python3 195: 54# 0x0000000000682973 in /usr/bin/python3 195: 55# 0x0000000000682273 in /usr/bin/python3 195: 56# 0x00000000006820AE in /usr/bin/python3 195: 57# Py_RunMain in /usr/bin/python3 195: 58# Py_BytesMain in /usr/bin/python3 195: 59# 0x00007F14FA014CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 61# _start in /usr/bin/python3 195: ---------- 195: **** 195: 192/236 Test #197: pyTestTrajectory ....................... Passed 0.31 sec test 198 Start 198: pyTestSGroups 198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testSGroups.py" 198: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 198: Test timeout computed to be: 1500 146: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 198: ............. 198: ---------------------------------------------------------------------- 198: Ran 13 tests in 0.041s 198: 198: OK 198: Testing SubstanceGroups wrapper 193/236 Test #198: pyTestSGroups .......................... Passed 0.20 sec test 199 Start 199: pyTestThreads 199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testThreads.py" 199: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 199: Test timeout computed to be: 1500 146: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 147: [09:36:01] Interrupted, cancelling conformer generation 147: Atoms: 147: 0 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[9 3 1 6] 147: 1 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[0 13 6 7] 147: 2 7 N chg: 0 deg: 3 exp: 3 imp: 0 hyb: SP2 arom?: 1 147: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 147: 4 7 N chg: 0 deg: 1 exp: 1 imp: 2 hyb: SP3 147: 5 6 C chg: 0 deg: 3 exp: 3 imp: 1 hyb: SP3 chi: CW nbrs:[4 11 7] 147: 6 7 N chg: 0 deg: 2 exp: 2 imp: 0 hyb: SP3 rad: 1 147: 7 7 N chg: 0 deg: 2 exp: 2 imp: 1 hyb: SP3 147: 8 7 N chg: 0 deg: 3 exp: 3 imp: 0 hyb: SP2 arom?: 1 147: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP3 147: 10 8 O chg: 0 deg: 1 exp: 2 imp: 0 hyb: SP2 147: 11 7 N chg: 0 deg: 2 exp: 2 imp: 1 hyb: SP2 147: 12 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 147: 13 8 O chg: 0 deg: 1 exp: 1 imp: 0 hyb: SP3 rad: 1 147: Bonds: 147: 0 0->9 order: 1 147: 1 0->3 order: 1 147: 2 1->0 order: 1 147: 3 1->13 order: 1 147: 4 2->8 order: a conj?: 1 aromatic?: 1 147: 5 2->12 order: a conj?: 1 aromatic?: 1 147: 6 3->10 order: 2 conj?: 1 147: 7 3->8 order: 1 conj?: 1 147: 8 5->4 order: 1 147: 9 11->5 order: 1 147: 10 6->1 order: 1 147: 11 6->0 order: 1 147: 12 7->1 order: 1 147: 13 7->5 order: 1 147: 14 8->12 order: a conj?: 1 aromatic?: 1 147: 15 11->2 order: 1 stereo: CCW bonds: (9 4 5) conj?: 1 147: =============================================================================== 147: All tests passed (12742 assertions in 21 test cases) 147: 194/236 Test #147: distGeomHelpersCatch ................... Passed 46.50 sec test 200 Start 200: pyTestMultithreadedMolSupplier 200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 200: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 200: Test timeout computed to be: 1500 195: ....................[09:36:01] Explicit valence for atom # 1 F, 2, is greater than permitted 195: [09:36:01] Explicit valence for atom # 6 F, 2, is greater than permitted 195: [09:36:01] Can't kekulize mol. Unkekulized atoms: 3 4 5 195: .................[09:36:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 200: .s. 200: ---------------------------------------------------------------------- 200: Ran 3 tests in 0.045s 200: 200: OK (skipped=1) 200: Testing Smiles and SD MultithreadedMolSupplier 195/236 Test #200: pyTestMultithreadedMolSupplier ......... Passed 0.20 sec test 201 Start 201: pyTestPropertyLists 201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testPropertyLists.py" 201: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 201: Test timeout computed to be: 1500 201: [09:36:02] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 201: [09:36:02] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 201: [09:36:02] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 201: .[09:36:02] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 201: [09:36:02] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 201: [09:36:02] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 201: ...[09:36:02] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 201: [09:36:02] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 201: [09:36:02] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 201: . 201: ---------------------------------------------------------------------- 201: Ran 5 tests in 0.006s 201: 201: OK 196/236 Test #201: pyTestPropertyLists .................... Passed 0.14 sec test 202 Start 202: pyCDXMLTest 202: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/test_cdxml.py" 202: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 202: Test timeout computed to be: 1500 197/236 Test #199: pyTestThreads .......................... Passed 0.76 sec test 203 Start 203: molStandardizeTest 203: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 203: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 203: Test timeout computed to be: 1500 202: . 202: ---------------------------------------------------------------------- 202: Ran 1 test in 0.005s 202: 202: OK 198/236 Test #202: pyCDXMLTest ............................ Passed 0.15 sec test 204 Start 204: molNormalizeTest 204: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 204: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 204: Test timeout computed to be: 1500 204: [09:36:02] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 204: [09:36:02] Initializing Normalizer 204: [09:36:02] Running Normalizer 204: [09:36:02] Rule applied: BrokenazidetoN=N+=N- 204: [09:36:02] Initializing Normalizer 204: [09:36:02] Running Normalizer 204: [09:36:02] Initializing Normalizer 204: [09:36:02] Running Normalizer 199/236 Test #204: molNormalizeTest ....................... Passed 0.07 sec test 205 Start 205: molValidateTest 205: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest 205: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 205: Test timeout computed to be: 1500 205: ERROR: [FeaturesValidation] Query atom 0 is not allowed 205: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed 205: ERROR: [FeaturesValidation] Query bond 0 is not allowed 205: ERROR: [FeaturesValidation] Bond 0 of aromatic type is not allowed 205: ERROR: [FeaturesValidation] Bond 1 of aromatic type is not allowed 205: ERROR: [FeaturesValidation] Bond 2 of aromatic type is not allowed 205: ERROR: [FeaturesValidation] Bond 3 of aromatic type is not allowed 205: ERROR: [FeaturesValidation] Bond 5 of aromatic type is not allowed 205: ERROR: [FeaturesValidation] Bond 6 of aromatic type is not allowed 205: ERROR: [FeaturesValidation] Bond 2 of dative type is not allowed 205: ERROR: [FeaturesValidation] Bond 3 of dative type is not allowed 205: ERROR: [FeaturesValidation] Atom 2 with alias 'CF3' is not allowed 205: ERROR: [FeaturesValidation] Enhanced stereochemistry features are not allowed 205: ERROR: [StereoValidation] Atom 3 has both unknown and wedged/dashed stereo bonds. 205: here 205: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. 205: there 205: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. 200/236 Test #205: molValidateTest ........................ Passed 0.03 sec test 206 Start 206: molChargeTest 206: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 206: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 206: Test timeout computed to be: 1500 201/236 Test #206: molChargeTest .......................... Passed 0.04 sec test 207 Start 207: molTautomerTest 207: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 207: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 207: Test timeout computed to be: 1500 146: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 207: [09:36:02] Tautomer enumeration stopped at 292 tautomers: max transforms reached 146: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] 202/236 Test #203: molStandardizeTest ..................... Passed 0.47 sec test 208 Start 208: molStandardizeSmallTest 208: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 208: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 208: Test timeout computed to be: 1500 203/236 Test #208: molStandardizeSmallTest ................ Passed 0.02 sec test 209 Start 209: molFragmentTest 209: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 209: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 209: Test timeout computed to be: 1500 209: [09:36:02] SMARTS Parse Error: syntax error while parsing: [Cl 209: [09:36:02] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' 204/236 Test #209: molFragmentTest ........................ Passed 0.03 sec test 210 Start 210: molStandardizeCatchTest 210: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 210: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 210: Test timeout computed to be: 1500 207: [09:36:02] Tautomer enumeration stopped at 292 tautomers: max transforms reached 207: [09:36:02] Tautomer enumeration stopped at 50 tautomers: max tautomers reached 210: Randomness seeded to: 247607439 210: * - * - * - * m1 210: * - * - * - * m2 210: * - * - * - * m1 210: * - * - * - * m2 210: [09:36:02] Can't kekulize mol. Unkekulized atoms: 3 7 210: [09:36:02] Can't kekulize mol. Unkekulized atoms: 3 8 210: [09:36:02] Can't kekulize mol. Unkekulized atoms: 2 3 4 207: [09:36:02] Tautomer enumeration stopped at 151 tautomers: canceled 207: Enumeration was canceled due to timeout (50 ms) 207: 375 207: Enumeration has completed 207: [09:36:03] Tautomer enumeration stopped at 151 tautomers: canceled 207: CN=c1cc[nH]cn1 207: CN=c1ccnc[nH]1 207: CNc1ccncn1 207: res: CNc1ccncn1 207: CN=c1cccc[nH]1 207: CNc1ccccn1 207: res: CNc1ccccn1 205/236 Test #207: molTautomerTest ........................ Passed 1.24 sec test 211 Start 211: molStandardizePipelineTest 211: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest 211: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 211: Test timeout computed to be: 1500 211: Randomness seeded to: 1420733301 211: 1 Counts line too short: '' on line4 211: 1 Could not instantiate a valid molecule from input 211: 8 Molecule has no atoms 211: [09:36:03] Explicit valence for atom # 1 N, 4, is greater than permitted 211: [09:36:03] Explicit valence for atom # 1 N, 4, is greater than permitted 211: 8 Explicit valence for atom # 1 N, 4, is greater than permitted 211: 128 An error occurred while preparing the molecule for standardization. 211: 8 The molecule contains an unknown isotope: 3C 211: 4 Query atom 0 is not allowed 211: 4 Bond 0 of aromatic type is not allowed 211: 4 Bond 1 of aromatic type is not allowed 211: 4 Bond 2 of aromatic type is not allowed 211: 4 Bond 3 of aromatic type is not allowed 211: 4 Bond 5 of aromatic type is not allowed 211: 4 Bond 6 of aromatic type is not allowed 211: 4 Bond 2 of dative type is not allowed 211: 4 Bond 3 of dative type is not allowed 211: 4 Enhanced stereochemistry features are not allowed 211: 8 The radical at atom 0 is not allowed 211: [09:36:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 211: 16 The molecule includes non-null Z coordinates 211: 32 Atom 0 too close to bond 2 211: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit 211: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds 211: 64 Atom 0 has adjacent stereo bonds with like orientation 211: [09:36:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 211: 16 The molecule includes non-null Z coordinates 211: 64 Atom 0 has adjacent stereo bonds with like orientation 211: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit 211: 8388608 One or more metal atoms were disconnected. 211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 211: 67108864 The protonation state was adjusted. 211: 16777216 The representation of some functional groups was adjusted. 211: 67108864 The protonation state was adjusted. 211: 16777216 The representation of some functional groups was adjusted. 211: 67108864 The protonation state was adjusted. 211: 16777216 The representation of some functional groups was adjusted. 211: 16777216 The representation of some functional groups was adjusted. 211: 67108864 The protonation state was adjusted. 211: 16777216 The representation of some functional groups was adjusted. 211: 67108864 The protonation state was adjusted. 211: 16777216 The representation of some functional groups was adjusted. 211: 67108864 The protonation state was adjusted. 211: 16777216 The representation of some functional groups was adjusted. 211: 67108864 The protonation state was adjusted. 211: 8388608 One or more metal atoms were disconnected. 211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 211: 67108864 The protonation state was adjusted. 211: 8388608 One or more metal atoms were disconnected. 211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 211: 67108864 The protonation state was adjusted. 211: 8388608 One or more metal atoms were disconnected. 211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 211: 67108864 The protonation state was adjusted. 211: 8388608 One or more metal atoms were disconnected. 211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 211: 67108864 The protonation state was adjusted. 211: 8388608 One or more metal atoms were disconnected. 211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 211: 67108864 The protonation state was adjusted. 211: 16777216 The "wavy" style of bond 4 was removed 211: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration 211: 16777216 The "wavy" style of bond 2 was removed 211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 211: 16777216 The "wavy" style of bond 1 was removed 211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 211: 16777216 The "wavy" style of bond 1 was removed 211: 16777216 The "wavy" style of bond 4 was removed 211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 211: 16777216 The "wavy" style of bond 3 was removed 211: 16777216 The representation of some functional groups was adjusted. 211: [09:36:03] Can't kekulize mol. Unkekulized atoms: 2 3 5 211: =============================================================================== 211: All tests passed (268 assertions in 5 test cases) 211: 206/236 Test #211: molStandardizePipelineTest ............. Passed 0.10 sec test 212 Start 212: pyMolStandardize 212: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" 212: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap 212: Test timeout computed to be: 1500 212: .....[09:36:04] Tautomer enumeration stopped at 292 tautomers: max transforms reached 212: [09:36:04] Tautomer enumeration stopped at 50 tautomers: max tautomers reached 212: .[09:36:04] Tautomer enumeration stopped at 120 tautomers: canceled 212: Enumeration was canceled due to timeout (50 ms) 212: Enumeration has completed 212: [09:36:04] Tautomer enumeration stopped at 122 tautomers: canceled 212: ..........[09:36:04] Explicit valence for atom # 1 N, 4, is greater than permitted 212: [09:36:04] Explicit valence for atom # 1 N, 4, is greater than permitted 212: [09:36:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 212: [09:36:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 212: ............[09:36:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 212: [09:36:05] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. 212: [09:36:05] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. 212: ........[09:36:05] Explicit valence for atom # 1 O, 3, is greater than permitted 212: .. 212: ---------------------------------------------------------------------- 212: Ran 38 tests in 1.316s 212: 212: OK 212: done 207/236 Test #212: pyMolStandardize ....................... Passed 1.47 sec test 213 Start 213: testScaffoldNetwork 213: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 213: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork 213: Test timeout computed to be: 1500 213: Randomness seeded to: 1838272332 213: =============================================================================== 213: All tests passed (273 assertions in 19 test cases) 213: 208/236 Test #213: testScaffoldNetwork .................... Passed 0.54 sec test 214 Start 214: pyScaffoldNetwork 214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 214: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 214: Test timeout computed to be: 1500 195: ..[09:36:05] 195: 195: **** 195: Pre-condition Violation 195: no owner 195: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h 195: Failed Expression: dp_mol 195: ---------- 195: Stacktrace: 195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 5# 0x00007F14F97D962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 16# 0x00007F14F6FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 17# 0x00007F14F6FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 18# 0x00007F14F6FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 19# 0x00007F14F6FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 20# 0x00007F14F6FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 26# 0x00007F14F97D63C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 195: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 31# 0x000000000064B89F in /usr/bin/python3 195: 32# 0x000000000069ECA0 in /usr/bin/python3 195: 33# _PyObject_MakeTpCall in /usr/bin/python3 195: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 35# 0x00000000005C30D9 in /usr/bin/python3 195: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 37# 0x000000000064B89F in /usr/bin/python3 195: 38# 0x000000000069ECA0 in /usr/bin/python3 195: 39# _PyObject_MakeTpCall in /usr/bin/python3 195: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 41# 0x00000000005C30D9 in /usr/bin/python3 195: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 43# 0x000000000064B89F in /usr/bin/python3 195: 44# 0x000000000069ECA0 in /usr/bin/python3 195: 45# _PyObject_MakeTpCall in /usr/bin/python3 195: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 47# 0x0000000000599C8E in /usr/bin/python3 195: 48# _PyObject_MakeTpCall in /usr/bin/python3 195: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 50# PyEval_EvalCode in /usr/bin/python3 195: 51# 0x000000000066DA21 in /usr/bin/python3 195: 52# 0x0000000000669A8C in /usr/bin/python3 195: 53# 0x0000000000682973 in /usr/bin/python3 195: 54# 0x0000000000682273 in /usr/bin/python3 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 195: 58# 0x00007F14FA014CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: 195: [09:36:05] 195: 195: **** 195: Pre-condition Violation 195: no owner 195: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h 195: Failed Expression: dp_mol 195: ---------- 195: Stacktrace: 195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 5# 0x00007F14F97D962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 16# 0x00007F14F6FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 17# 0x00007F14F6FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 18# 0x00007F14F6FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 19# 0x00007F14F6FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 20# 0x00007F14F6FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 26# 0x00007F14F97D63C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 195: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 31# 0x000000000064B89F in /usr/bin/python3 195: 32# 0x000000000069ECA0 in /usr/bin/python3 195: 33# _PyObject_MakeTpCall in /usr/bin/python3 195: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 35# 0x00000000005C30D9 in /usr/bin/python3 195: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 37# 0x000000000064B89F in /usr/bin/python3 195: 38# 0x000000000069ECA0 in /usr/bin/python3 195: 39# _PyObject_MakeTpCall in /usr/bin/python3 195: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 41# 0x00000000005C30D9 in /usr/bin/python3 195: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 43# 0x000000000064B89F in /usr/bin/python3 195: 44# 0x000000000069ECA0 in /usr/bin/python3 195: 45# _PyObject_MakeTpCall in /usr/bin/python3 195: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 47# 0x0000000000599C8E in /usr/bin/python3 195: 48# _PyObject_MakeTpCall in /usr/bin/python3 195: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 50# PyEval_EvalCode in /usr/bin/python3 195: 51# 0x000000000066DA21 in /usr/bin/python3 195: 52# 0x0000000000669A8C in /usr/bin/python3 195: 53# 0x0000000000682973 in /usr/bin/python3 195: 54# 0x0000000000682273 in /usr/bin/python3 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 195: 58# 0x00007F14FA014CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: 195: [09:36:05] 195: 195: **** 195: Pre-condition Violation 195: no owner 195: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h 195: Failed Expression: dp_mol 195: ---------- 195: Stacktrace: 195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 5# 0x00007F14F97D962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 16# 0x00007F14F6FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 17# 0x00007F14F6FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 18# 0x00007F14F6FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 19# 0x00007F14F6FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 20# 0x00007F14F6FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 26# 0x00007F14F97D63C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 195: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 31# 0x000000000064B89F in /usr/bin/python3 195: 32# 0x000000000069ECA0 in /usr/bin/python3 195: 33# _PyObject_MakeTpCall in /usr/bin/python3 195: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 35# 0x00000000005C30D9 in /usr/bin/python3 195: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 37# 0x000000000064B89F in /usr/bin/python3 195: 38# 0x000000000069ECA0 in /usr/bin/python3 195: 39# _PyObject_MakeTpCall in /usr/bin/python3 195: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 41# 0x00000000005C30D9 in /usr/bin/python3 195: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 43# 0x000000000064B89F in /usr/bin/python3 195: 44# 0x000000000069ECA0 in /usr/bin/python3 195: 45# _PyObject_MakeTpCall in /usr/bin/python3 195: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 47# 0x0000000000599C8E in /usr/bin/python3 195: 48# _PyObject_MakeTpCall in /usr/bin/python3 195: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 50# PyEval_EvalCode in /usr/bin/python3 195: 51# 0x000000000066DA21 in /usr/bin/python3 195: 52# 0x0000000000669A8C in /usr/bin/python3 195: 53# 0x0000000000682973 in /usr/bin/python3 195: 54# 0x0000000000682273 in /usr/bin/python3 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 195: 58# 0x00007F14FA014CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: 195: [09:36:05] 195: 195: **** 195: Pre-condition Violation 195: no owner 195: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h 195: Failed Expression: dp_mol 195: ---------- 195: Stacktrace: 195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 5# 0x00007F14F97D962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 16# 0x00007F14F6FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 17# 0x00007F14F6FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 18# 0x00007F14F6FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 19# 0x00007F14F6FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 20# 0x00007F14F6FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 26# 0x00007F14F97D63C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 195: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 31# 0x000000000064B89F in /usr/bin/python3 195: 32# 0x000000000069ECA0 in /usr/bin/python3 195: 33# _PyObject_MakeTpCall in /usr/bin/python3 195: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 35# 0x00000000005C30D9 in /usr/bin/python3 195: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 37# 0x000000000064B89F in /usr/bin/python3 195: 38# 0x000000000069ECA0 in /usr/bin/python3 195: 39# _PyObject_MakeTpCall in /usr/bin/python3 195: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 41# 0x00000000005C30D9 in /usr/bin/python3 195: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 43# 0x000000000064B89F in /usr/bin/python3 195: 44# 0x000000000069ECA0 in /usr/bin/python3 195: 45# _PyObject_MakeTpCall in /usr/bin/python3 195: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 47# 0x0000000000599C8E in /usr/bin/python3 195: 48# _PyObject_MakeTpCall in /usr/bin/python3 195: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 50# PyEval_EvalCode in /usr/bin/python3 195: 51# 0x000000000066DA21 in /usr/bin/python3 195: 52# 0x0000000000669A8C in /usr/bin/python3 195: 53# 0x0000000000682973 in /usr/bin/python3 195: 54# 0x0000000000682273 in /usr/bin/python3 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 195: 58# 0x00007F14FA014CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: 195: [09:36:05] 195: 195: **** 195: Pre-condition Violation 195: no owner 195: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h 195: Failed Expression: dp_mol 195: ---------- 195: Stacktrace: 195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 5# 0x00007F14F97D962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 16# 0x00007F14F6FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 17# 0x00007F14F6FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 18# 0x00007F14F6FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 19# 0x00007F14F6FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 20# 0x00007F14F6FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 26# 0x00007F14F97D63C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 195: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 31# 0x000000000064B89F in /usr/bin/python3 195: 32# 0x000000000069ECA0 in /usr/bin/python3 195: 33# _PyObject_MakeTpCall in /usr/bin/python3 195: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 35# 0x00000000005C30D9 in /usr/bin/python3 195: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 37# 0x000000000064B89F in /usr/bin/python3 195: 38# 0x000000000069ECA0 in /usr/bin/python3 195: 39# _PyObject_MakeTpCall in /usr/bin/python3 195: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 41# 0x00000000005C30D9 in /usr/bin/python3 195: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 43# 0x000000000064B89F in /usr/bin/python3 195: 44# 0x000000000069ECA0 in /usr/bin/python3 195: 45# _PyObject_MakeTpCall in /usr/bin/python3 195: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 47# 0x0000000000599C8E in /usr/bin/python3 195: 48# _PyObject_MakeTpCall in /usr/bin/python3 195: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 50# PyEval_EvalCode in /usr/bin/python3 195: 51# 0x000000000066DA21 in /usr/bin/python3 195: 52# 0x0000000000669A8C in /usr/bin/python3 195: 53# 0x0000000000682973 in /usr/bin/python3 195: 54# 0x0000000000682273 in /usr/bin/python3 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 195: 58# 0x00007F14FA014CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: 195: .....[09:36:05] 195: 195: **** 195: Range Error 195: atomIdx1 195: Violation occurred on line 498 in file ./Code/GraphMol/RWMol.cpp 195: Failed Expression: 0 < 0 195: ---------- 195: Stacktrace: 195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 5# 0x00007F14F97D962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 16# 0x00007F14F6FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 17# 0x00007F14F6FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 18# 0x00007F14F6FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 19# 0x00007F14F6FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 20# 0x00007F14F6FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 26# 0x00007F14F97D63C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 195: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 31# 0x000000000064B89F in /usr/bin/python3 195: 32# 0x000000000069ECA0 in /usr/bin/python3 195: 33# _PyObject_MakeTpCall in /usr/bin/python3 195: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 35# 0x00000000005C30D9 in /usr/bin/python3 195: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 37# 0x000000000064B89F in /usr/bin/python3 195: 38# 0x000000000069ECA0 in /usr/bin/python3 195: 39# _PyObject_MakeTpCall in /usr/bin/python3 195: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 41# 0x00000000005C30D9 in /usr/bin/python3 195: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 43# 0x000000000064B89F in /usr/bin/python3 195: 44# 0x000000000069ECA0 in /usr/bin/python3 195: 45# _PyObject_MakeTpCall in /usr/bin/python3 195: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 47# 0x0000000000599C8E in /usr/bin/python3 195: 48# _PyObject_MakeTpCall in /usr/bin/python3 195: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 50# PyEval_EvalCode in /usr/bin/python3 195: 51# 0x000000000066DA21 in /usr/bin/python3 195: 52# 0x0000000000669A8C in /usr/bin/python3 195: 53# 0x0000000000682973 in /usr/bin/python3 195: 54# 0x0000000000682273 in /usr/bin/python3 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 195: 58# 0x00007F14FA014CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: 195: ......[09:36:05] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 195: [09:36:05] ERROR: Smiles parse error on line 0 195: [09:36:05] ERROR: Cannot create molecule from : 'c1ccccc' 195: [09:36:05] SMILES Parse Error: extra open parentheses while parsing: C(C 195: [09:36:05] SMILES Parse Error: check for mistakes around position 2: 195: [09:36:05] C(C 195: [09:36:05] ~^ 195: [09:36:05] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' 195: [09:36:05] ERROR: Smiles parse error on line 3 195: [09:36:05] ERROR: Cannot create molecule from : 'C(C' 195: [09:36:05] Explicit valence for atom # 1 C, 5, is greater than permitted 195: [09:36:05] ERROR: Could not sanitize molecule on line 6 195: [09:36:05] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted 195: [09:36:05] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 195: [09:36:05] ERROR: Smiles parse error on line 0 195: [09:36:05] ERROR: Cannot create molecule from : 'c1ccccc' 195: [09:36:05] SMILES Parse Error: extra open parentheses while parsing: C(C 195: [09:36:05] SMILES Parse Error: check for mistakes around position 2: 195: [09:36:05] C(C 195: [09:36:05] ~^ 195: [09:36:05] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' 195: [09:36:05] ERROR: Smiles parse error on line 3 195: [09:36:05] ERROR: Cannot create molecule from : 'C(C' 195: [09:36:05] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' 195: [09:36:05] ERROR: Smiles parse error on line 6 195: [09:36:05] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' 195: [09:36:05] Explicit valence for atom # 1 F, 2, is greater than permitted 195: [09:36:05] ERROR: Could not sanitize molecule ending on line 21 195: [09:36:05] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 195: [09:36:05] ERROR: EOF hit while reading atoms 195: [09:36:05] ERROR: moving to the beginning of the next molecule 195: [09:36:05] Explicit valence for atom # 1 F, 2, is greater than permitted 195: [09:36:05] ERROR: Could not sanitize molecule ending on line 21 195: [09:36:05] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 195: [09:36:05] ERROR: EOF hit while reading atoms 195: [09:36:05] ERROR: moving to the beginning of the next molecule 195: ....[09:36:05] 195: 195: **** 195: Pre-condition Violation 195: RingInfo not initialized 195: Violation occurred on line 170 in file ./Code/GraphMol/RingInfo.cpp 195: Failed Expression: df_init 195: ---------- 195: Stacktrace: 195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 5# 0x00007F14F97D962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 16# 0x00007F14F6FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 17# 0x00007F14F6FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 18# 0x00007F14F6FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 19# 0x00007F14F6FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 20# 0x00007F14F6FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 26# 0x00007F14F97D63C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 195: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 31# 0x000000000064B89F in /usr/bin/python3 195: 32# 0x000000000069ECA0 in /usr/bin/python3 195: 33# _PyObject_MakeTpCall in /usr/bin/python3 195: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 35# 0x00000000005C30D9 in /usr/bin/python3 195: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 37# 0x000000000064B89F in /usr/bin/python3 195: 38# 0x000000000069ECA0 in /usr/bin/python3 195: 39# _PyObject_MakeTpCall in /usr/bin/python3 195: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 41# 0x00000000005C30D9 in /usr/bin/python3 195: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 43# 0x000000000064B89F in /usr/bin/python3 195: 44# 0x000000000069ECA0 in /usr/bin/python3 195: 45# _PyObject_MakeTpCall in /usr/bin/python3 195: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 47# 0x0000000000599C8E in /usr/bin/python3 195: 48# _PyObject_MakeTpCall in /usr/bin/python3 195: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 50# PyEval_EvalCode in /usr/bin/python3 195: 51# 0x000000000066DA21 in /usr/bin/python3 195: 52# 0x0000000000669A8C in /usr/bin/python3 195: 53# 0x0000000000682973 in /usr/bin/python3 195: 54# 0x0000000000682273 in /usr/bin/python3 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 195: 58# 0x00007F14FA014CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: 195: .............[09:36:05] 195: 195: **** 195: Range Error 195: idx 195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 195: Failed Expression: 3 < 1 195: ---------- 195: Stacktrace: 195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 5# 0x00007F14F97D962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 16# 0x00007F14F6FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 17# 0x00007F14F6FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 18# 0x00007F14F6FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 19# 0x00007F14F6FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 20# 0x00007F14F6FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 26# 0x00007F14F97D63C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 195: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 31# 0x000000000064B89F in /usr/bin/python3 195: 32# 0x000000000069ECA0 in /usr/bin/python3 195: 33# _PyObject_MakeTpCall in /usr/bin/python3 195: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 35# 0x00000000005C30D9 in /usr/bin/python3 195: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 37# 0x000000000064B89F in /usr/bin/python3 195: 38# 0x000000000069ECA0 in /usr/bin/python3 195: 39# _PyObject_MakeTpCall in /usr/bin/python3 195: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 41# 0x00000000005C30D9 in /usr/bin/python3 195: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 43# 0x000000000064B89F in /usr/bin/python3 195: 44# 0x000000000069ECA0 in /usr/bin/python3 195: 45# _PyObject_MakeTpCall in /usr/bin/python3 195: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 47# 0x0000000000599C8E in /usr/bin/python3 195: 48# _PyObject_MakeTpCall in /usr/bin/python3 195: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 50# PyEval_EvalCode in /usr/bin/python3 195: 51# 0x000000000066DA21 in /usr/bin/python3 195: 52# 0x0000000000669A8C in /usr/bin/python3 195: 53# 0x0000000000682973 in /usr/bin/python3 195: 54# 0x0000000000682273 in /usr/bin/python3 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 195: 58# 0x00007F14FA014CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: 195: ...[09:36:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 195: ............................[09:36:05] SMILES Parse Error: unclosed ring for input: 'C1CC' 195: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| 195: 1000 195: ..[09:36:05] WARNING: not removing hydrogen atom without neighbors 195: [09:36:05] WARNING: not removing hydrogen atom with dummy atom neighbors 195: [09:36:05] WARNING: not removing hydrogen atom with wedged bond 195: [09:36:05] WARNING: not removing hydrogen atom without neighbors 195: [09:36:05] WARNING: not removing hydrogen atom with dummy atom neighbors 214: ....... 214: ---------------------------------------------------------------------- 214: Ran 7 tests in 0.019s 214: 214: OK 209/236 Test #214: pyScaffoldNetwork ...................... Passed 0.17 sec test 215 Start 215: pyScaffoldNetworkPickling 215: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" 215: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 215: Test timeout computed to be: 1500 195: ......[09:36:05] Explicit valence for atom # 1 F, 2, is greater than permitted 195: [09:36:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 195: .[09:36:05] Explicit valence for atom # 1 F, 2, is greater than permitted 195: [09:36:05] Explicit valence for atom # 1 F, 2, is greater than permitted 195: [09:36:05] Explicit valence for atom # 1 F, 2, is greater than permitted 195: [09:36:05] Explicit valence for atom # 1 F, 2, is greater than permitted 195: [09:36:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 195: [09:36:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 195: [09:36:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 195: ..........[09:36:05] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname 195: [09:36:05] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' 195: .[09:36:05] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname 195: [09:36:05] SMILES Parse Error: check for mistakes around position 4: 195: [09:36:05] CCC |$foo;;bar$| ourname 195: [09:36:05] ~~~^ 195: [09:36:05] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' 195: ..[09:36:05] SMILES Parse Error: syntax error while parsing: error 195: [09:36:05] SMILES Parse Error: check for mistakes around position 1: 195: [09:36:05] error 195: [09:36:05] ^ 195: [09:36:05] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' 195: [09:36:05] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' 195: [09:36:05] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' 195: [09:36:05] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' 195: .........................[09:36:05] SMILES Parse Error: syntax error while parsing: garbage_0 195: [09:36:05] SMILES Parse Error: check for mistakes around position 1: 195: [09:36:05] garbage_0 195: [09:36:05] ^ 195: [09:36:05] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' 195: [09:36:05] SMILES Parse Error: syntax error while parsing: garbage_2 195: [09:36:05] SMILES Parse Error: check for mistakes around position 1: 195: [09:36:05] garbage_2 195: [09:36:05] ^ 195: [09:36:05] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' 195: [09:36:05] SMILES Parse Error: syntax error while parsing: garbage_4 195: [09:36:05] SMILES Parse Error: check for mistakes around position 1: 195: [09:36:05] garbage_4 195: [09:36:05] ^ 195: [09:36:05] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' 195: ............ 195: ---------------------------------------------------------------------- 195: Ran 279 tests in 5.055s 195: 195: OK 195: supplier: 195: supplier: 195: supplier: 210/236 Test #195: pyGraphMolWrap ......................... Passed 5.29 sec test 216 Start 216: testMolEnumerator 216: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 216: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator 216: Test timeout computed to be: 1500 216: Randomness seeded to: 2719379852 216: [09:36:06] can only enumerate SRUs with CONNECT=HT or CONNECT=HH 216: =============================================================================== 216: All tests passed (321 assertions in 16 test cases) 216: 211/236 Test #216: testMolEnumerator ...................... Passed 0.04 sec test 217 Start 217: pyMolEnumerator 217: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 217: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 217: Test timeout computed to be: 1500 215: . 215: ---------------------------------------------------------------------- 215: Ran 1 test in 0.006s 215: 215: OK 212/236 Test #215: pyScaffoldNetworkPickling .............. Passed 0.14 sec test 218 Start 218: testAbbreviations 218: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 218: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations 218: Test timeout computed to be: 1500 218: Randomness seeded to: 1832873838 218: [09:36:06] SMARTS Parse Error: syntax error while parsing: *fail 218: [09:36:06] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' 218: [09:36:06] no suitable SubstanceGroups found 218: =============================================================================== 218: All tests passed (195 assertions in 12 test cases) 218: 213/236 Test #218: testAbbreviations ...................... Passed 0.02 sec test 219 Start 219: pyAbbreviations 219: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 219: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 219: Test timeout computed to be: 1500 217: ... 217: ---------------------------------------------------------------------- 217: Ran 3 tests in 0.006s 217: 217: OK 214/236 Test #217: pyMolEnumerator ........................ Passed 0.14 sec test 220 Start 220: generalizedSubstructCatch 220: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 220: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 220: Test timeout computed to be: 1500 219: ....... 219: ---------------------------------------------------------------------- 219: Ran 7 tests in 0.009s 219: 219: OK 215/236 Test #219: pyAbbreviations ........................ Passed 0.14 sec test 221 Start 221: pyGeneralizedSubstruct 221: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 221: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 221: Test timeout computed to be: 1500 220: Randomness seeded to: 113701996 220: =============================================================================== 220: All tests passed (486 assertions in 10 test cases) 220: 216/236 Test #220: generalizedSubstructCatch .............. Passed 0.11 sec test 222 Start 222: testMolProcessing 222: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing 222: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing 222: Test timeout computed to be: 1500 221: ....... 221: ---------------------------------------------------------------------- 221: Ran 7 tests in 0.181s 221: 221: OK 217/236 Test #221: pyGeneralizedSubstruct ................. Passed 0.32 sec test 223 Start 223: pyMolProcessing 223: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" 223: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap 223: Test timeout computed to be: 1500 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 0.289s 223: 223: OK 218/236 Test #223: pyMolProcessing ........................ Passed 0.61 sec test 224 Start 224: testMIF 224: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF 224: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields 224: Test timeout computed to be: 1500 224: Randomness seeded to: 1678401397 224: =============================================================================== 224: All tests passed (27926 assertions in 8 test cases) 224: 219/236 Test #224: testMIF ................................ Passed 0.04 sec test 225 Start 225: pyMIF 225: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" 225: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap 225: Test timeout computed to be: 1500 146: [09:36:07] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:36:03] --------------------------------- 146: [09:36:03] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system 146: [09:36:03] --------------------------------- 146: [09:36:03] More ChEMBL molecules failing bounds smoothing. 146: [09:36:03] --------------------------------- 146: [09:36:03] ugly conformations can be generated for highly constrained ring systems. 146: [09:36:03] --------------------------------- 146: [09:36:03] test embed parameters structure. 146: [09:36:03] --------------------------------- 146: [09:36:03] test github 1227: Hs being used in RMSD filtering. 146: [09:36:03] --------------------------------- 146: [09:36:03] Failure to embed larger aromatic rings. 146: [09:36:04] --------------------------------- 146: [09:36:04] Deterministic with large random seeds 146: [09:36:06] --------------------------------- 146: [09:36:06] Github #1990: seg fault after RemoveHs 146: [09:36:06] --------------------------------- 146: [09:36:06] Github #2246: Use coordMap when starting embedding from random coords 146: [09:36:07] --------------------------------- 146: [09:36:07] Providing a distance bounds matrix. 146: [09:36:07] --------------------------------- 146: [09:36:07] Disabling fragmentation. 146: [09:36:07] --------------------------------- 146: [09:36:07] Using symmetry in conformation pruning. 146: [09:36:07] --------------------------------- 146: [09:36:07] Force trans amides. 146: [09:36:07] --------------------------------- 146: [09:36:07] test missing Hs warning. 146: [09:36:07] --------------------------------- 146: [09:36:07] basic H bond support. 146: [09:36:07] ******************************************************* 220/236 Test #146: testDistGeomHelpers .................... Passed 52.10 sec test 226 Start 226: testQuery 226: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Query/testQuery 226: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Query 226: Test timeout computed to be: 1500 226: Query 226: Query2 226: Equality 226: Greater 226: GreaterEqual 226: Less 226: LessEqual 226: Open Range 226: Closed Range 226: Float 226: With Tolerance 226: Set 226: And 226: Or 226: XOr 226: pointer and copy foo 226: Set2 221/236 Test #226: testQuery .............................. Passed 0.00 sec test 227 Start 227: testBaseFeatures 227: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features/testBaseFeatures 227: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features 227: Test timeout computed to be: 1500 227: ------------------------------------- 227: Basics for ExplicitFeatures. 227: done 227: ------------------------------------- 227: Basics for ImplicitFeatures. 227: done 227: ------------------------------------- 227: ExplicitFeatures 2D, string type. 227: done 222/236 Test #227: testBaseFeatures ....................... Passed 0.00 sec test 228 Start 228: testMatCalc 228: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc 228: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc 228: Test timeout computed to be: 1500 228: 1.68022e+08 228: 1.73149e+08 228: 1.05549e+08 228: 7.20603e+07 228: 1.41535e+08 228: 1.08592e+08 228: 1.11334e+08 228: 2.05553e+08 228: 1.54962e+08 228: 8.08231e+07 228: 5.61421e+07 228: 1.28874e+08 228: 1.59011e+08 228: 8.69902e+07 228: 1.31367e+08 228: 2.27389e+08 228: 1.60289e+08 228: 7.79813e+07 228: 1.61001e+08 228: 2.07599e+08 228: 2.24432e+08 228: 1.39725e+08 228: 2.42614e+08 228: 1.77578e+08 228: 1.05908e+08 228: 9.06742e+07 228: 1.8087e+08 228: 1.98182e+08 228: 2.03052e+08 228: 1.7673e+08 228: 9.32798e+07 228: 1.37969e+08 228: 1.83778e+08 228: 2.1228e+08 228: 5.06157e+07 228: 1.566e+08 228: 2.37142e+08 228: 1.49345e+08 228: 7.05819e+07 228: 1.71633e+08 228: 1.96817e+08 228: 2.18246e+08 228: 9.49496e+07 228: 2.25618e+08 228: 1.30219e+08 223/236 Test #228: testMatCalc ............................ Passed 0.00 sec test 229 Start 229: pyMatCalc 229: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 229: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 229: Test timeout computed to be: 1500 225: ....... 225: ---------------------------------------------------------------------- 225: Ran 7 tests in 0.033s 225: 225: OK 225: Testing MIF wrapper 224/236 Test #225: pyMIF .................................. Passed 0.19 sec test 230 Start 230: testSimDivPickers 230: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers 230: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers 230: Test timeout computed to be: 1500 230: [09:36:07] ------------------------------------- 230: [09:36:07] Testing github issue 1421: MaxMinPicker picking non-existent element. 230: [09:36:07] Done 230: [09:36:07] ------------------------------------- 230: [09:36:07] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. 230: [09:36:07] Done 225/236 Test #230: testSimDivPickers ...................... Passed 0.00 sec test 231 Start 231: pickersTestsCatch 231: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 231: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers 231: Test timeout computed to be: 1500 231: Randomness seeded to: 2486141801 231: =============================================================================== 231: All tests passed (21267 assertions in 1 test case) 231: 226/236 Test #231: pickersTestsCatch ...................... Passed 0.04 sec test 232 Start 232: pySimDivPickers 232: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap/testPickers.py" 232: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap 232: Test timeout computed to be: 1500 229: ..... 229: ---------------------------------------------------------------------- 229: Ran 5 tests in 0.134s 229: 229: OK 227/236 Test #229: pyMatCalc .............................. Passed 0.25 sec test 233 Start 233: pyRanker 233: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/testRanker.py" 233: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap 233: Test timeout computed to be: 1500 232: [09:36:07] the useCache argument is deprecated and ignored 233: ..[09:36:07] 233: 233: **** 233: Invariant Violation 233: Can't rank more bits than the ensemble size 233: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp 233: Failed Expression: num <= dp_maskBits->getNumOnBits() 233: ---------- 233: Stacktrace: 233: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 233: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 233: 2# RDInfoTheory::InfoBitRanker::getTopN(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitInfoTheory.so.1 233: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 233: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 233: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 233: 6# 0x00007EFE216DF62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 233: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 233: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 233: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 233: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 233: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 233: 12# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 233: 13# 0x00007EFE216DC3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 233: 14# _PyObject_MakeTpCall in /usr/bin/python3 233: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 233: 16# 0x00000000005C30D9 in /usr/bin/python3 233: 17# _PyEval_EvalFrameDefault in /usr/bin/python3 233: 18# 0x000000000064B89F in /usr/bin/python3 233: 19# 0x000000000069ECA0 in /usr/bin/python3 233: 20# _PyObject_MakeTpCall in /usr/bin/python3 233: 21# _PyEval_EvalFrameDefault in /usr/bin/python3 233: 22# 0x00000000005C30D9 in /usr/bin/python3 233: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 233: 24# 0x000000000064B89F in /usr/bin/python3 233: 25# 0x000000000069ECA0 in /usr/bin/python3 233: 26# _PyObject_MakeTpCall in /usr/bin/python3 233: 27# _PyEval_EvalFrameDefault in /usr/bin/python3 233: 28# 0x00000000005C30D9 in /usr/bin/python3 233: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 233: 30# 0x000000000064B89F in /usr/bin/python3 233: 31# 0x000000000069ECA0 in /usr/bin/python3 233: 32# _PyObject_MakeTpCall in /usr/bin/python3 233: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 233: 34# 0x0000000000599C8E in /usr/bin/python3 233: 35# _PyObject_MakeTpCall in /usr/bin/python3 233: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 233: 37# PyEval_EvalCode in /usr/bin/python3 233: 38# 0x000000000066DA21 in /usr/bin/python3 233: 39# 0x0000000000669A8C in /usr/bin/python3 233: 40# 0x0000000000682973 in /usr/bin/python3 233: 41# 0x0000000000682273 in /usr/bin/python3 233: 42# 0x00000000006820AE in /usr/bin/python3 233: 43# Py_RunMain in /usr/bin/python3 233: 44# Py_BytesMain in /usr/bin/python3 233: 45# 0x00007EFE22954CA8 in /lib/x86_64-linux-gnu/libc.so.6 233: 46# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 233: 47# _start in /usr/bin/python3 233: ---------- 233: **** 233: 233: ... 233: ---------------------------------------------------------------------- 233: Ran 5 tests in 0.010s 233: 233: OK 228/236 Test #233: pyRanker ............................... Passed 0.13 sec test 234 Start 234: testChemicalFeatures 234: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures 234: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures 234: Test timeout computed to be: 1500 234: ----------------------------------------- 234: Test1 234: Done 229/236 Test #234: testChemicalFeatures ................... Passed 0.00 sec test 235 Start 235: pyFeatures 235: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/testFeatures.py" 235: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap 235: Test timeout computed to be: 1500 232: ...[09:36:07] the useCache argument is deprecated and ignored 232: [09:36:07] the useCache argument is deprecated and ignored 232: .[09:36:07] the useCache argument is deprecated and ignored 222: Randomness seeded to: 247307928 222: =============================================================================== 222: All tests passed (203 assertions in 1 test case) 222: 230/236 Test #222: testMolProcessing ...................... Passed 1.39 sec test 236 Start 236: pythonProjectTests 236: Test command: /usr/bin/python3 "-m" "pytest" 236: Working Directory: /build/reproducible-path/rdkit-202503.1/Projects 236: Test timeout computed to be: 1500 235: .. 235: ---------------------------------------------------------------------- 235: Ran 2 tests in 0.000s 235: 235: OK 235: Testing ChemicalFeatures Wrapper code: 231/236 Test #235: pyFeatures ............................. Passed 0.13 sec 232: ....... 232: ---------------------------------------------------------------------- 232: Ran 11 tests in 0.514s 232: 232: OK 232/236 Test #232: pySimDivPickers ........................ Passed 0.63 sec 236: ============================= test session starts ============================== 236: platform linux -- Python 3.13.3, pytest-8.3.5, pluggy-1.5.0 236: rootdir: /build/reproducible-path/rdkit-202503.1/Projects 236: configfile: pytest.ini 236: collected 12 items 236: 210: [09:36:08] Explicit valence for atom # 0 Br, 1, is greater than permitted 210: =============================================================================== 210: All tests passed (38344 assertions in 51 test cases) 210: 233/236 Test #210: molStandardizeCatchTest ................ Passed 6.11 sec 170: =============================================================================== 170: All tests passed (3590 assertions in 35 test cases) 170: 234/236 Test #170: testRascalMCES ......................... Passed 39.07 sec 236: DbCLI/UnitTestDbCLI.py ............ [100%] 236: 236: =============================== warnings summary =============================== 236: ../obj-x86_64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20 236: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) 236: decBase = declarative_base() 236: 236: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 236: ======================== 12 passed, 1 warning in 9.66s ========================= 235/236 Test #236: pythonProjectTests ..................... Passed 9.87 sec 174: Randomness seeded to: 3121451933 174: =============================================================================== 174: All tests passed (28 assertions in 2 test cases) 174: 236/236 Test #174: testSynthonSpaceRascalSearch ........... Passed 35.67 sec 100% tests passed, 0 tests failed out of 236 Total Test time (real) = 84.15 sec make[2]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' create-stamp debian/debhelper-build-stamp dh_testroot -i -O--buildsystem=cmake dh_prep -i -O--buildsystem=cmake dh_installdirs -i -O--buildsystem=cmake debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' dh_auto_install cd obj-x86_64-linux-gnu && make -j6 install DESTDIR=/build/reproducible-path/rdkit-202503.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202503.1 -B/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Geometry -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Geometry/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/conftest.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbInfo.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbUtils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/StorageUtils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbConnection.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbModule.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbResultSet.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Avalon -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Avalon/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDLogger.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/TestRunner.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Filter.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Output.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Supply.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SDSupply.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbMolSupply.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesSupply.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/demo.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Node.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Transform.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/Metric -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/Metric/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/listutils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemutils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/retest.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/fileutils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/spiral.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/cactvs.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw_qax.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitRank.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/entropy.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitClusterer.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/MLData.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/DataUtils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/FindQuantBounds.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Transforms.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Stats.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/SplitData.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Quantize.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/Risk.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/files.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/Scoring.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Murtagh.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Butina.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/murtagh_test.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Standardize.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Resemblance.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Clusters.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterUtils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterVis.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Parser.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Descriptors.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/CompoundDescriptors.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MatOps.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/VoteImg.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDRandom.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/SimilarityPickers.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pid.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/pidSVG.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/formatted-strings.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pidtest.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/testallps.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pstests.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/HTMLPiddler.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfdoc.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfutils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfmetrics.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgeom.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgen.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pidPDF.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/utils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/stringformat.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/latin1MetricsCache.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/fontinfo.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/pidPS.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/psmetrics.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil -- Installing: 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Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pagesizes.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/pidTK.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/pidPyart.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/Fontmapping.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/__init__.py -- 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-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/SimilarityMaps.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/BuilderUtils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/demoCombined.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeObjects.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeBuilder.py -- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DataStructs/DiscreteValueVect.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DataStructs/RealValueVect.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DataStructs/ExplicitBitVect.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DataStructs/SparseBitVect.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DataStructs/SparseIntVect.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DataStructs/FPBReader.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DataStructs/MultiFPBReader.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/cDataStructs.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDGeometryLib.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDGeometryLib.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDGeometryLib.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Geometry/Grid3D.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Geometry/GridUtils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Geometry/point.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Geometry/Transform2D.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Geometry/Transform3D.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Geometry/Transform.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Geometry/UniformGrid3D.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Geometry/UniformRealValueGrid3D.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Geometry/Utils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Geometry/rdGeometry.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitAlignment.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitAlignment.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitAlignment.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Numerics/Alignment/AlignPoints.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics/rdAlignment.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitEigenSolvers.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitEigenSolvers.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitEigenSolvers.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Numerics/EigenSolvers/PowerEigenSolver.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitOptimizer.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitOptimizer.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitOptimizer.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Numerics/Optimizer/BFGSOpt.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Numerics/Matrix.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Numerics/SquareMatrix.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Numerics/SymmMatrix.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Numerics/Vector.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Numerics/Conrec.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitForceField.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitForceField.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitForceField.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/Contrib.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/ForceField.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/AngleConstraints.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/DistanceConstraints.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/UFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/UFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/UFF/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/UFF/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/UFF/Nonbonded.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/UFF/Params.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/UFF/Utils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/UFF/Inversion.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/UFF/Inversions.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/MMFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/MMFF/StretchBend.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/MMFF/OopBend.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/MMFF/Nonbonded.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/MMFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/MMFF/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/MMFF/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ForceField/MMFF/Params.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField/rdForceField.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitDistGeometry.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitDistGeometry.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitDistGeometry.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DistGeom/BoundsMatrix.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DistGeom/ChiralSet.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DistGeom/ChiralViolationContribs.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DistGeom/DistGeomUtils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DistGeom/DistViolationContribs.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DistGeom/FourthDimContribs.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DistGeom/TriangleSmooth.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry/DistGeom.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitCatalogs.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitCatalogs.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitCatalogs.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Catalogs/CatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Catalogs/Catalog.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Catalogs/CatalogParams.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitGraphMol.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitGraphMol.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitGraphMol.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Atom.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/atomic_data.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/AtomIterators.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Atropisomers.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Bond.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/BondIterators.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Canon.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Chirality.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Conformer.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/details.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/GraphMol.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolOps.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolPickler.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/PeriodicTable.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/QueryAtom.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/QueryBond.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/QueryOps.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/RDKitBase.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/RDKitQueries.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Resonance.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/RingInfo.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Rings.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ROMol.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/RWMol.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SanitException.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SubstanceGroup.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/StereoGroup.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MonomerInfo.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/new_canon.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolBundle.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSmilesParse.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSmilesParse.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSmilesParse.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmartsWrite.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParse.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesWrite.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/CanonicalizeStereoGroups.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesJSONParsers.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitDepictor.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitDepictor.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitDepictor.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Depictor/DepictUtils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Depictor/EmbeddedFrag.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Depictor/RDDepictor.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdDepictor.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMarvinParser.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMarvinParser.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMarvinParser.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MarvinParse/MarvinParser.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitFileParsers.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitFileParsers.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitFileParsers.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/CDXMLParser.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParsers.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParserUtils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolFileStereochem.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileWriters.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.v1API.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolWriters.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceParsers.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceWriters.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/GeneralFileReader.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSDMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/PNGParser.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSubstructMatch.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructUtils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitGenericGroups.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitGenericGroups.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitGenericGroups.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/GenericGroups/GenericGroups.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitChemReactions.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitChemReactions.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitChemReactions.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Reaction.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionParser.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionPickler.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionFingerprints.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionUtils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionRunner.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/PreprocessRxn.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/SanitizeRxn.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/Enumerate.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateBase.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/CartesianProduct.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSample.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdChemReactions.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitChemTransforms.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitChemTransforms.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitChemTransforms.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/MolFragmenterJSONParser.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitTautomerQuery.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/TautomerQuery/TautomerQuery.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdTautomerQuery.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSubgraphs.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSubgraphs.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSubgraphs.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/Subgraphs.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/SubgraphUtils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitFilterCatalog.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalog.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatcherBase.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatchers.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdfiltercatalog.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitFragCatalog.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitFragCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitFragCatalog.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatGenerator.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatParams.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragFPGenerator.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdfragcatalog.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitDescriptors.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitDescriptors.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitDescriptors.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Crippen.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/BCUT.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Lipinski.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolSurf.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/ConnectivityDescriptors.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MQN.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RegisterDescriptor.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Property.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR2D.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Data3Ddescriptors.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolData3Ddescriptors.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/USRDescriptor.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AtomFeat.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/OxidationNumbers.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/DCLV.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors3D.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/EEM.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PBF.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PMI.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR3D.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RDF.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MORSE.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/GETAWAY.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/WHIM.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/CoulombMat.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolDescriptors.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitFingerprints.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitFingerprints.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitFingerprints.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairs.h -- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/TopologicalTorsionGenerator.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintUtil.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdFingerprintGenerator.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMHFPFingerprint.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitPartialCharges.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitPartialCharges.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitPartialCharges.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerCharges.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerParams.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdPartialCharges.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolTransforms.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolTransforms.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolTransforms.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolTransforms/MolTransforms.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolTransforms.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1.2025.03.1 -- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/MMFF.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdForceFieldHelpers.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/Embedder.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdDistGeom.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolAlign.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolAlign.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolAlign.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitO3AAlign.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitO3AAlign.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitO3AAlign.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/AlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/O3AAlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolAlign.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/FeatureParser.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitShapeHelpers.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeUtils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdShapeHelpers.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolCatalog.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolCatalog.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalog.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolCatalog.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2Dwx.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DHelpers.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolDraw2D.so -- 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMMPA.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRascalMCES.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRascalMCES.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRascalMCES.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalMCES.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalOptions.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalClusterOptions.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalResult.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdRascalMCES.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSynthonSpaceSearch.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSynthonSpaceSearch.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpace.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSet.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/Synthon.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SearchResults.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceRascalSearcher.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdSynthonSpaceSearch.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitCIPLabeler.so -- 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitTrajectory.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitTrajectory.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitTrajectory.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Snapshot.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Trajectory.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSubstructLibrary.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/PatternFactory.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdSubstructLibrary.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecompParams.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecompJSONParsers.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdRGroupDecomposition.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolInterchange.so.1.2025.03.1 -- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolStandardize.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolStandardize.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolStandardize.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Pipeline.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/MolStandardize.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Metal.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Normalize.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Validate.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Charge.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Tautomer.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Fragment.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h -- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdGeneralizedSubstruct.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolProcessing.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolProcessing.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolProcessing.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolProcessing/MolProcessing.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolProcessing.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolInteractionFields.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolInteractionFields.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitMolInteractionFields.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/GraphMol/MolInteractionFields/MIFDescriptors.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMIF.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Query/AndQuery.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Query/EqualityQuery.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Query/GreaterEqualQuery.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Query/GreaterQuery.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Query/LessEqualQuery.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Query/LessQuery.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Query/NullQueryAlgebra.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Query/OrQuery.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Query/Query.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Query/QueryObjects.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Query/RangeQuery.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Query/SetQuery.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Query/XOrQuery.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/Features/Feature.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricFuncs.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/SimDivPickers/DistPicker.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/SimDivPickers/LeaderPicker.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/SimDivPickers/HierarchicalClusterPicker.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/SimDivPickers/MaxMinPicker.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/rdSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKithc.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKithc.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKithc.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Clustering.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitInfoTheory.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitInfoTheory.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/rdInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/cQuantize.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ChemicalFeatures/ChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/ChemicalFeatures/FreeChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdChemicalFeatures.so ===================================================================== PostgreSQL cartridge installation succeeded. ===================================================================== Restart the PostgreSQL service before using the PostgreSQL RDKit cartridge. ===================================================================== -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDPaths.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets.cmake -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets-none.cmake -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/cmake/rdkit/rdkit-config.cmake -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/cmake/rdkit/rdkit-config-version.cmake -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-targets.cmake -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-targets-none.cmake -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-config.cmake -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-config-version.cmake make[2]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' mkdir -p /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3 mv /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3/dist-packages rm -f -rf /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13 ln -sf /usr/share/fonts/truetype/freefont/FreeSans.ttf /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/FreeSans.ttf dh_install -ppython3-rdkit /usr/lib/python3 dh_install: warning: All requested packages have been excluded (e.g. via a Build-Profile or due to architecture restrictions). rm -f -rf /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3/dist-packages/rdkit/docs/ rm -f -rf /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/__pycache__ dh_numpy3 Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. dh_install for v in $(pg_buildext supported-versions); do \ mkdir -p debian/postgresql-$v-rdkit/usr/lib/postgresql/$v/lib/ debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ cp Code/PgSQL/rdkit/build-$v/librdkit.so debian/postgresql-$v-rdkit/usr/lib/postgresql/$v/lib/rdkit.so; \ cp Code/PgSQL/rdkit/build-$v/rdkit*.sql debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ cp Code/PgSQL/rdkit/build-$v/update_sql/rdkit*.sql debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ cp Code/PgSQL/rdkit/rdkit.control debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ done mkdir -p /build/reproducible-path/rdkit-202503.1/debian/rdkit-doc/usr/share/doc/rdkit/ # cp /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/RDKit.pdf /build/reproducible-path/rdkit-202503.1/debian/rdkit-doc/usr/share/doc/rdkit/ cp -a /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html /build/reproducible-path/rdkit-202503.1/debian/rdkit-doc/usr/share/doc/rdkit/ ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202503.1/debian/rdkit-doc/usr/share/doc/rdkit//html/cppapi/jquery.js ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202503.1/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/jquery.js ln -sf /usr/share/javascript/underscore/underscore.js /build/reproducible-path/rdkit-202503.1/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/underscore.js make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' dh_installdocs -i -O--buildsystem=cmake debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' dh_installchangelogs ReleaseNotes.md make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' dh_python3 -ppython3-rdkit dh_numpy3 -ppython3-rdkit Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. dh_numpy3: warning: All requested packages have been excluded (e.g. via a Build-Profile or due to architecture restrictions). make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' dh_installsystemduser -i -O--buildsystem=cmake dh_perl -i -O--buildsystem=cmake dh_link -i -O--buildsystem=cmake dh_strip_nondeterminism -i -O--buildsystem=cmake dh_compress -i -O--buildsystem=cmake dh_fixperms -i -O--buildsystem=cmake debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' dh_missing --list-missing dh_missing: warning: usr/lib/postgresql/17/lib/rdkit.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Avalon/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/AllChem.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Pairs.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Sheridan.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Torsions.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Utils.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/BRICS.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/BuildFragmentCatalog.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/AlignDepict.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/BulkTester.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/DescriptorUtilities.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/SDFToCSV.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/TemplateExpand.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/ChemicalFeatures.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/ChemicalForceFields.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Crippen.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/DSViewer.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Descriptors.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Descriptors3D.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Draw/FreeSans.ttf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Draw/IPythonConsole.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Draw/InteractiveRenderer.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Draw/MolDrawing.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Draw/SimilarityMaps.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Draw/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Draw/rdMolDraw2D.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/EState/AtomTypes.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/EState/EState.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/EState/EState_VSA.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/EState/Fingerprinter.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/EState/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/EnumerateHeterocycles.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/EnumerateStereoisomers.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/FastSDMolSupplier.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/FeatFinderCLI.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapParser.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapPoint.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapUtils.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMaps.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Features/FeatDirUtilsRD.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Features/ShowFeats.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Features/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/FilterCatalog.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/ClusterMols.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/DbFpSupplier.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/FingerprintMols.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/MolSimilarity.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/SimilarityScreener.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Fraggle/FraggleSim.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Fraggle/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/FragmentCatalog.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/FragmentMatcher.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Fragments.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/FunctionalGroups.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/GraphDescriptors.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Graphs.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Lipinski.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MACCSkeys.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MCS.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MolCatalog.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MolDb/FingerprintUtils.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader_orig.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader_sa.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MolDb/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MolKey/InchiInfo.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MolKey/MolKey.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MolKey/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/rdMolStandardize.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/MolSurf.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/PandasPatcher.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/PandasTools.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Generate.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/LazyGenerator.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Matcher.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/SigFactory.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Utils.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/EmbedLib.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/ExcludedVolume.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/Pharmacophore.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/PropertyMol.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/PyMol.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/QED.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Randomize.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/Recap.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/ReducedGraphs.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/RegistrationHash.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/SATIS.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/SaltRemover.py exists in debian/tmp but is not installed to 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but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdFingerprintGenerator.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdForceFieldHelpers.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdGeneralizedSubstruct.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdMHFPFingerprint.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdMIF.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdMMPA.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdMolAlign.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdMolCatalog.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdMolChemicalFeatures.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdMolDescriptors.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdMolEnumerator.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdMolHash.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdMolInterchange.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/Chem/rdMolProcessing.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: 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exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmartsRemover.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesOutput.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesSupply.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/demo.py exists in debian/tmp but 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usr/lib/python3/dist-packages/rdkit/sping/PIL/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pidPIL.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-10.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-12.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-14.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-18.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-24.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/metrics.dat exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/removemedium.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-10.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-10.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-12.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-12.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-14.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-14.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-18.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-18.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-24.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-24.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-8.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-8.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PS/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PS/fontinfo.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PS/latin1MetricsCache.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PS/pidPS.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/PS/psmetrics.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/Pyart/Fontmapping.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/Pyart/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/Pyart/pidPyart.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/Qt/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/Qt/pidQt.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/Qt/pidQt4.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/README exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/ReportLab/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/ReportLab/pidReportLab.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/SVG/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/SVG/pidSVG.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/TK/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/TK/pidTK.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/WX/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/WX/pidWX.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/WX/pidWxDc.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/colors.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/examples/formatted-strings.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/pagesizes.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1.1.diff exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/pid.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/stringformat.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/tests/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/tests/pidtest.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/tests/pstests.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/tests/testallps.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/util/HTMLPiddler.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/util/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/sping/utils.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/utils/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/utils/cactvs.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/utils/chemdraw.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/utils/chemdraw_qax.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/utils/chemutils.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/utils/fileutils.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/utils/listutils.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/utils/retest.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/python3/dist-packages/rdkit/utils/spiral.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/CMakeLists.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/FindMyRDKit.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example1.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example10.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example11.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example12.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example13.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example14.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example15.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example16.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example17.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example2.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example3.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example4.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example5.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: 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exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_or2_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_trans_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.ai exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.inkscape.svg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.lrg.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo_plain.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/compounds.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/RD.css exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/README.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/FeatFinderCLI.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/PythonFormat.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/README.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/create_deb_packages.sh exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/gen_rdkit_stubs/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/gen_rdkit_stubs/__main__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/gen_rdkit_stubs/worker.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/patch_rdkit_docstrings/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/patch_rdkit_docstrings/__main__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/patch_rdkit_docstrings/clang_worker.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/test.sh exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/license.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--3.8--4.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.0--4.0.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.0.1--4.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.1--4.1.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.1.1--4.2.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.2--4.3.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.3.0--4.4.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.4.0--4.5.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.5.0--4.6.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.6.0--4.6.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.6.1--4.7.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.7.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit.control exists in debian/tmp but is not installed to anywhere The following debhelper tools have reported what they installed (with files per package) * dh_install: librdkit-dev (64), librdkit1t64 (124), postgresql-17-rdkit (0), python3-rdkit (0), rdkit-data (3), rdkit-doc (0) * dh_installdocs: librdkit-dev (0), librdkit1t64 (0), postgresql-17-rdkit (0), python3-rdkit (0), rdkit-data (0), rdkit-doc (0) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.md.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built If the omission is intentional or no other helper can take care of this consider adding the paths to debian/not-installed. make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' dh_installdeb -i -O--buildsystem=cmake dh_gencontrol -i -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -i -O--buildsystem=cmake dh_builddeb -i -O--buildsystem=cmake dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202503.1-4_all.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202503.1-4_all.deb'. dpkg-genbuildinfo --build=all -O../rdkit_202503.1-4_all.buildinfo dpkg-genchanges --build=all -O../rdkit_202503.1-4_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2025-07-28T09:37:09Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 28 Jul 2025 09:37:10 +0000 | +------------------------------------------------------------------------------+ rdkit_202503.1-4_all.changes: ----------------------------- Format: 1.8 Date: Tue, 29 Apr 2025 09:27:17 -0400 Source: rdkit Binary: rdkit-data rdkit-doc Architecture: all Version: 202503.1-4 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Andrius Merkys Description: rdkit-data - Collection of cheminformatics and machine-learning software (data rdkit-doc - Collection of cheminformatics and machine-learning software (docu Closes: 1104363 Changes: rdkit (202503.1-4) unstable; urgency=medium . * Update debian/control.in according to debian/control (Closes: #1104363) Checksums-Sha1: 26642f0b174ad8f41dc42b0aecf0e78ed840eba6 13179164 rdkit-data_202503.1-4_all.deb 6f7a445ae63bb7e14693639a90f3099f8133424b 6888552 rdkit-doc_202503.1-4_all.deb c79502b89330e3c1ce86b6a163e83ca627096f68 15883 rdkit_202503.1-4_all.buildinfo Checksums-Sha256: 82641970ca98ba9ef7d38ed01a1ec462de262c9206ec6243edff59990282c987 13179164 rdkit-data_202503.1-4_all.deb 9279dd3dfae6b3907443ca3cd57975bfbf6f6ce20546f0f67514f9b088020997 6888552 rdkit-doc_202503.1-4_all.deb 319013d44bd87c81f6dd9cc109883ffd7dc67835b4dff2be235470d54c63ca72 15883 rdkit_202503.1-4_all.buildinfo Files: 43d4037ea218ee1e9a0d43716d6aecad 13179164 science optional rdkit-data_202503.1-4_all.deb 36903a4e54d63771e375a4e8726577e3 6888552 doc optional rdkit-doc_202503.1-4_all.deb 78ac235fc542cf837c3e1fc9fe69994a 15883 science optional rdkit_202503.1-4_all.buildinfo +------------------------------------------------------------------------------+ | Buildinfo Mon, 28 Jul 2025 09:37:11 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: rdkit Binary: rdkit-data rdkit-doc Architecture: all Version: 202503.1-4 Checksums-Md5: 43d4037ea218ee1e9a0d43716d6aecad 13179164 rdkit-data_202503.1-4_all.deb 36903a4e54d63771e375a4e8726577e3 6888552 rdkit-doc_202503.1-4_all.deb Checksums-Sha1: 26642f0b174ad8f41dc42b0aecf0e78ed840eba6 13179164 rdkit-data_202503.1-4_all.deb 6f7a445ae63bb7e14693639a90f3099f8133424b 6888552 rdkit-doc_202503.1-4_all.deb Checksums-Sha256: 82641970ca98ba9ef7d38ed01a1ec462de262c9206ec6243edff59990282c987 13179164 rdkit-data_202503.1-4_all.deb 9279dd3dfae6b3907443ca3cd57975bfbf6f6ce20546f0f67514f9b088020997 6888552 rdkit-doc_202503.1-4_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 28 Jul 2025 09:37:09 +0000 Build-Path: /build/reproducible-path/rdkit-202503.1 Installed-Build-Depends: adduser (= 3.150), architecture-properties (= 0.2.6), autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 13.7), base-passwd (= 3.6.7), bash (= 5.2.37-2), binutils (= 2.44-3), binutils-common (= 2.44-3), binutils-x86-64-linux-gnu (= 2.44-3), bison (= 2:3.8.2+dfsg-1+b2), bsdextrautils (= 2.41-4), bsdutils (= 1:2.41-4), build-essential (= 12.12), bzip2 (= 1.0.8-6), ca-certificates (= 20250419), catch2 (= 3.7.1-0.5), clang-19 (= 1:19.1.7-3), cmake (= 3.31.6-2), cmake-data (= 3.31.6-2), coreutils (= 9.7-2), cpp (= 4:14.2.0-1), cpp-14 (= 14.2.0-19), cpp-14-x86-64-linux-gnu (= 14.2.0-19), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.24.2), debianutils (= 5.22), dh-autoreconf (= 20), dh-python (= 6.20250414), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), docutils-common (= 0.21.2+dfsg-2), doxygen (= 1.9.8+ds-2.1), dpkg (= 1.22.18), dpkg-dev (= 1.22.18), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), flex (= 2.6.4-8.2+b4), fontconfig (= 2.15.0-2.3), fontconfig-config (= 2.15.0-2.3), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), fonts-lmodern (= 2.005-1), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-19), g++-14-x86-64-linux-gnu (= 14.2.0-19), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-14 (= 14.2.0-19), gcc-14-base (= 14.2.0-19), gcc-14-x86-64-linux-gnu (= 14.2.0-19), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2), gettext-base (= 0.23.1-2), girepository-tools (= 2.84.1-2), grep (= 3.11-4), groff-base (= 1.23.0-7), gzip (= 1.13-1), hicolor-icon-theme (= 0.18-2), hostname (= 3.25), icu-devtools (= 76.1-3), imagemagick (= 8:7.1.1.47+dfsg1-1), imagemagick-7-common (= 8:7.1.1.47+dfsg1-1), imagemagick-7.q16 (= 8:7.1.1.47+dfsg1-1), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), latexmk (= 1:4.86~ds-1), libacl1 (= 2.3.2-2+b1), libapache-pom-java (= 33-2), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.7.4-3), libasan8 (= 14.2.0-19), libatomic1 (= 14.2.0-19), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b2), libbinutils (= 2.44-3), libblas3 (= 3.12.1-2), libblkid-dev (= 2.41-4), libblkid1 (= 2.41-4), libboost-atomic1.83-dev (= 1.83.0-4.2), libboost-atomic1.83.0 (= 1.83.0-4.2), libboost-chrono1.83-dev (= 1.83.0-4.2), libboost-chrono1.83.0t64 (= 1.83.0-4.2), libboost-date-time1.83-dev (= 1.83.0-4.2), libboost-date-time1.83.0 (= 1.83.0-4.2), libboost-dev (= 1.83.0.2+b2), libboost-iostreams-dev (= 1.83.0.2+b2), libboost-iostreams1.83-dev (= 1.83.0-4.2), libboost-iostreams1.83.0 (= 1.83.0-4.2), libboost-numpy-dev (= 1.83.0.2+b2), libboost-numpy1.83-dev (= 1.83.0-4.2), libboost-numpy1.83.0 (= 1.83.0-4.2), libboost-program-options-dev (= 1.83.0.2+b2), libboost-program-options1.83-dev (= 1.83.0-4.2), libboost-program-options1.83.0 (= 1.83.0-4.2), libboost-python-dev (= 1.83.0.2+b2), libboost-python1.83-dev (= 1.83.0-4.2), libboost-python1.83.0 (= 1.83.0-4.2), libboost-regex-dev (= 1.83.0.2+b2), libboost-regex1.83-dev (= 1.83.0-4.2), libboost-regex1.83.0 (= 1.83.0-4.2), libboost-serialization1.83-dev (= 1.83.0-4.2), libboost-serialization1.83.0 (= 1.83.0-4.2), libboost-system-dev (= 1.83.0.2+b2), libboost-system1.83-dev (= 1.83.0-4.2), libboost-system1.83.0 (= 1.83.0-4.2), libboost-thread-dev (= 1.83.0.2+b2), libboost-thread1.83-dev (= 1.83.0-4.2), libboost-thread1.83.0 (= 1.83.0-4.2), libboost1.83-dev (= 1.83.0-4.2), libbrotli-dev (= 1.1.0-2+b7), libbrotli1 (= 1.1.0-2+b7), libbsd0 (= 0.12.2-2), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.41-7), libc-dev-bin (= 2.41-7), libc6 (= 2.41-7), libc6-dev (= 2.41-7), libcairo-gobject2 (= 1.18.4-1+b1), libcairo-script-interpreter2 (= 1.18.4-1+b1), libcairo2 (= 1.18.4-1+b1), libcairo2-dev (= 1.18.4-1+b1), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-7), libcatch2-dev (= 3.7.1-0.5), libcc1-0 (= 14.2.0-19), libclang-common-19-dev (= 1:19.1.7-3), libclang-cpp19 (= 1:19.1.7-3), libclang1-19 (= 1:19.1.7-3), libcom-err2 (= 1.47.2-1+b1), libcommons-logging-java (= 1.3.0-1), libcommons-parent-java (= 56-1), libcoordgen-dev (= 3.0.2-1+b2), libcoordgen3 (= 3.0.2-1+b2), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.44-3), libctf0 (= 2.44-3), libcurl4t64 (= 8.13.0-5), libdatrie1 (= 0.2.13-3+b1), libdav1d7 (= 1.5.1-1), libdb5.3t64 (= 5.3.28+dfsg2-9), libde265-0 (= 1.0.15-1+b3), libdebconfclient0 (= 0.278), libdebhelper-perl (= 13.24.2), libdeflate0 (= 1.23-2), libdpkg-perl (= 1.22.18), libedit2 (= 3.1-20250104-1), libeigen3-dev (= 3.4.0-4), libelf1t64 (= 0.192-4), libexpat1 (= 2.7.1-1), libexpat1-dev (= 2.7.1-1), libffi-dev (= 3.4.8-2), libffi8 (= 3.4.8-2), libfftw3-double3 (= 3.3.10-2+b1), libfile-stripnondeterminism-perl (= 1.14.1-2), libfmt10 (= 10.1.1+ds1-4), libfontbox-java (= 1:1.8.16-5), libfontconfig-dev (= 2.15.0-2.3), libfontconfig1 (= 2.15.0-2.3), libfontenc1 (= 1:1.1.8-1+b2), libfreetype-dev (= 2.13.3+dfsg-1), libfreetype6 (= 2.13.3+dfsg-1), libfribidi0 (= 1.0.16-1), libgc1 (= 1:8.2.8-1), libgcc-14-dev (= 14.2.0-19), libgcc-s1 (= 14.2.0-19), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgdk-pixbuf-2.0-0 (= 2.42.12+dfsg-2), libgdk-pixbuf2.0-common (= 2.42.12+dfsg-2), libgfortran5 (= 14.2.0-19), libgio-2.0-dev (= 2.84.1-2), libgio-2.0-dev-bin (= 2.84.1-2), libgirepository-2.0-0 (= 2.84.1-2), libglib2.0-0t64 (= 2.84.1-2), libglib2.0-bin (= 2.84.1-2), libglib2.0-data (= 2.84.1-2), libglib2.0-dev (= 2.84.1-2), libglib2.0-dev-bin (= 2.84.1-2), libgmp10 (= 2:6.3.0+dfsg-3), libgnutls30t64 (= 3.8.9-2), libgomp1 (= 14.2.0-19), libgprofng0 (= 2.44-3), libgraphite2-3 (= 1.3.14-2+b1), libgssapi-krb5-2 (= 1.21.3-5), libharfbuzz0b (= 10.2.0-1+b1), libheif-plugin-dav1d (= 1.19.8-1), libheif-plugin-libde265 (= 1.19.8-1), libheif1 (= 1.19.8-1), libhogweed6t64 (= 3.10.1-1), libhwasan0 (= 14.2.0-19), libice-dev (= 2:1.1.1-1), libice6 (= 2:1.1.1-1), libicu-dev (= 76.1-3), libicu76 (= 76.1-3), libidn2-0 (= 2.3.8-2), libimagequant0 (= 2.18.0-1+b2), libinchi-dev (= 1.07.3+dfsg-1), libinchi1.07 (= 1.07.3+dfsg-1), libio-pty-perl (= 1:1.20-1+b3), libipc-run-perl (= 20231003.0-2), libisl23 (= 0.27-1), libitm1 (= 14.2.0-19), libjansson4 (= 2.14-2+b3), libjbig0 (= 2.1-6.1+b2), libjpeg62-turbo (= 1:2.1.5-3.1), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-sphinxdoc (= 8.1.3-5), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libjson-perl (= 4.10000-1), libjsoncpp26 (= 1.9.6-3), libk5crypto3 (= 1.21.3-5), libkeyutils1 (= 1.6.3-6), libkpathsea6 (= 2024.20240313.70630+ds-6), libkrb5-3 (= 1.21.3-5), libkrb5support0 (= 1.21.3-5), liblapack3 (= 3.12.1-2), liblastlog2-2 (= 2.41-4), liblcms2-2 (= 2.16-2), libldap2 (= 2.6.9+dfsg-2), liblerc4 (= 4.0.0+ds-5), libllvm19 (= 1:19.1.7-3), liblqr-1-0 (= 0.4.2-2.1+b2), liblsan0 (= 14.2.0-19), libltdl7 (= 2.5.4-4), liblua5.4-0 (= 5.4.7-1+b2), liblz4-1 (= 1.10.0-4), liblzma5 (= 5.8.1-1), liblzo2-2 (= 2.10-3+b1), libmaeparser-dev (= 1.3.1-1+b2), libmaeparser1 (= 1.3.1-1+b2), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmagickcore-7.q16-10 (= 8:7.1.1.47+dfsg1-1), libmagickwand-7.q16-10 (= 8:7.1.1.47+dfsg1-1), libmd0 (= 1.1.0-2+b1), libmount-dev (= 2.41-4), libmount1 (= 2.41-4), libmpc3 (= 1.3.1-1+b3), libmpfi0 (= 1.5.4+ds-4), libmpfr6 (= 4.2.2-1), libncurses-dev (= 6.5+20250216-2), libncurses6 (= 6.5+20250216-2), libncursesw6 (= 6.5+20250216-2), libnettle8t64 (= 3.10.1-1), libnghttp2-14 (= 1.64.0-1.1), libnghttp3-9 (= 1.8.0-1), libnuma1 (= 2.0.19-1), libobjc-14-dev (= 14.2.0-19), libobjc4 (= 14.2.0-19), libopenjp2-7 (= 2.5.3-2), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.7.0-3), libpam-modules-bin (= 1.7.0-3), libpam-runtime (= 1.7.0-3), libpam0g (= 1.7.0-3), libpango-1.0-0 (= 1.56.3-1), libpangocairo-1.0-0 (= 1.56.3-1), libpangoft2-1.0-0 (= 1.56.3-1), libpaper-utils (= 2.2.5-0.3+b2), libpaper2 (= 2.2.5-0.3+b2), libpcre2-16-0 (= 10.45-1), libpcre2-32-0 (= 10.45-1), libpcre2-8-0 (= 10.45-1), libpcre2-dev (= 10.45-1), libpcre2-posix3 (= 10.45-1), libpdfbox-java (= 1:1.8.16-5), libperl5.40 (= 5.40.1-3), libpfm4 (= 4.13.0+git99-gc5587f9-1), libpipeline1 (= 1.5.8-1), libpixman-1-0 (= 0.44.0-3), libpixman-1-dev (= 0.44.0-3), libpkgconf3 (= 1.8.1-4), libpng-dev (= 1.6.47-1.1), libpng16-16t64 (= 1.6.47-1.1), libpotrace0 (= 1.16-2+b2), libpq-dev (= 17.4-2), libpq5 (= 17.4-2), libproc2-0 (= 2:4.0.4-8), libpsl5t64 (= 0.21.2-1.1+b1), libptexenc1 (= 2024.20240313.70630+ds-6), libpython3-dev (= 3.13.3-1), libpython3-stdlib (= 3.13.3-1), libpython3.13 (= 3.13.3-2), libpython3.13-dev (= 3.13.3-2), libpython3.13-minimal (= 3.13.3-2), libpython3.13-stdlib (= 3.13.3-2), libquadmath0 (= 14.2.0-19), libraqm0 (= 0.10.2-1), libraw23t64 (= 0.21.4-2), libreadline8t64 (= 8.2-6), librhash1 (= 1.4.5-1), librsvg2-2 (= 2.60.0+dfsg-1), librsvg2-bin (= 2.60.0+dfsg-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libsasl2-2 (= 2.1.28+dfsg1-9), libsasl2-modules-db (= 2.1.28+dfsg1-9), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libselinux1-dev (= 3.8.1-1), libsemanage-common (= 3.8.1-1), libsemanage2 (= 3.8.1-1), libsepol-dev (= 3.8.1-1), libsepol2 (= 3.8.1-1), libsframe1 (= 2.44-3), libsharpyuv0 (= 1.5.0-0.1), libsm-dev (= 2:1.2.6-1), libsm6 (= 2:1.2.6-1), libsmartcols1 (= 2.41-4), libsqlite3-0 (= 3.46.1-3), libsqlite3-dev (= 3.46.1-3), libssh2-1t64 (= 1.11.1-1), libssl-dev (= 3.5.0-1), libssl3t64 (= 3.5.0-1), libstdc++-14-dev (= 14.2.0-19), libstdc++6 (= 14.2.0-19), libsynctex2 (= 2024.20240313.70630+ds-6), libsysprof-capture-4-dev (= 48.0-2), libsystemd0 (= 257.5-2), libtasn1-6 (= 4.20.0-2), libteckit0 (= 2.5.12+ds1-1+b1), libtexlua53-5 (= 2024.20240313.70630+ds-6), libtext-charwidth-perl (= 0.04-11+b4), libtext-wrapi18n-perl (= 0.06-10), libthai-data (= 0.1.29-2), libthai0 (= 0.1.29-2+b1), libtiff6 (= 4.7.0-3), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 14.2.0-19), libubsan1 (= 14.2.0-19), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.5-2), libunistring5 (= 1.3-2), libuuid1 (= 2.41-4), libuv1t64 (= 1.50.0-2), libwebp7 (= 1.5.0-0.1), libwebpdemux2 (= 1.5.0-0.1), libwebpmux3 (= 1.5.0-0.1), libx11-6 (= 2:1.8.12-1), libx11-data (= 2:1.8.12-1), libx11-dev (= 2:1.8.12-1), libxapian30 (= 1.4.29-2), libxau-dev (= 1:1.0.11-1), libxau6 (= 1:1.0.11-1), libxaw7 (= 2:1.0.16-1), libxcb-render0 (= 1.17.0-2+b1), libxcb-render0-dev (= 1.17.0-2+b1), libxcb-shm0 (= 1.17.0-2+b1), libxcb-shm0-dev (= 1.17.0-2+b1), libxcb1 (= 1.17.0-2+b1), libxcb1-dev (= 1.17.0-2+b1), libxdmcp-dev (= 1:1.1.5-1), libxdmcp6 (= 1:1.1.5-1), libxext-dev (= 2:1.3.4-1+b3), libxext6 (= 2:1.3.4-1+b3), libxi6 (= 2:1.8.2-1), libxml2 (= 2.12.7+dfsg+really2.9.14-0.4), libxml2-dev (= 2.12.7+dfsg+really2.9.14-0.4), libxmu6 (= 2:1.1.3-3+b4), libxpm4 (= 1:3.5.17-1+b3), libxrender-dev (= 1:0.9.12-1), libxrender1 (= 1:0.9.12-1), libxt6t64 (= 1:1.2.1-1.2+b2), libxxhash0 (= 0.8.3-2), libyaml-0-2 (= 0.2.5-2), libz3-4 (= 4.13.3-1), libz3-dev (= 4.13.3-1), libzstd1 (= 1.5.7+dfsg-1), libzzip-0-13t64 (= 0.13.78+dfsg.1-0.1), linux-libc-dev (= 6.12.25-1), llvm-19 (= 1:19.1.7-3), llvm-19-dev (= 1:19.1.7-3), llvm-19-linker-tools (= 1:19.1.7-3), llvm-19-runtime (= 1:19.1.7-3), llvm-19-tools (= 1:19.1.7-3), login.defs (= 1:4.17.4-2), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.0-1), mawk (= 1.3.4.20250131-1), media-types (= 13.0.0), native-architecture (= 0.2.6), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), netbase (= 6.5), openssl (= 3.5.0-1), openssl-provider-legacy (= 3.5.0-1), pandoc (= 3.1.11.1+ds-2), pandoc-data (= 3.1.11.1-3), passwd (= 1:4.17.4-2), patch (= 2.8-1), perl (= 5.40.1-3), perl-base (= 5.40.1-3), perl-modules-5.40 (= 5.40.1-3), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), postgresql-client-17 (= 17.4-2), postgresql-client-common (= 277), postgresql-common (= 277), postgresql-common-dev (= 277), postgresql-server-dev-17 (= 17.4-2), postgresql-server-dev-all (= 277), preview-latex-style (= 13.2-1), procps (= 2:4.0.4-8), python-babel-localedata (= 2.17.0-1), python3 (= 3.13.3-1), python3-alabaster (= 0.7.16-0.1), python3-babel (= 2.17.0-1), python3-certifi (= 2025.1.31+ds-1), python3-chardet (= 5.2.0+dfsg-2), python3-charset-normalizer (= 3.4.1-1+b1), python3-commonmark (= 0.9.1-8), python3-dateutil (= 2.9.0-4), python3-defusedxml (= 0.7.1-3), python3-dev (= 3.13.3-1), python3-docutils (= 0.21.2+dfsg-2), python3-greenlet (= 3.1.0-1+b2), python3-idna (= 3.10-1), python3-imagesize (= 1.4.1-1), python3-iniconfig (= 1.1.1-2), python3-jinja2 (= 3.1.6-1), python3-markdown-it (= 3.0.0-2), python3-markupsafe (= 2.1.5-1+b3), python3-mdit-py-plugins (= 0.4.2-1), python3-mdurl (= 0.1.2-1), python3-minimal (= 3.13.3-1), python3-myst-parser (= 4.0.1-1), python3-numpy (= 1:2.2.4+ds-1), python3-numpy-dev (= 1:2.2.4+ds-1), python3-packaging (= 25.0-1), python3-pandas (= 2.2.3+dfsg-9), python3-pandas-lib (= 2.2.3+dfsg-9), python3-pil (= 11.1.0-5+b1), python3-pluggy (= 1.5.0-1), python3-pygments (= 2.18.0+dfsg-2), python3-pytest (= 8.3.5-2), python3-pytz (= 2025.2-2), python3-recommonmark (= 0.7.1+ds-8), python3-requests (= 2.32.3+dfsg-5), python3-roman (= 5.0-1), python3-snowballstemmer (= 2.2.0-4), python3-sphinx (= 8.1.3-5), python3-sqlalchemy (= 2.0.40+ds1-1), python3-typing-extensions (= 4.13.2-1), python3-urllib3 (= 2.3.0-2), python3-yaml (= 6.0.2-1+b2), python3.13 (= 3.13.3-2), python3.13-dev (= 3.13.3-2), python3.13-minimal (= 3.13.3-2), rapidjson-dev (= 1.1.0+dfsg2-7.4), readline-common (= 8.2-6), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sgml-base (= 1.31+nmu1), shared-mime-info (= 2.4-5+b2), sphinx-common (= 8.1.3-5), ssl-cert (= 1.1.3), sysvinit-utils (= 3.14-4), t1utils (= 1.41-4), tar (= 1.35+dfsg-3.1), tex-common (= 6.19), tex-gyre (= 20180621-6), texlive-base (= 2024.20250309-1), texlive-binaries (= 2024.20240313.70630+ds-6), texlive-fonts-recommended (= 2024.20250309-1), texlive-latex-base (= 2024.20250309-1), texlive-latex-extra (= 2024.20250309-2), texlive-latex-recommended (= 2024.20250309-1), texlive-pictures (= 2024.20250309-1), tzdata (= 2025b-2), ucf (= 3.0051), util-linux (= 2.41-4), uuid-dev (= 2.41-4), x11-common (= 1:7.7+24), x11proto-dev (= 2024.1-1), xdg-utils (= 1.2.1-2), xfonts-encodings (= 1:1.0.4-2.2), xfonts-utils (= 1:7.7+7), xml-core (= 0.19), xorg-sgml-doctools (= 1:1.11-1.1), xtrans-dev (= 1.4.0-1), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=6" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1745933237" +------------------------------------------------------------------------------+ | Package contents Mon, 28 Jul 2025 09:37:11 +0000 | +------------------------------------------------------------------------------+ rdkit-data_202503.1-4_all.deb ----------------------------- new Debian package, version 2.0. size 13179164 bytes: control archive=6784 bytes. 441 bytes, 14 lines control 19086 bytes, 221 lines md5sums Package: rdkit-data Source: rdkit Version: 202503.1-4 Architecture: all Maintainer: Debichem Team Installed-Size: 59394 Section: science Priority: optional Homepage: http://www.rdkit.org Description: Collection of cheminformatics and machine-learning software (data files) RDKit is a Python/C++ based cheminformatics and machine-learning software environment. . This package contains data files. drwxr-xr-x root/root 0 2025-04-29 13:27 ./ drwxr-xr-x root/root 0 2025-04-29 13:27 ./usr/ drwxr-xr-x root/root 0 2025-04-29 13:27 ./usr/share/ drwxr-xr-x root/root 0 2025-04-29 13:27 ./usr/share/RDKit/ drwxr-xr-x root/root 0 2025-04-29 13:27 ./usr/share/RDKit/Contrib/ drwxr-xr-x root/root 0 2025-04-29 13:27 ./usr/share/RDKit/Contrib/AtomAtomSimilarity/ -rw-r--r-- root/root 14150 2025-03-31 18:11 ./usr/share/RDKit/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py -rw-r--r-- root/root 37 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CMakeLists.txt drwxr-xr-x root/root 0 2025-04-29 13:27 ./usr/share/RDKit/Contrib/CalcLigRMSD/ -rw-r--r-- root/root 3355 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py -rw-r--r-- root/root 25816 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb -rw-r--r-- root/root 3966 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/README.md drwxr-xr-x root/root 0 2025-04-29 13:27 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/ -rw-r--r-- root/root 2576 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/1C9_renamed.pdb -rw-r--r-- root/root 3812 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb -rw-r--r-- root/root 4174 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb -rw-r--r-- root/root 3340 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb -rw-r--r-- root/root 2290 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/4i23_1C9.pdb -rw-r--r-- root/root 2908 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/4i24_1C9.pdb -rw-r--r-- root/root 2197 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb -rw-r--r-- root/root 219105 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/5dpv.pdb -rw-r--r-- root/root 396495 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/5dt0.pdb -rw-r--r-- root/root 853659 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/6c83.pdb -rw-r--r-- root/root 3217 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb -rw-r--r-- root/root 3217 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb -rw-r--r-- root/root 2884 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb -rw-r--r-- root/root 3853 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/AKI_renamed.pdb -rw-r--r-- root/root 3811 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/BEG_test.pdb -rw-r--r-- root/root 2017 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/JVE_renamed.pdb -rw-r--r-- root/root 3076 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/N15_renamed.pdb -rw-r--r-- root/root 2805 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb -rw-r--r-- root/root 2576 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb -rw-r--r-- root/root 351089 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb -rw-r--r-- root/root 180441 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb -rw-r--r-- root/root 6611 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb -rw-r--r-- root/root 7365 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb -rw-r--r-- root/root 3999 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb -rw-r--r-- root/root 6027 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb -rw-r--r-- root/root 5595 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb -rw-r--r-- root/root 6256 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb -rw-r--r-- root/root 2805 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb drwxr-xr-x root/root 0 2025-04-29 13:27 ./usr/share/RDKit/Contrib/CalcLigRMSD/figures/ -rw-r--r-- root/root 742146 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/figures/1C9.png -rw-r--r-- root/root 551613 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/figures/5dpv_complex.png -rw-r--r-- root/root 588511 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/figures/6c83_complex.png -rw-r--r-- root/root 493752 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/figures/AKI.png -rw-r--r-- root/root 4701 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png -rw-r--r-- root/root 424439 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/figures/JVE.png -rw-r--r-- root/root 429769 2025-03-31 18:11 ./usr/share/RDKit/Contrib/CalcLigRMSD/figures/N15.png drwxr-xr-x root/root 0 2025-04-29 13:27 ./usr/share/RDKit/Contrib/ChiralPairs/ -rw-r--r-- root/root 16038 2025-03-31 18:11 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./usr/share/doc/rdkit-data/copyright rdkit-doc_202503.1-4_all.deb ---------------------------- new Debian package, version 2.0. size 6888552 bytes: control archive=115076 bytes. 486 bytes, 15 lines control 513071 bytes, 5107 lines md5sums Package: rdkit-doc Source: rdkit Version: 202503.1-4 Architecture: all Maintainer: Debichem Team Installed-Size: 82568 Depends: libjs-jquery, libjs-underscore Section: doc Priority: optional Homepage: http://www.rdkit.org Description: Collection of cheminformatics and machine-learning software (documentation) RDKit is a Python/C++ based cheminformatics and machine-learning software environment. . 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./usr/share/doc/rdkit/html/source/rdkit.utils.listutils.html -rw-r--r-- root/root 5250 2025-04-29 13:27 ./usr/share/doc/rdkit/html/source/rdkit.utils.spiral.html +------------------------------------------------------------------------------+ | Post Build Mon, 28 Jul 2025 09:37:12 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 28 Jul 2025 09:37:12 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 28 Jul 2025 09:37:17 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: all Build-Space: 5683340 Build-Time: 1287 Distribution: unstable Host Architecture: amd64 Install-Time: 8 Job: /srv/rebuilderd/tmp/rebuilderd3HfAy5/inputs/rdkit_202503.1-4.dsc Machine Architecture: amd64 Package: rdkit Package-Time: 1353 Source-Version: 202503.1-4 Space: 5683340 Status: successful Version: 202503.1-4 -------------------------------------------------------------------------------- Finished at 2025-07-28T09:37:09Z Build needed 00:22:33, 5683340k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderd3HfAy5/out checking rdkit-data_202503.1-4_all.deb: size... md5... sha256... sha1... all OK checking rdkit-doc_202503.1-4_all.deb: size differs for rdkit-doc_202503.1-4_all.deb