=============================================================================== 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/rebuilderd4rQZSi/inputs/mdtraj_1.11.1.post1-3_amd64.buildinfo Source: mdtraj Version: 1.11.1.post1-3 rebuilderd-worker node: osuosl41-amd64 +------------------------------------------------------------------------------+ | Downloading sources Wed, 04 Mar 2026 06:38:20 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [140 kB] Get:2 https://deb.debian.org/debian-security trixie-security InRelease [43.4 kB] Get:3 https://deb.debian.org/debian trixie-updates InRelease [47.3 kB] Get:4 https://deb.debian.org/debian trixie-proposed-updates InRelease [57.6 kB] Get:5 https://deb.debian.org/debian trixie-backports InRelease [54.0 kB] Get:6 https://deb.debian.org/debian forky InRelease [137 kB] Get:7 https://deb.debian.org/debian sid InRelease [187 kB] Get:8 https://deb.debian.org/debian experimental InRelease [91.7 kB] Get:9 https://deb.debian.org/debian trixie/non-free-firmware Sources [6,552 B] Get:10 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:11 https://deb.debian.org/debian-security trixie-security/main Sources [137 kB] Get:12 https://deb.debian.org/debian-security trixie-security/non-free-firmware Sources [696 B] Get:13 https://deb.debian.org/debian trixie-updates/main Sources [2,788 B] Get:14 https://deb.debian.org/debian trixie-proposed-updates/main Sources [102 kB] Get:15 https://deb.debian.org/debian trixie-backports/main Sources [154 kB] Get:16 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [2,464 B] Get:17 https://deb.debian.org/debian forky/main Sources [10.7 MB] Get:18 https://deb.debian.org/debian forky/non-free-firmware Sources [8,308 B] Get:19 https://deb.debian.org/debian sid/non-free-firmware Sources [10.5 kB] Get:20 https://deb.debian.org/debian sid/main Sources [11.4 MB] Get:21 https://deb.debian.org/debian experimental/non-free-firmware Sources [2,572 B] Get:22 https://deb.debian.org/debian experimental/main Sources [442 kB] Fetched 34.2 MB in 3s (10.1 MB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.11.1.post1-3.dsc' mdtraj_1.11.1.post1-3.dsc 2914 SHA256:804fa5bde050873d69e69ffc25f8f2f84c67fab5b9421b358ab8b8f2b7c5b0a2 'https://deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.11.1.post1.orig.tar.gz' mdtraj_1.11.1.post1.orig.tar.gz 22729550 SHA256:8a46153ba6102b851639bc61ab6db5387b4c5d5b46d09a72a519e845b3c1f390 'https://deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.11.1.post1-3.debian.tar.xz' mdtraj_1.11.1.post1-3.debian.tar.xz 301808 SHA256:5379a71153de26c9329136774ae225ba9e1a70ced7e3192397733087177ef578 8a46153ba6102b851639bc61ab6db5387b4c5d5b46d09a72a519e845b3c1f390 mdtraj_1.11.1.post1.orig.tar.gz 5379a71153de26c9329136774ae225ba9e1a70ced7e3192397733087177ef578 mdtraj_1.11.1.post1-3.debian.tar.xz 804fa5bde050873d69e69ffc25f8f2f84c67fab5b9421b358ab8b8f2b7c5b0a2 mdtraj_1.11.1.post1-3.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Wed, 04 Mar 2026 06:38:25 +0000 | +------------------------------------------------------------------------------+ Rebuilding mdtraj=1.11.1.post1-3 in /srv/rebuilderd/tmp/rebuilderd4rQZSi/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderd4rQZSi/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderd4rQZSi/inputs/mdtraj_1.11.1.post1-3_amd64.buildinfo /srv/rebuilderd/tmp/rebuilderd4rQZSi/inputs/mdtraj_1.11.1.post1-3_amd64.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/mdtraj-1.11.1.post1 I: verifying dsc... successful! Get:1 http://deb.debian.org/debian unstable InRelease [187 kB] Get:2 http://snapshot.debian.org/archive/debian/20260302T143911Z forky InRelease [137 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 Packages [10.3 MB] Get:4 http://snapshot.debian.org/archive/debian/20260302T143911Z forky/main amd64 Packages [9588 kB] Fetched 20.2 MB in 2s (12.2 MB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20260302T143911Z/dists/forky/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://deb.debian.org/debian unstable/main amd64 diffutils amd64 1:3.12-1 [405 kB] Fetched 405 kB in 0s (0 B/s) dpkg-name: info: moved 'diffutils_1%3a3.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpncr5fdqu/diffutils_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Fetched 877 kB in 0s (72.1 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-4_all.deb' to '/srv/rebuilderd/tmp/tmpgsllf1yo/automake_1.18.1-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-cffi-backend amd64 2.0.0-3 [111 kB] Fetched 111 kB in 0s (2438 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3p8lrauc/python3-cffi-backend_2.0.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.6+repack-2 [64.7 kB] Fetched 64.7 kB in 0s (3548 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkhbxm33g/libhdf5-hl-310_1.14.6+repack-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-9 [540 kB] Fetched 540 kB in 0s (52.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfs3969y4/libtool_2.5.4-9_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbinutils amd64 2.46-2 [548 kB] Fetched 548 kB in 0s (54.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppacv7zck/libbinutils_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgomp1 amd64 15.2.0-14 [140 kB] Fetched 140 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpill8wq3v/libgomp1_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Fetched 216 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw7aoaxa6/po-debconf_1.0.22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.12-1 [1974 kB] Fetched 1974 kB in 0s (118 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprfyj3jhf/libpython3.13-stdlib_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-netcdf4 amd64 1.7.4-1 [892 kB] Fetched 892 kB in 0s (32.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9ndacout/python3-netcdf4_1.7.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.14-minimal amd64 3.14.3-1 [2406 kB] Fetched 2406 kB in 0s (6774 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpks4bbxnk/python3.14-minimal_3.14.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.14-dev amd64 3.14.3-1 [5433 kB] Fetched 5433 kB in 1s (4254 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp51nfiv5/libpython3.14-dev_3.14.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Fetched 10.9 kB in 1s (12.0 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8im7bnu6/sgml-base_1.31+nmu1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libubsan1 amd64 15.2.0-14 [1108 kB] Fetched 1108 kB in 0s (81.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqw7qnw8j/libubsan1_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.3.3+dfsg-3 [2935 kB] Fetched 2935 kB in 1s (5375 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi2k2msz4/python3-pandas_2.3.3+dfsg-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-traitlets all 5.14.3+really5.14.3-3 [71.1 kB] Fetched 71.1 kB in 0s (1568 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk1c1fnqe/python3-traitlets_5.14.3+really5.14.3-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-cpuinfo all 9.0.0+git20221119-3 [23.5 kB] Fetched 23.5 kB in 0s (1099 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpka3xflld/python3-cpuinfo_9.0.0+git20221119-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils-common amd64 2.46-2 [2635 kB] Fetched 2635 kB in 0s (127 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmrt41ksq/binutils-common_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-15-dev amd64 15.2.0-14 [2718 kB] Fetched 2718 kB in 0s (133 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_pbpc3mb/libgcc-15-dev_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl-modules-5.40 all 5.40.1-7 [3012 kB] Fetched 3012 kB in 0s (140 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph58_p6_k/perl-modules-5.40_5.40.1-7_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-attr all 25.4.0-1 [73.1 kB] Fetched 73.1 kB in 0s (2224 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyjj8mgee/python3-attr_25.4.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.22.4+dfsg-1 [433 kB] Fetched 433 kB in 0s (10.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmponmmzb3q/python3-docutils_0.22.4+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.3.3+dfsg-3 [6583 kB] Fetched 6583 kB in 0s (26.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprulfnzad/python3-pandas-lib_2.3.3+dfsg-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-rpds-py amd64 0.28.0-1 [341 kB] Fetched 341 kB in 0s (7243 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkq3e1gt3/python3-rpds-py_0.28.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 3.0.1-1 [63.5 kB] Fetched 63.5 kB in 0s (2231 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0iwgpdwx/python3-snowballstemmer_3.0.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.12-1 [5298 kB] Fetched 5298 kB in 0s (27.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_68oarrf/libpython3.13-dev_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.9.2-1 [18.4 kB] Fetched 18.4 kB in 0s (1329 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiwcnxxfc/python3-platformdirs_4.9.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libatomic1 amd64 15.2.0-14 [9536 B] Fetched 9536 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0l_mm8fr/libatomic1_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 make amd64 4.4.1-3 [463 kB] Fetched 463 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmj1hdqpr/make_4.4.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-2 [56.7 kB] Fetched 56.7 kB in 0s (5492 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvlvn_wvj/python3-packaging_25.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.12-3 [1520 kB] Fetched 1520 kB in 0s (105 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4_mmew73/libgnutls30t64_3.8.12-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Fetched 18.6 kB in 0s (647 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptysivztf/python3-installer_0.7.0+dfsg1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB] Fetched 30.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplshkj59y/media-types_14.0.0_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python-tinycss2-common all 1.5.1-1 [45.1 kB] Fetched 45.1 kB in 0s (2285 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkdng0olz/python-tinycss2-common_1.5.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7+b1 [209 kB] Fetched 209 kB in 0s (3047 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1hwopwsi/libblas3_3.12.1-7+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++-15-dev amd64 15.2.0-14 [2446 kB] Fetched 2446 kB in 0s (128 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9m2640cc/libstdc++-15-dev_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Fetched 108 kB in 0s (5912 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdmookxg1/python3-chardet_5.2.0+dfsg-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.11-1 [41.7 kB] Fetched 41.7 kB in 0s (2113 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9qi_u6nl/python3-idna_3.11-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.2.3-12 [478 kB] Fetched 478 kB in 0s (2177 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp49ok71g3/python3-sphinx_8.2.3-12_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libncursesw6 amd64 6.6+20251231-1 [137 kB] Fetched 137 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3j1yoey0/libncursesw6_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-webencodings all 0.5.1-5 [11.1 kB] Fetched 11.1 kB in 0s (658 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq4n5ixze/python3-webencodings_0.5.1-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Fetched 8812 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjq0sr0pg/dh-strip-nondeterminism_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm6t64 amd64 1.26-1+b1 [78.9 kB] Fetched 78.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfhi92sy1/libgdbm6t64_1.26-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.12-1 [776 kB] Fetched 776 kB in 0s (67.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb2x9bll2/python3.13_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11 [710 kB] Fetched 710 kB in 0s (63.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2k5qzoyq/libdb5.3t64_5.3.28+dfsg2-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-referencing all 0.36.2-2 [23.8 kB] Fetched 23.8 kB in 0s (1522 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdmju66bx/python3-referencing_0.36.2-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.6-1 [18.8 kB] Fetched 18.8 kB in 0s (938 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzn7nlsjz/libsz2_1.1.6-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 9.0.2-2 [275 kB] Fetched 275 kB in 0s (1483 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp699dmf_b/python3-pytest_9.0.2-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg amd64 1.23.5 [1527 kB] Fetched 1527 kB in 0s (105 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8pcdrsah/dpkg_1.23.5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-12 [27.9 kB] Fetched 27.9 kB in 0s (1232 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa86quirq/libjs-sphinxdoc_8.2.3-12_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcrypt1 amd64 1:4.5.1-1 [98.0 kB] Fetched 98.0 kB in 0s (0 B/s) dpkg-name: info: moved 'libcrypt1_1%3a4.5.1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpjg8m9ijk/libcrypt1_4.5.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Fetched 332 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3qhii3k9/m4_1.4.21-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp amd64 4:15.2.0-5 [1564 B] Fetched 1564 B in 0s (0 B/s) dpkg-name: info: moved 'cpp_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpb32yax0o/cpp_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-5 [5324 B] Fetched 5324 B in 0s (0 B/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp8_23e4pk/cpp-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtsan2 amd64 15.2.0-14 [2491 kB] Fetched 2491 kB in 0s (118 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpes5ki5dq/libtsan2_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuuid1 amd64 2.41.3-4 [39.1 kB] Fetched 39.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsozflumq/libuuid1_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-nbclient all 0.10.4-1 [29.8 kB] Fetched 29.8 kB in 0s (1685 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzg2hn3cw/python3-nbclient_0.10.4-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-5 [1436 B] Fetched 1436 B in 0s (0 B/s) dpkg-name: info: moved 'gcc-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpe_pqt20l/gcc-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.22.4+dfsg-1 [128 kB] Fetched 128 kB in 0s (5779 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptmmw1jpm/docutils-common_0.22.4+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.1.6+dfsg-2+b1 [3313 kB] Fetched 3313 kB in 0s (8304 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr6l6ce43/cython3_3.1.6+dfsg-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.2.3-12 [619 kB] Fetched 619 kB in 0s (7971 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcg9iv9vp/sphinx-common_8.2.3-12_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.9-3 [1072 B] Fetched 1072 B in 0s (33.6 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpckcpv0zq/libpython3-all-dev_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Fetched 19.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5y95mgdl/libfile-stripnondeterminism-perl_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b8 [25.1 kB] Fetched 25.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwmr0ngpf/libcom-err2_1.47.2-3+b8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-10 [57.8 kB] Fetched 57.8 kB in 0s (301 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa5tg7_1a/libsasl2-2_2.1.28+dfsg1-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwasan0 amd64 15.2.0-14 [1538 kB] Fetched 1538 kB in 0s (105 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpazxmusqy/libhwasan0_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1+b1 [245 kB] Fetched 245 kB in 0s (3548 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgwhtke9a/libssh2-1t64_1.11.1-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Fetched 185 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2gercaew/libelf1t64_0.194-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxxhash0 amd64 0.8.3-2+b1 [28.1 kB] Fetched 28.1 kB in 0s (736 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf5dag651/libxxhash0_0.8.3-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Fetched 27.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqaobafgt/sensible-utils_0.0.26_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5+b1 [338 kB] Fetched 338 kB in 0s (0 B/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp20nel2c_/libmagic-mgc_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libctf-nobfd0 amd64 2.46-2 [160 kB] Fetched 160 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvlhisk1r/libctf-nobfd0_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils amd64 2.46-2 [282 kB] Fetched 282 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy0gkdrf4/binutils_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libisl23 amd64 0.27-1+b1 [663 kB] Fetched 663 kB in 0s (64.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvesjga34/libisl23_0.27-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsqlite3-0 amd64 3.46.1-9+b1 [918 kB] Fetched 918 kB in 0s (69.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg9nslzh2/libsqlite3-0_3.46.1-9+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-ossl0 amd64 1.16.0-1 [27.5 kB] Fetched 27.5 kB in 0s (1213 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpueeqx9e8/libngtcp2-crypto-ossl0_1.16.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1+b2 [163 kB] Fetched 163 kB in 0s (4455 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzj0sv6u7/libpgm-5.3-0t64_5.3.128~dfsg-2.1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-13 [1123 kB] Fetched 1123 kB in 0s (86.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr_v55unu/libc-gconv-modules-extra_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Fetched 68.4 kB in 0s (2419 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5glafruu/libnghttp3-9_1.12.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bzip2 amd64 1.0.8-6+b1 [41.0 kB] Fetched 41.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9q7y01wr/bzip2_1.0.8-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.9-3 [10.8 kB] Fetched 10.8 kB in 0s (151 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu2rin23c/libpython3-dev_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-3 [89.0 kB] Fetched 89.0 kB in 0s (0 B/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.1-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpl0qhb78e/zlib1g_1.3.dfsg+really1.3.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.26.2-2 [470 kB] Fetched 470 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6l_fa_rv/libp11-kit0_0.26.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpc3 amd64 1.3.1-2+b1 [52.2 kB] Fetched 52.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9s9k_xq0/libmpc3_1.3.1-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpcre2-8-0 amd64 10.46-1+b1 [298 kB] Fetched 298 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpskhw0f3k/libpcre2-8-0_10.46-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.4.2-4 [24.1 MB] Fetched 24.1 MB in 1s (28.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn67ojt18/python3-networkx_3.4.2-4_all.deb' Get:1 http://deb.debian.org/debian unstable/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/tmpgr73kr2k/hostname_3.25_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-python all 7.20260125 [119 kB] Fetched 119 kB in 0s (4227 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp6lc0ur0/dh-python_7.20260125_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-2 [337 kB] Fetched 337 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp93ocvlwu/libkrb5-3_1.22.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Fetched 12.0 kB in 0s (291 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv8bveuef/python3-jaraco.functools_4.1.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.14-stdlib amd64 3.14.3-1 [2263 kB] Fetched 2263 kB in 0s (31.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplicx2y86/libpython3.14-stdlib_3.14.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsmartcols1 amd64 2.41.3-4 [145 kB] Fetched 145 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_esfezdy/libsmartcols1_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsodium23 amd64 1.0.18-2 [166 kB] Fetched 166 kB in 0s (3837 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprcx2yvdy/libsodium23_1.0.18-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblosc1 amd64 1.21.5+ds-2+b1 [49.3 kB] Fetched 49.3 kB in 0s (2107 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptlmyn5_t/libblosc1_1.21.5+ds-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-tables-lib amd64 3.11.0-3 [708 kB] Fetched 708 kB in 0s (5744 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq4bd8dzv/python3-tables-lib_3.11.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.17.0-2 [117 kB] Fetched 117 kB in 0s (5048 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw0xlt2gb/python3-babel_2.17.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.19.0~rc3-1 [401 kB] Fetched 401 kB in 0s (7045 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd4e4lifa/libcurl3t64-gnutls_8.19.0~rc3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b2 [57.4 kB] Fetched 57.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprq12a9mo/liblzo2-2_2.10-3+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.19.2+dfsg-1 [847 kB] Fetched 847 kB in 0s (7148 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9k8lsyxp/python3-pygments_2.19.2+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 tar amd64 1.35+dfsg-4 [817 kB] Fetched 817 kB in 0s (71.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp1v48sls/tar_1.35+dfsg-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5+b1 [110 kB] Fetched 110 kB in 0s (0 B/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpe6n79rh6/libmagic1t64_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-3 [919 kB] Fetched 919 kB in 0s (78.4 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.1-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpb423ss0_/zlib1g-dev_1.3.dfsg+really1.3.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssl3t64 amd64 3.5.5-1 [2449 kB] Fetched 2449 kB in 0s (126 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp70twuaav/libssl3t64_3.5.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-bin amd64 6.6+20251231-1 [445 kB] Fetched 445 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwe40d3th/ncurses-bin_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pytz all 2025.2-5 [31.8 kB] Fetched 31.8 kB in 0s (1051 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4yq2jcr2/python3-pytz_2025.2-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbz2-1.0 amd64 1.0.8-6+b1 [40.4 kB] Fetched 40.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu3t9epqn/libbz2-1.0_1.0.8-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Fetched 1469 kB in 0s (98.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5cr2bjp1/man-db_2.13.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Fetched 43.4 kB in 0s (866 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps394uapg/python3-defusedxml_0.7.1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcc1-0 amd64 15.2.0-14 [42.6 kB] Fetched 42.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgukqikn4/libcc1-0_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Fetched 79.4 kB in 0s (1167 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr8d_wfes/python3-dateutil_2.9.0-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15 amd64 15.2.0-14 [1276 B] Fetched 1276 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3qj0gc5w/cpp-15_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdpkg-perl all 1.23.5 [668 kB] Fetched 668 kB in 0s (54.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyolvrvyd/libdpkg-perl_1.23.5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6 amd64 2.42-13 [1814 kB] Fetched 1814 kB in 0s (77.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2f2wkfwp/libc6_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++6 amd64 15.2.0-14 [736 kB] Fetched 736 kB in 0s (57.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6t858zvp/libstdc++6_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.9-3 [1068 B] Fetched 1068 B in 0s (27.4 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2_lid_ka/python3-all-dev_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgprofng0 amd64 2.46-2 [820 kB] Fetched 820 kB in 0s (71.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo4m1h2kv/libgprofng0_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libasan8 amd64 15.2.0-14 [2779 kB] Fetched 2779 kB in 0s (128 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgpo90qd0/libasan8_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/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/tmp5gyj82y9/autotools-dev_20240727.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaudit-common all 1:4.1.2-1 [14.3 kB] Fetched 14.3 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit-common_1%3a4.1.2-1_all.deb' to '/srv/rebuilderd/tmp/tmpwoodn0id/libaudit-common_4.1.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 linux-libc-dev all 6.18.15-1 [1964 kB] Fetched 1964 kB in 0s (106 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb00wbnr0/linux-libc-dev_6.18.15-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-bs4 all 4.14.3-2 [118 kB] Fetched 118 kB in 0s (5422 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnc2nt2z0/python3-bs4_4.14.3-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaudit1 amd64 1:4.1.2-1+b1 [60.2 kB] Fetched 60.2 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit1_1%3a4.1.2-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmph4y7dhl1/libaudit1_4.1.2-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.12-1 [2267 kB] Fetched 2267 kB in 0s (80.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp03tb6uka/python3.13-minimal_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debianutils amd64 5.23.2 [92.4 kB] Fetched 92.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_xuxsplr/debianutils_5.23.2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Fetched 20.1 kB in 0s (1046 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpteifzkkg/xml-core_0.19_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.9-3 [26.0 kB] Fetched 26.0 kB in 0s (1753 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4u3rkgvb/python3-dev_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-dev-bin amd64 2.42-13 [61.5 kB] Fetched 61.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbrfqs37u/libc-dev-bin_2.42-13_amd64.deb' Downloading dependency 1 of 315: diffutils:amd64=1:3.12-1 Downloading dependency 2 of 315: automake:amd64=1:1.18.1-4 Downloading dependency 3 of 315: python3-cffi-backend:amd64=2.0.0-3 Downloading dependency 4 of 315: libhdf5-hl-310:amd64=1.14.6+repack-2 Downloading dependency 5 of 315: libtool:amd64=2.5.4-9 Downloading dependency 6 of 315: libbinutils:amd64=2.46-2 Downloading dependency 7 of 315: libgomp1:amd64=15.2.0-14 Downloading dependency 8 of 315: po-debconf:amd64=1.0.22 Downloading dependency 9 of 315: libpython3.13-stdlib:amd64=3.13.12-1 Downloading dependency 10 of 315: python3-netcdf4:amd64=1.7.4-1 Downloading dependency 11 of 315: python3.14-minimal:amd64=3.14.3-1 Downloading dependency 12 of 315: libpython3.14-dev:amd64=3.14.3-1 Downloading dependency 13 of 315: 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python3-bs4:amd64=4.14.3-2 Downloading dependency 122 of 315: libaudit1:amd64=1:4.1.2-1+b1 Downloading dependency 123 of 315: python3.13-minimal:amd64=3.13.12-1 Downloading dependency 124 of 315: debianutils:amd64=5.23.2 Downloading dependency 125 of 315: xml-core:amd64=0.19 Downloading dependency 126 of 315: python3-dev:amd64=3.13.9-3 Downloading dependency 127 of 315: libc-dev-bin:amd64=2.42-13 Downloading dependency 128 of 315: cpp-15-x86-64-linux-gnu:amd64=15.2.0-14Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-14 [12.1 MB] Fetched 12.1 MB in 0s (187 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyvhtqft_/cpp-15-x86-64-linux-gnu_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssl-provider-legacy amd64 3.5.5-1 [311 kB] Fetched 311 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq5tu3ht1/openssl-provider-legacy_3.5.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-2 [92.5 kB] Fetched 92.5 kB in 0s (1415 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2qk7lqf_/python3-typing-extensions_4.15.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7+b1 [2550 kB] Fetched 2550 kB in 0s (22.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7xyjjva2/liblapack3_3.12.1-7+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.9-3 [27.6 kB] Fetched 27.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl9yu67q4/python3-minimal_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.14-dev amd64 3.14.3-1 [507 kB] Fetched 507 kB in 0s (12.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprgppf0hd/python3.14-dev_3.14.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Fetched 738 kB in 0s (3894 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5uhc0tu8/python3-setuptools_78.1.1-0.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 1.0.0-1 [20.4 kB] Fetched 20.4 kB in 0s (616 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv0naejq5/python3-alabaster_1.0.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.4-1 [116 kB] Fetched 116 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp4hsvxj1/libexpat1_2.7.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl-base amd64 5.40.1-7 [1679 kB] Fetched 1679 kB in 0s (106 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpams4ix5f/perl-base_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-base amd64 15.2.0-14 [55.0 kB] Fetched 55.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa6qksvwm/gcc-15-base_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-bleach all 6.3.0-1 [51.4 kB] Fetched 51.4 kB in 0s (2557 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp421h83zg/python3-bleach_6.3.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mawk amd64 1.3.4.20260129-1 [143 kB] Fetched 143 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1li_vzwh/mawk_1.3.4.20260129-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpanj5j8sw/dwz_0.16-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblz4-1 amd64 1.10.0-8 [70.1 kB] Fetched 70.1 kB in 0s (3272 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzxcx_m0g/liblz4-1_1.10.0-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl amd64 5.40.1-7 [267 kB] Fetched 267 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8wlr7qju/perl_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnorm1t64 amd64 1.5.9+dfsg-4 [225 kB] Fetched 225 kB in 0s (3504 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzhyouthb/libnorm1t64_1.5.9+dfsg-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bash amd64 5.3-2 [1561 kB] Fetched 1561 kB in 0s (107 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpolgxqdog/bash_5.3-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.9-3 [1048 B] Fetched 1048 B in 0s (33.4 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjnkd5yfo/python3-all_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-passwd amd64 3.6.8 [54.6 kB] Fetched 54.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwh2912xh/base-passwd_3.6.8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6-dev amd64 2.42-13 [2016 kB] Fetched 2016 kB in 0s (114 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmu1lsus7/libc6-dev_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Fetched 11.0 kB in 0s (190 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi7wcoz_o/python3-zipp_3.23.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2+b1 [466 kB] Fetched 466 kB in 0s (41.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf7zk89an/libunistring5_1.3-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-versioneer all 0.29-2 [43.2 kB] Fetched 43.2 kB in 0s (1864 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbp0fxr1e/python3-versioneer_0.29-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Fetched 320 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvk47r_7r/libbrotli1_1.2.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.12-1 [2187 kB] Fetched 2187 kB in 0s (27.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuxwh6y37/libpython3.13_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-tables all 3.11.0-3 [354 kB] Fetched 354 kB in 0s (9438 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvdbny0ih/python3-tables_3.11.0-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnettle8t64 amd64 3.10.2-1 [307 kB] Fetched 307 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzzmheksx/libnettle8t64_3.10.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.6+repack-2 [1360 kB] Fetched 1360 kB in 0s (3174 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3ghn97r3/libhdf5-310_1.14.6+repack-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 3.0.3-1+b1 [14.3 kB] Fetched 14.3 kB in 0s (236 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4l87g55q/python3-markupsafe_3.0.3-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-tornado amd64 6.5.4-0.1 [358 kB] Fetched 358 kB in 0s (1116 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1_1ixfau/python3-tornado_6.5.4-0.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.6.3-1 [120 kB] Fetched 120 kB in 0s (370 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1mxacmv1/python3-urllib3_2.6.3-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b2 [59.8 kB] Fetched 59.8 kB in 0s (903 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptc89na_f/libpsl5t64_0.21.2-1.1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libzstd1 amd64 1.5.7+dfsg-3+b1 [308 kB] Fetched 308 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdv8l3fju/libzstd1_1.5.7+dfsg-3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-nbformat all 5.10.4-1 [44.0 kB] Fetched 44.0 kB in 0s (2720 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg08g7j8f/python3-nbformat_5.10.4-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 util-linux amd64 2.41.3-4 [1166 kB] Fetched 1166 kB in 0s (90.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr6bpjnj8/util-linux_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-bin amd64 2.42-13 [644 kB] Fetched 644 kB in 0s (57.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt3knnxak/libc-bin_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-3+b1 [26.4 kB] Fetched 26.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi5nfyvmk/libffi8_3.5.2-3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-html5lib all 1.2-3 [92.1 kB] Fetched 92.1 kB in 0s (1422 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4512pvzn/python3-html5lib_1.2-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.4-1 [169 kB] Fetched 169 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9k40q8a1/libexpat1-dev_2.7.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtinfo6 amd64 6.6+20251231-1 [354 kB] Fetched 354 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8g989d47/libtinfo6_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-2 [139 kB] Fetched 139 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0ap6raj2/libgssapi-krb5-2_1.22.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.14 amd64 3.14.3-1 [836 kB] Fetched 836 kB in 0s (3301 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpohutr5dl/python3.14_3.14.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.14 amd64 3.14.3-1 [2372 kB] Fetched 2372 kB in 0s (6573 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1l3cb5mb/libpython3.14_3.14.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gzip amd64 1.13-1 [138 kB] Fetched 138 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu7w2mi1l/gzip_1.13-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1+b1 [195 kB] Fetched 195 kB in 0s (4317 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwoyqw53g/libldap2_2.6.10+dfsg-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Fetched 87.5 kB in 0s (3343 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp898_v3r0/libjson-perl_4.10000-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.21.0-2 [50.4 kB] Fetched 50.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdhf2_ca5/libtasn1-6_4.21.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Fetched 5667 kB in 0s (23.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4n3rsc5u/libjs-mathjax_2.7.9+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libctf0 amd64 2.46-2 [92.2 kB] Fetched 92.2 kB in 0s (8453 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp57ujgf6m/libctf0_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg-dev all 1.23.5 [1318 kB] Fetched 1318 kB in 0s (91.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1_s5bg7b/dpkg-dev_1.23.5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam0g amd64 1.7.0-5+b1 [70.4 kB] Fetched 70.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbx7rzrb1/libpam0g_1.7.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema-specifications all 2023.12.1-4 [9092 B] Fetched 9092 B in 0s (840 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjtq42elz/python3-jsonschema-specifications_2023.12.1-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sysvinit-utils amd64 3.15-6 [35.0 kB] Fetched 35.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4mbp1a70/sysvinit-utils_3.15-6_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.2-2+b1 [29.3 kB] Fetched 29.3 kB in 0s (190 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6eo5co5e/libsnappy1v5_1.2.2-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcap-ng0 amd64 0.9.1-1 [17.4 kB] Fetched 17.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqjcs58dt/libcap-ng0_0.9.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblsan0 amd64 15.2.0-14 [1249 kB] Fetched 1249 kB in 0s (94.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp6z5j28p/liblsan0_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-nbsphinx all 0.9.5+ds-1 [39.9 kB] Fetched 39.9 kB in 0s (1925 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpku_k369g/python3-nbsphinx_0.9.5+ds-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5+b1 [43.8 kB] Fetched 43.8 kB in 0s (0 B/s) dpkg-name: info: moved 'file_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpegtwdicz/file_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 build-essential amd64 12.12 [4624 B] Fetched 4624 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6dgxhj1e/build-essential_12.12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.2-1 [1687 kB] Fetched 1687 kB in 0s (111 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt_t6klvt/gettext_0.23.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Fetched 6688 B in 0s (213 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1p4mej3o/python3-imagesize_1.4.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.31 [75.7 kB] Fetched 75.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps4n4wf9_/libdebhelper-perl_13.31_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15 amd64 15.2.0-14 [26.1 kB] Fetched 26.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1xxglaa1/g++-15_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-fastjsonschema all 2.21.1-1 [22.4 kB] Fetched 22.4 kB in 0s (981 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8aw904s4/python3-fastjsonschema_2.21.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblosc2-7 amd64 2.23.0+ds-1 [202 kB] Fetched 202 kB in 0s (1939 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgzgf6nxw/libblosc2-7_2.23.0+ds-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/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/tmpesog6gfg/rpcsvc-proto_1.4.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-cftime amd64 1.6.5-1+b1 [504 kB] Fetched 504 kB in 0s (6777 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnmr90s8f/python3-cftime_1.6.5-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.4.0-1 [38.8 kB] Fetched 38.8 kB in 0s (2480 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa_v_bevt/python3-build_1.4.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnetcdf22 amd64 1:4.10.0-1 [526 kB] Fetched 526 kB in 0s (9664 kB/s) dpkg-name: info: moved 'libnetcdf22_1%3a4.10.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpgj_bwlur/libnetcdf22_4.10.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20260223 [158 kB] Fetched 158 kB in 0s (3173 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxb3ytpil/ca-certificates_20260223_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.2-1 [772 kB] Fetched 772 kB in 0s (64.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwc7ds7tg/autopoint_0.23.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-client all 8.7.0-1 [93.3 kB] Fetched 93.3 kB in 0s (2383 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaltslw4i/python3-jupyter-client_8.7.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-10 [1194 kB] Fetched 1194 kB in 0s (84.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp73gtawuq/groff-base_1.23.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-mistune all 3.1.4-1 [35.7 kB] Fetched 35.7 kB in 0s (1112 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphp0hdcaq/python3-mistune_3.1.4-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 2.1.0-2 [7540 B] Fetched 7540 B in 0s (66.1 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp86nsc2ym/python3-iniconfig_2.1.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 findutils amd64 4.10.0-3 [700 kB] Fetched 700 kB in 0s (65.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxgwd81gb/findutils_4.10.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-14 [13.2 MB] Fetched 13.2 MB in 0s (184 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx5e7kjrp/g++-15-x86-64-linux-gnu_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Fetched 33.0 kB in 0s (1156 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz1auqt16/python3-decorator_5.2.1-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-2 [33.1 kB] Fetched 33.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkhx4a3ls/libkrb5support0_1.22.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-10 [19.8 kB] Fetched 19.8 kB in 0s (1562 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8xzd9925/libsasl2-modules-db_2.1.28+dfsg1-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm-compat4t64 amd64 1.26-1+b1 [53.1 kB] Fetched 53.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2df9ry62/libgdbm-compat4t64_1.26-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debconf all 1.5.92 [123 kB] Fetched 123 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqeqqwiw2/debconf_1.5.92_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.6.0-2 [27.2 kB] Fetched 27.2 kB in 0s (1330 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqcz4rho0/python3-pluggy_1.6.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15 amd64 15.2.0-14 [536 kB] Fetched 536 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6rdxe9it/gcc-15_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-8 [250 kB] Fetched 250 kB in 0s (6659 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd8lfei82/libqhull-r8.0_2020.2-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.5.5-1 [1500 kB] Fetched 1500 kB in 0s (20.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn37viyx1/openssl_3.5.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5+b1 [561 kB] Fetched 561 kB in 0s (53.9 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpnm3b0xkf/libgmp10_6.3.0+dfsg-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Fetched 11.7 kB in 0s (492 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph4lbfjgy/python3-pyproject-hooks_1.2.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.14-minimal amd64 3.14.3-1 [897 kB] Fetched 897 kB in 0s (24.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5ee3iy9w/libpython3.14-minimal_3.14.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebconfclient0 amd64 0.282+b2 [11.2 kB] Fetched 11.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp06k7dd3i/libdebconfclient0_0.282+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 grep amd64 3.12-1 [443 kB] Fetched 443 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfagusmn2/grep_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-2 [37.2 kB] Fetched 37.2 kB in 0s (1354 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu2i2vusc/python3-typeguard_4.4.4-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmount1 amd64 2.41.3-4 [212 kB] Fetched 212 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy0d2muw_/libmount1_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python-tables-data all 3.11.0-3 [45.8 kB] Fetched 45.8 kB in 0s (1953 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp97wfqo_d/python-tables-data_3.11.0-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.4-2 [171 kB] Fetched 171 kB in 0s (1532 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1imfvt0y/python3-charset-normalizer_3.4.4-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-5 [494 kB] Fetched 494 kB in 0s (46.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk95niioq/autoconf_2.72-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules-bin amd64 1.7.0-5+b1 [49.8 kB] Fetched 49.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu39pnzoo/libpam-modules-bin_1.7.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [138 kB] Fetched 138 kB in 0s (3736 kB/s) dpkg-name: info: moved 'python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpzj7fd07g/python3-numpy-dev_2.3.5+ds-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.46.3-2 [27.5 kB] Fetched 27.5 kB in 0s (850 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbegtv_g_/python3-wheel_0.46.3-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmd0 amd64 1.1.0-2+b2 [36.2 kB] Fetched 36.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjctwmowz/libmd0_1.1.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsframe3 amd64 2.46-2 [84.6 kB] Fetched 84.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptn9t_vke/libsframe3_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.19.0~rc3-1 [408 kB] Fetched 408 kB in 0s (8679 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqgiskzg9/libcurl4t64_8.19.0~rc3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 init-system-helpers all 1.69 [39.3 kB] Fetched 39.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe7wqbpgo/init-system-helpers_1.69_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-core all 5.9.1-1 [36.5 kB] Fetched 36.5 kB in 0s (1390 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn2o41rke/python3-jupyter-core_5.9.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Fetched 224 kB in 0s (3969 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv0b9h3s8/python3-pkg-resources_78.1.1-0.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libattr1 amd64 1:2.5.2-4 [23.0 kB] Fetched 23.0 kB in 0s (0 B/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp0ks5f_f4/libattr1_2.5.2-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-gsd amd64 4.2.0-1 [206 kB] Fetched 206 kB in 0s (8277 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpojwshobx/python3-gsd_4.2.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-numexpr amd64 2.14.1-1+b1 [145 kB] Fetched 145 kB in 0s (659 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp69x163yp/python3-numexpr_2.14.1-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-2+b1 [641 kB] Fetched 641 kB in 0s (62.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd5mn4r4n/libxml2-16_2.15.1+dfsg-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 patch amd64 2.8-2 [134 kB] Fetched 134 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd5qwkp2t/patch_2.8-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnawfy_vv/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pandocfilters all 1.5.1-1 [23.7 kB] Fetched 23.7 kB in 0s (788 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxgq6lp2d/python3-pandocfilters_1.5.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/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/tmp8uxlv7on/netbase_6.5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.68.0-2 [79.2 kB] Fetched 79.2 kB in 0s (204 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2w_qc6vp/libnghttp2-14_1.68.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhogweed6t64 amd64 3.10.2-1 [336 kB] Fetched 336 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmon21gi8/libhogweed6t64_3.10.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpfr6 amd64 4.2.2-2+b1 [729 kB] Fetched 729 kB in 0s (65.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_7lamvlu/libmpfr6_4.2.2-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2026.2.25+ds-1 [9612 B] Fetched 9612 B in 0s (376 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0yqeve3h/python3-certifi_2026.2.25+ds-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3+b1 [60.7 kB] Fetched 60.7 kB in 0s (2348 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptbzc25cg/librtmp1_2.4+20151223.gitfa8646d.1-3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-2 [81.1 kB] Fetched 81.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3ytm0l28/libk5crypto3_1.22.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-4 [13.7 kB] Fetched 13.7 kB in 0s (350 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp43hrli_d/python3-autocommand_2.2.2-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-nbconvert all 7.17.0-1 [163 kB] Fetched 163 kB in 0s (2728 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6m0qdr8x/python3-nbconvert_7.17.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-4 [74.8 kB] Fetched 74.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvht48e6g/readline-common_8.3-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libseccomp2 amd64 2.6.0-2+b1 [52.2 kB] Fetched 52.2 kB in 0s (4547 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpymlw3e04/libseccomp2_2.6.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libperl5.40 amd64 5.40.1-7 [4317 kB] Fetched 4317 kB in 0s (153 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5_oad9bg/libperl5.40_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Fetched 33.0 kB in 0s (2120 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfbjn2r8r/python3-inflect_7.5.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-psutil amd64 7.1.0-1 [224 kB] Fetched 224 kB in 0s (9244 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0mfyfx1w/python3-psutil_7.1.0-1_amd64.deb' Downloading dependency 129 of 315: openssl-provider-legacy:amd64=3.5.5-1 Downloading dependency 130 of 315: python3-typing-extensions:amd64=4.15.0-2 Downloading dependency 131 of 315: liblapack3:amd64=3.12.1-7+b1 Downloading dependency 132 of 315: python3-minimal:amd64=3.13.9-3 Downloading dependency 133 of 315: python3.14-dev:amd64=3.14.3-1 Downloading dependency 134 of 315: python3-setuptools:amd64=78.1.1-0.1 Downloading dependency 135 of 315: python3-alabaster:amd64=1.0.0-1 Downloading dependency 136 of 315: libexpat1:amd64=2.7.4-1 Downloading dependency 137 of 315: perl-base:amd64=5.40.1-7 Downloading dependency 138 of 315: gcc-15-base:amd64=15.2.0-14 Downloading dependency 139 of 315: python3-bleach:amd64=6.3.0-1 Downloading dependency 140 of 315: mawk:amd64=1.3.4.20260129-1 Downloading dependency 141 of 315: 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dependency 234 of 315: libattr1:amd64=1:2.5.2-4 Downloading dependency 235 of 315: python3-gsd:amd64=4.2.0-1 Downloading dependency 236 of 315: python3-numexpr:amd64=2.14.1-1+b1 Downloading dependency 237 of 315: libxml2-16:amd64=2.15.1+dfsg-2+b1 Downloading dependency 238 of 315: patch:amd64=2.8-2 Downloading dependency 239 of 315: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 240 of 315: python3-pandocfilters:amd64=1.5.1-1 Downloading dependency 241 of 315: netbase:amd64=6.5 Downloading dependency 242 of 315: libnghttp2-14:amd64=1.68.0-2 Downloading dependency 243 of 315: libhogweed6t64:amd64=3.10.2-1 Downloading dependency 244 of 315: libmpfr6:amd64=4.2.2-2+b1 Downloading dependency 245 of 315: python3-certifi:amd64=2026.2.25+ds-1 Downloading dependency 246 of 315: librtmp1:amd64=2.4+20151223.gitfa8646d.1-3+b1 Downloading dependency 247 of 315: libk5crypto3:amd64=1.22.1-2 Downloading dependency 248 of 315: python3-autocommand:amd64=2.2.2-4 Downloading dependency 249 of 315: python3-nbconvert:amd64=7.17.0-1 Downloading dependency 250 of 315: readline-common:amd64=8.3-4 Downloading dependency 251 of 315: libseccomp2:amd64=2.6.0-2+b1 Downloading dependency 252 of 315: libperl5.40:amd64=5.40.1-7 Downloading dependency 253 of 315: python3-inflect:amd64=7.5.0-1 Downloading dependency 254 of 315: python3-psutil:amd64=7.1.0-1 Downloading dependency 255 of 315: python3-jupyterlab-pygments:amd64=0.2.2-3Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Fetched 6096 B in 0s (342 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7su0rprp/python3-jupyterlab-pygments_0.2.2-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.31 [932 kB] Fetched 932 kB in 0s (80.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp42qsml4w/debhelper_13.31_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libselinux1 amd64 3.9-4+b1 [86.1 kB] Fetched 86.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwb7k578e/libselinux1_3.9-4+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-runtime all 1.7.0-5 [249 kB] Fetched 249 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt6vgmfco/libpam-runtime_1.7.0-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblkid1 amd64 2.41.3-4 [174 kB] Fetched 174 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp60vzx05j/libblkid1_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 xz-utils amd64 5.8.2-2 [706 kB] Fetched 706 kB in 0s (67.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3oui87uh/xz-utils_5.8.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pybuild-plugin-pyproject all 7.20260125 [13.0 kB] Fetched 13.0 kB in 0s (456 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv8mhk6rw/pybuild-plugin-pyproject_7.20260125_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.3-4 [98.9 kB] Fetched 98.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn_5fsao_/bsdextrautils_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libacl1 amd64 2.3.2-3 [32.7 kB] Fetched 32.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptgavi388/libacl1_2.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.9-3 [27.6 kB] Fetched 27.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplhte66k9/python3_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-2 [8184 B] Fetched 8184 B in 0s (388 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp637scpib/python3-jaraco.context_6.0.1-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.9-3 [10.5 kB] Fetched 10.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfq05nv8f/libpython3-stdlib_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc amd64 4:15.2.0-5 [5160 B] Fetched 5160 B in 0s (0 B/s) dpkg-name: info: moved 'gcc_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp698oke8a/gcc_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.3-1 [148 kB] Fetched 148 kB in 0s (1082 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp57raejxl/python3-pyparsing_3.1.3-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-s1 amd64 15.2.0-14 [71.5 kB] Fetched 71.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl48q0g8f/libgcc-s1_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Fetched 71.7 kB in 0s (2071 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpog1qj88z/python3-more-itertools_10.8.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-tinycss2 all 1.5.1-1 [25.9 kB] Fetched 25.9 kB in 0s (1195 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk6b3kvxk/python3-tinycss2_1.5.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.16.3-4 [18.6 MB] Fetched 18.6 MB in 1s (23.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1otae8gl/python3-scipy_1.16.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules amd64 1.7.0-5+b1 [179 kB] Fetched 179 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphqaf_3oq/libpam-modules_1.7.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Fetched 136 kB in 0s (6402 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnv2s0x32/libngtcp2-16_1.16.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 coreutils amd64 9.10-1 [3142 kB] Fetched 3142 kB in 0s (131 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbrl9o5i1/coreutils_9.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblzma5 amd64 5.8.2-2 [327 kB] Fetched 327 kB in 0s (31.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppekqkrc5/liblzma5_5.8.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsystemd0 amd64 260~rc1-2 [445 kB] Fetched 445 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplv41lpbv/libsystemd0_260~rc1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-soupsieve all 2.8.3-1 [39.6 kB] Fetched 39.6 kB in 0s (2011 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu_5ghf_i/python3-soupsieve_2.8.3-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.5+dfsg-1 [72.4 kB] Fetched 72.4 kB in 0s (4073 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjvk3tmi9/python3-requests_2.32.5+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libquadmath0 amd64 15.2.0-14 [145 kB] Fetched 145 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp04fjh50j/libquadmath0_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.46-2 [1058 kB] Fetched 1058 kB in 0s (85.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfplcfs4v/binutils-x86-64-linux-gnu_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-files amd64 14 [72.9 kB] Fetched 72.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwnh67xzv/base-files_14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-base all 6.6+20251231-1 [277 kB] Fetched 277 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpla89oa2r/ncurses-base_6.6+20251231-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-14 [862 kB] Fetched 862 kB in 0s (8727 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6135e86s/libgfortran5_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sed amd64 4.9-2 [329 kB] Fetched 329 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp78rusjvw/sed_4.9-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/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/tmpxedpy3l5/dash_0.5.12-12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.2-1 [245 kB] Fetched 245 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnsp3koe5/gettext-base_0.23.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-2+b1 [132 kB] Fetched 132 kB in 0s (3233 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpll_q3nv_/libbsd0_0.12.2-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [7487 kB] Fetched 7487 kB in 0s (49.8 MB/s) dpkg-name: info: moved 'python3-numpy_1%3a2.3.5+ds-3_amd64.deb' to '/srv/rebuilderd/tmp/tmple54grnb/python3-numpy_2.3.5+ds-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.16.0-1 [25.2 kB] Fetched 25.2 kB in 0s (1453 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr7lbu5p0/libngtcp2-crypto-gnutls8_1.16.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.6-1 [107 kB] Fetched 107 kB in 0s (3607 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuef2lth7/python3-jinja2_3.1.6-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-zmq amd64 27.1.0-1+b1 [215 kB] Fetched 215 kB in 0s (4671 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk99sd0f6/python3-zmq_27.1.0-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-5 [1200 B] Fetched 1200 B in 0s (0 B/s) dpkg-name: info: moved 'g++-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp23yyn8f2/g++-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.12-1 [504 kB] Fetched 504 kB in 0s (5300 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaxh8ppmf/python3.13-dev_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b1 [9784 B] Fetched 9784 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp948ed55o/libkeyutils1_1.6.3-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/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/tmponcn0djr/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4+b1 [110 kB] Fetched 110 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk7z0fdeq/libidn2-0_2.3.8-4+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema all 4.26.0-1 [74.5 kB] Fetched 74.5 kB in 0s (1537 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8lfa_ogb/python3-jsonschema_4.26.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Fetched 12.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6fx3xin9/dh-autoreconf_22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libitm1 amd64 15.2.0-14 [26.5 kB] Fetched 26.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm1a6f2j3/libitm1_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libudev1 amd64 260~rc1-2 [131 kB] Fetched 131 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdd5i4svo/libudev1_260~rc1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Fetched 11.4 kB in 0s (572 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa0wd60id/python3-jaraco.text_4.0.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b1 [68.8 kB] Fetched 68.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwli6n4qx/libuchardet0_0.0.8-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pytest-rerunfailures all 16.1-1 [18.2 kB] Fetched 18.2 kB in 0s (726 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu5srgp2h/python3-pytest-rerunfailures_16.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-4 [181 kB] Fetched 181 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn1nh_ov_/libreadline8t64_8.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-14 [23.4 MB] Fetched 23.4 MB in 0s (198 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb08eepqm/gcc-15-x86-64-linux-gnu_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Fetched 2210 kB in 0s (22.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbhuzryqy/fonts-mathjax_2.7.9+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-roman-numerals all 4.1.0-1 [9196 B] Fetched 9196 B in 0s (342 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx1inmo0l/python3-roman-numerals_4.1.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.12-1 [866 kB] Fetched 866 kB in 0s (73.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_ob2wu15/libpython3.13-minimal_3.13.12-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260302T143911Z forky/main amd64 tzdata all 2025c-3 [263 kB] Fetched 263 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpia2mie2m/tzdata_2025c-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjansson4 amd64 2.14-2+b4 [40.1 kB] Fetched 40.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqxpzlj3j/libjansson4_2.14-2+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++ amd64 4:15.2.0-5 [1344 B] Fetched 1344 B in 0s (0 B/s) dpkg-name: info: moved 'g++_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp2ygpsi_b/g++_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-2 [42.1 kB] Fetched 42.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp30vy3u_p/libpipeline1_1.5.8-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.17.0-2 [6052 kB] Fetched 6052 kB in 0s (37.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf0xatot_/python-babel-localedata_2.17.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libzmq5 amd64 4.3.5-1+b4 [298 kB] Fetched 298 kB in 0s (5873 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxcg6i7xq/libzmq5_4.3.5-1+b4_amd64.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-source --before-build . dpkg-buildpackage: info: host architecture amd64 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/tmpmjm2u8hj/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.18Kx5cUxPH as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.18Kx5cUxPH 127.0.0.1 - - [04/Mar/2026 06:40:29] code 404, message File not found 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:45753 ./ InRelease 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:45753 ./ Release [462 B] 127.0.0.1 - - [04/Mar/2026 06:40:29] code 404, message File not found 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:45753 ./ Release.gpg 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:45753 ./ Packages [389 kB] Fetched 390 kB in 0s (26.5 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 - - [04/Mar/2026 06:40:29] "GET /./gcc-15-base_15.2.0-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./libc-gconv-modules-extra_2.42-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./libc6_2.42-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./libgcc-s1_15.2.0-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./mawk_1.3.4.20260129-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./base-files_14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./libtinfo6_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./debianutils_5.23.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./bash_5.3-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./libacl1_2.3.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./libattr1_2.5.2-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Mar/2026 06:40:29] "GET /./libgmp10_6.3.0%2bdfsg-5%2bb1_amd64.deb HTTP/1.1" 200 - 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I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.18Kx5cUxPH 127.0.0.1 - - [04/Mar/2026 06:40:31] code 404, message File not found 127.0.0.1 - - [04/Mar/2026 06:40:31] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:45753 ./ InRelease 127.0.0.1 - - [04/Mar/2026 06:40:31] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:45753 ./ Release 127.0.0.1 - - [04/Mar/2026 06:40:31] code 404, message File not found 127.0.0.1 - - [04/Mar/2026 06:40:31] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:45753 ./ 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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127.0.0.1 - - [04/Mar/2026 06:40:48] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpmjm2u8hj/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.18Kx5cUxPH Reading package lists... Building dependency tree... Reading state information... diffutils is already the newest version (1:3.12-1). automake is already the newest version (1:1.18.1-4). automake set to manually installed. python3-cffi-backend is already the newest version (2.0.0-3). python3-cffi-backend set to manually installed. libhdf5-hl-310 is already the newest version (1.14.6+repack-2). libhdf5-hl-310 set to manually installed. libtool is already the newest version (2.5.4-9). libtool set to manually installed. libbinutils is already the newest version (2.46-2). libbinutils set to manually installed. libgomp1 is already the newest version (15.2.0-14). libgomp1 set to manually installed. po-debconf is already the newest version (1.0.22). po-debconf set to manually installed. libpython3.13-stdlib is already the newest version (3.13.12-1). libpython3.13-stdlib set to manually installed. python3-netcdf4 is already the newest version (1.7.4-1). python3-netcdf4 set to manually installed. python3.14-minimal is already the newest version (3.14.3-1). python3.14-minimal set to manually installed. libpython3.14-dev is already the newest version (3.14.3-1). libpython3.14-dev set to manually installed. sgml-base is already the newest version (1.31+nmu1). sgml-base set to manually installed. libubsan1 is already the newest version (15.2.0-14). libubsan1 set to manually installed. python3-pandas is already the newest version (2.3.3+dfsg-3). python3-pandas set to manually installed. python3-traitlets is already the newest version (5.14.3+really5.14.3-3). python3-traitlets set to manually installed. python3-cpuinfo is already the newest version (9.0.0+git20221119-3). python3-cpuinfo set to manually installed. binutils-common is already the newest version (2.46-2). binutils-common set to manually installed. libgcc-15-dev is already the newest version (15.2.0-14). libgcc-15-dev set to manually installed. perl-modules-5.40 is already the newest version (5.40.1-7). perl-modules-5.40 set to manually installed. python3-attr is already the newest version (25.4.0-1). python3-attr set to manually installed. python3-docutils is already the newest version (0.22.4+dfsg-1). python3-docutils set to manually installed. python3-pandas-lib is already the newest version (2.3.3+dfsg-3). python3-pandas-lib set to manually installed. python3-rpds-py is already the newest version (0.28.0-1). python3-rpds-py set to manually installed. python3-snowballstemmer is already the newest version (3.0.1-1). python3-snowballstemmer set to manually installed. libpython3.13-dev is already the newest version (3.13.12-1). libpython3.13-dev set to manually installed. python3-platformdirs is already the newest version (4.9.2-1). python3-platformdirs set to manually installed. libatomic1 is already the newest version (15.2.0-14). libatomic1 set to manually installed. make is already the newest version (4.4.1-3). make set to manually installed. python3-packaging is already the newest version (25.0-2). python3-packaging set to manually installed. libgnutls30t64 is already the newest version (3.8.12-3). libgnutls30t64 set to manually installed. python3-installer is already the newest version (0.7.0+dfsg1-3). python3-installer set to manually installed. media-types is already the newest version (14.0.0). media-types set to manually installed. python-tinycss2-common is already the newest version (1.5.1-1). python-tinycss2-common set to manually installed. libblas3 is already the newest version (3.12.1-7+b1). libblas3 set to manually installed. libstdc++-15-dev is already the newest version (15.2.0-14). libstdc++-15-dev set to manually installed. python3-chardet is already the newest version (5.2.0+dfsg-2). python3-chardet set to manually installed. python3-idna is already the newest version (3.11-1). python3-idna set to manually installed. python3-sphinx is already the newest version (8.2.3-12). python3-sphinx set to manually installed. libncursesw6 is already the newest version (6.6+20251231-1). libncursesw6 set to manually installed. python3-webencodings is already the newest version (0.5.1-5). python3-webencodings set to manually installed. dh-strip-nondeterminism is already the newest version (1.15.0-1). dh-strip-nondeterminism set to manually installed. libgdbm6t64 is already the newest version (1.26-1+b1). libgdbm6t64 set to manually installed. python3.13 is already the newest version (3.13.12-1). python3.13 set to manually installed. libdb5.3t64 is already the newest version (5.3.28+dfsg2-11). python3-referencing is already the newest version (0.36.2-2). python3-referencing set to manually installed. libsz2 is already the newest version (1.1.6-1). libsz2 set to manually installed. python3-pytest is already the newest version (9.0.2-2). python3-pytest set to manually installed. dpkg is already the newest version (1.23.5). libjs-sphinxdoc is already the newest version (8.2.3-12). libjs-sphinxdoc set to manually installed. libcrypt1 is already the newest version (1:4.5.1-1). m4 is already the newest version (1.4.21-1). m4 set to manually installed. cpp is already the newest version (4:15.2.0-5). cpp set to manually installed. cpp-x86-64-linux-gnu is already the newest version (4:15.2.0-5). cpp-x86-64-linux-gnu set to manually installed. libtsan2 is already the newest version (15.2.0-14). libtsan2 set to manually installed. libuuid1 is already the newest version (2.41.3-4). python3-nbclient is already the newest version (0.10.4-1). python3-nbclient set to manually installed. gcc-x86-64-linux-gnu is already the newest version (4:15.2.0-5). gcc-x86-64-linux-gnu set to manually installed. docutils-common is already the newest version (0.22.4+dfsg-1). docutils-common set to manually installed. cython3 is already the newest version (3.1.6+dfsg-2+b1). cython3 set to manually installed. sphinx-common is already the newest version (8.2.3-12). sphinx-common set to manually installed. libpython3-all-dev is already the newest version (3.13.9-3). libpython3-all-dev set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.15.0-1). libfile-stripnondeterminism-perl set to manually installed. libcom-err2 is already the newest version (1.47.2-3+b8). libcom-err2 set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-10). libsasl2-2 set to manually installed. libhwasan0 is already the newest version (15.2.0-14). libhwasan0 set to manually installed. libssh2-1t64 is already the newest version (1.11.1-1+b1). libssh2-1t64 set to manually installed. libelf1t64 is already the newest version (0.194-1). libelf1t64 set to manually installed. libxxhash0 is already the newest version (0.8.3-2+b1). libxxhash0 set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils set to manually installed. libmagic-mgc is already the newest version (1:5.46-5+b1). libmagic-mgc set to manually installed. libctf-nobfd0 is already the newest version (2.46-2). libctf-nobfd0 set to manually installed. binutils is already the newest version (2.46-2). binutils set to manually installed. libisl23 is already the newest version (0.27-1+b1). libisl23 set to manually installed. libsqlite3-0 is already the newest version (3.46.1-9+b1). libsqlite3-0 set to manually installed. libngtcp2-crypto-ossl0 is already the newest version (1.16.0-1). libngtcp2-crypto-ossl0 set to manually installed. libpgm-5.3-0t64 is already the newest version (5.3.128~dfsg-2.1+b2). libpgm-5.3-0t64 set to manually installed. libc-gconv-modules-extra is already the newest version (2.42-13). libnghttp3-9 is already the newest version (1.12.0-1). libnghttp3-9 set to manually installed. bzip2 is already the newest version (1.0.8-6+b1). bzip2 set to manually installed. libpython3-dev is already the newest version (3.13.9-3). libpython3-dev set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.1-3). libp11-kit0 is already the newest version (0.26.2-2). libp11-kit0 set to manually installed. libmpc3 is already the newest version (1.3.1-2+b1). libmpc3 set to manually installed. libpcre2-8-0 is already the newest version (10.46-1+b1). python3-networkx is already the newest version (3.4.2-4). python3-networkx set to manually installed. hostname is already the newest version (3.25). dh-python is already the newest version (7.20260125). dh-python set to manually installed. libkrb5-3 is already the newest version (1.22.1-2). libkrb5-3 set to manually installed. python3-jaraco.functools is already the newest version (4.1.0-1). python3-jaraco.functools set to manually installed. libpython3.14-stdlib is already the newest version (3.14.3-1). libpython3.14-stdlib set to manually installed. libsmartcols1 is already the newest version (2.41.3-4). libsodium23 is already the newest version (1.0.18-2). libsodium23 set to manually installed. libblosc1 is already the newest version (1.21.5+ds-2+b1). libblosc1 set to manually installed. python3-tables-lib is already the newest version (3.11.0-3). python3-tables-lib set to manually installed. python3-babel is already the newest version (2.17.0-2). python3-babel set to manually installed. libcurl3t64-gnutls is already the newest version (8.19.0~rc3-1). libcurl3t64-gnutls set to manually installed. liblzo2-2 is already the newest version (2.10-3+b2). liblzo2-2 set to manually installed. python3-pygments is already the newest version (2.19.2+dfsg-1). python3-pygments set to manually installed. tar is already the newest version (1.35+dfsg-4). libmagic1t64 is already the newest version (1:5.46-5+b1). libmagic1t64 set to manually installed. zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.1-3). zlib1g-dev set to manually installed. libssl3t64 is already the newest version (3.5.5-1). ncurses-bin is already the newest version (6.6+20251231-1). python3-pytz is already the newest version (2025.2-5). python3-pytz set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6+b1). man-db is already the newest version (2.13.1-1). man-db set to manually installed. python3-defusedxml is already the newest version (0.7.1-3). python3-defusedxml set to manually installed. libcc1-0 is already the newest version (15.2.0-14). libcc1-0 set to manually installed. python3-dateutil is already the newest version (2.9.0-4). python3-dateutil set to manually installed. cpp-15 is already the newest version (15.2.0-14). cpp-15 set to manually installed. libdpkg-perl is already the newest version (1.23.5). libdpkg-perl set to manually installed. libc6 is already the newest version (2.42-13). libstdc++6 is already the newest version (15.2.0-14). libstdc++6 set to manually installed. python3-all-dev is already the newest version (3.13.9-3). python3-all-dev set to manually installed. libgprofng0 is already the newest version (2.46-2). libgprofng0 set to manually installed. libasan8 is already the newest version (15.2.0-14). libasan8 set to manually installed. autotools-dev is already the newest version (20240727.1). autotools-dev set to manually installed. libaudit-common is already the newest version (1:4.1.2-1). linux-libc-dev is already the newest version (6.18.15-1). linux-libc-dev set to manually installed. python3-bs4 is already the newest version (4.14.3-2). python3-bs4 set to manually installed. libaudit1 is already the newest version (1:4.1.2-1+b1). python3.13-minimal is already the newest version (3.13.12-1). python3.13-minimal set to manually installed. debianutils is already the newest version (5.23.2). xml-core is already the newest version (0.19). xml-core set to manually installed. python3-dev is already the newest version (3.13.9-3). python3-dev set to manually installed. libc-dev-bin is already the newest version (2.42-13). libc-dev-bin set to manually installed. cpp-15-x86-64-linux-gnu is already the newest version (15.2.0-14). cpp-15-x86-64-linux-gnu set to manually installed. openssl-provider-legacy is already the newest version (3.5.5-1). python3-typing-extensions is already the newest version (4.15.0-2). python3-typing-extensions set to manually installed. liblapack3 is already the newest version (3.12.1-7+b1). liblapack3 set to manually installed. python3-minimal is already the newest version (3.13.9-3). python3-minimal set to manually installed. python3.14-dev is already the newest version (3.14.3-1). python3.14-dev set to manually installed. python3-setuptools is already the newest version (78.1.1-0.1). python3-setuptools set to manually installed. python3-alabaster is already the newest version (1.0.0-1). python3-alabaster set to manually installed. libexpat1 is already the newest version (2.7.4-1). libexpat1 set to manually installed. perl-base is already the newest version (5.40.1-7). gcc-15-base is already the newest version (15.2.0-14). python3-bleach is already the newest version (6.3.0-1). python3-bleach set to manually installed. mawk is already the newest version (1.3.4.20260129-1). dwz is already the newest version (0.16-2). dwz set to manually installed. liblz4-1 is already the newest version (1.10.0-8). liblz4-1 set to manually installed. perl is already the newest version (5.40.1-7). perl set to manually installed. libnorm1t64 is already the newest version (1.5.9+dfsg-4). libnorm1t64 set to manually installed. bash is already the newest version (5.3-2). python3-all is already the newest version (3.13.9-3). python3-all set to manually installed. base-passwd is already the newest version (3.6.8). libc6-dev is already the newest version (2.42-13). libc6-dev set to manually installed. python3-zipp is already the newest version (3.23.0-1). python3-zipp set to manually installed. libunistring5 is already the newest version (1.3-2+b1). libunistring5 set to manually installed. python3-versioneer is already the newest version (0.29-2). python3-versioneer set to manually installed. libbrotli1 is already the newest version (1.2.0-3). libbrotli1 set to manually installed. libpython3.13 is already the newest version (3.13.12-1). libpython3.13 set to manually installed. python3-tables is already the newest version (3.11.0-3). python3-tables set to manually installed. libnettle8t64 is already the newest version (3.10.2-1). libnettle8t64 set to manually installed. libhdf5-310 is already the newest version (1.14.6+repack-2). libhdf5-310 set to manually installed. python3-markupsafe is already the newest version (3.0.3-1+b1). python3-markupsafe set to manually installed. python3-tornado is already the newest version (6.5.4-0.1). python3-tornado set to manually installed. python3-urllib3 is already the newest version (2.6.3-1). python3-urllib3 set to manually installed. libpsl5t64 is already the newest version (0.21.2-1.1+b2). libpsl5t64 set to manually installed. libzstd1 is already the newest version (1.5.7+dfsg-3+b1). python3-nbformat is already the newest version (5.10.4-1). python3-nbformat set to manually installed. util-linux is already the newest version (2.41.3-4). libc-bin is already the newest version (2.42-13). libffi8 is already the newest version (3.5.2-3+b1). libffi8 set to manually installed. python3-html5lib is already the newest version (1.2-3). python3-html5lib set to manually installed. libexpat1-dev is already the newest version (2.7.4-1). libexpat1-dev set to manually installed. libtinfo6 is already the newest version (6.6+20251231-1). libgssapi-krb5-2 is already the newest version (1.22.1-2). libgssapi-krb5-2 set to manually installed. python3.14 is already the newest version (3.14.3-1). python3.14 set to manually installed. libpython3.14 is already the newest version (3.14.3-1). libpython3.14 set to manually installed. gzip is already the newest version (1.13-1). libldap2 is already the newest version (2.6.10+dfsg-1+b1). libldap2 set to manually installed. libjson-perl is already the newest version (4.10000-1). libjson-perl set to manually installed. libtasn1-6 is already the newest version (4.21.0-2). libtasn1-6 set to manually installed. libjs-mathjax is already the newest version (2.7.9+dfsg-1). libjs-mathjax set to manually installed. libctf0 is already the newest version (2.46-2). libctf0 set to manually installed. dpkg-dev is already the newest version (1.23.5). dpkg-dev set to manually installed. libpam0g is already the newest version (1.7.0-5+b1). python3-jsonschema-specifications is already the newest version (2023.12.1-4). python3-jsonschema-specifications set to manually installed. sysvinit-utils is already the newest version (3.15-6). libsnappy1v5 is already the newest version (1.2.2-2+b1). libsnappy1v5 set to manually installed. libcap-ng0 is already the newest version (0.9.1-1). liblsan0 is already the newest version (15.2.0-14). liblsan0 set to manually installed. python3-nbsphinx is already the newest version (0.9.5+ds-1). python3-nbsphinx set to manually installed. file is already the newest version (1:5.46-5+b1). file set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. gettext is already the newest version (0.23.2-1). gettext set to manually installed. python3-imagesize is already the newest version (1.4.1-1). python3-imagesize set to manually installed. libdebhelper-perl is already the newest version (13.31). libdebhelper-perl set to manually installed. g++-15 is already the newest version (15.2.0-14). g++-15 set to manually installed. python3-fastjsonschema is already the newest version (2.21.1-1). python3-fastjsonschema set to manually installed. libblosc2-7 is already the newest version (2.23.0+ds-1). libblosc2-7 set to manually installed. rpcsvc-proto is already the newest version (1.4.3-1). rpcsvc-proto set to manually installed. python3-cftime is already the newest version (1.6.5-1+b1). python3-cftime set to manually installed. python3-build is already the newest version (1.4.0-1). python3-build set to manually installed. libnetcdf22 is already the newest version (1:4.10.0-1). libnetcdf22 set to manually installed. ca-certificates is already the newest version (20260223). ca-certificates set to manually installed. autopoint is already the newest version (0.23.2-1). autopoint set to manually installed. python3-jupyter-client is already the newest version (8.7.0-1). python3-jupyter-client set to manually installed. groff-base is already the newest version (1.23.0-10). groff-base set to manually installed. python3-mistune is already the newest version (3.1.4-1). python3-mistune set to manually installed. python3-iniconfig is already the newest version (2.1.0-2). python3-iniconfig set to manually installed. findutils is already the newest version (4.10.0-3). g++-15-x86-64-linux-gnu is already the newest version (15.2.0-14). g++-15-x86-64-linux-gnu set to manually installed. python3-decorator is already the newest version (5.2.1-2). python3-decorator set to manually installed. libkrb5support0 is already the newest version (1.22.1-2). libkrb5support0 set to manually installed. libsasl2-modules-db is already the newest version (2.1.28+dfsg1-10). libsasl2-modules-db set to manually installed. libgdbm-compat4t64 is already the newest version (1.26-1+b1). libgdbm-compat4t64 set to manually installed. debconf is already the newest version (1.5.92). python3-pluggy is already the newest version (1.6.0-2). python3-pluggy set to manually installed. gcc-15 is already the newest version (15.2.0-14). gcc-15 set to manually installed. libqhull-r8.0 is already the newest version (2020.2-8). libqhull-r8.0 set to manually installed. openssl is already the newest version (3.5.5-1). openssl set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-5+b1). python3-pyproject-hooks is already the newest version (1.2.0-1). python3-pyproject-hooks set to manually installed. libpython3.14-minimal is already the newest version (3.14.3-1). libpython3.14-minimal set to manually installed. libdebconfclient0 is already the newest version (0.282+b2). grep is already the newest version (3.12-1). python3-typeguard is already the newest version (4.4.4-2). python3-typeguard set to manually installed. libmount1 is already the newest version (2.41.3-4). python-tables-data is already the newest version (3.11.0-3). python-tables-data set to manually installed. python3-charset-normalizer is already the newest version (3.4.4-2). python3-charset-normalizer set to manually installed. autoconf is already the newest version (2.72-5). autoconf set to manually installed. libpam-modules-bin is already the newest version (1.7.0-5+b1). python3-numpy-dev is already the newest version (1:2.3.5+ds-3). python3-numpy-dev set to manually installed. python3-wheel is already the newest version (0.46.3-2). python3-wheel set to manually installed. libmd0 is already the newest version (1.1.0-2+b2). libsframe3 is already the newest version (2.46-2). libsframe3 set to manually installed. libcurl4t64 is already the newest version (8.19.0~rc3-1). libcurl4t64 set to manually installed. init-system-helpers is already the newest version (1.69). python3-jupyter-core is already the newest version (5.9.1-1). python3-jupyter-core set to manually installed. python3-pkg-resources is already the newest version (78.1.1-0.1). python3-pkg-resources set to manually installed. libattr1 is already the newest version (1:2.5.2-4). python3-gsd is already the newest version (4.2.0-1). python3-gsd set to manually installed. python3-numexpr is already the newest version (2.14.1-1+b1). python3-numexpr set to manually installed. libxml2-16 is already the newest version (2.15.1+dfsg-2+b1). libxml2-16 set to manually installed. patch is already the newest version (2.8-2). patch set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. python3-pandocfilters is already the newest version (1.5.1-1). python3-pandocfilters set to manually installed. netbase is already the newest version (6.5). netbase set to manually installed. libnghttp2-14 is already the newest version (1.68.0-2). libnghttp2-14 set to manually installed. libhogweed6t64 is already the newest version (3.10.2-1). libhogweed6t64 set to manually installed. libmpfr6 is already the newest version (4.2.2-2+b1). libmpfr6 set to manually installed. python3-certifi is already the newest version (2026.2.25+ds-1). python3-certifi set to manually installed. librtmp1 is already the newest version (2.4+20151223.gitfa8646d.1-3+b1). librtmp1 set to manually installed. libk5crypto3 is already the newest version (1.22.1-2). libk5crypto3 set to manually installed. python3-autocommand is already the newest version (2.2.2-4). python3-autocommand set to manually installed. python3-nbconvert is already the newest version (7.17.0-1). python3-nbconvert set to manually installed. readline-common is already the newest version (8.3-4). readline-common set to manually installed. libseccomp2 is already the newest version (2.6.0-2+b1). libseccomp2 set to manually installed. libperl5.40 is already the newest version (5.40.1-7). libperl5.40 set to manually installed. python3-inflect is already the newest version (7.5.0-1). python3-inflect set to manually installed. python3-psutil is already the newest version (7.1.0-1). python3-psutil set to manually installed. python3-jupyterlab-pygments is already the newest version (0.2.2-3). python3-jupyterlab-pygments set to manually installed. debhelper is already the newest version (13.31). debhelper set to manually installed. libselinux1 is already the newest version (3.9-4+b1). libpam-runtime is already the newest version (1.7.0-5). libblkid1 is already the newest version (2.41.3-4). xz-utils is already the newest version (5.8.2-2). xz-utils set to manually installed. pybuild-plugin-pyproject is already the newest version (7.20260125). pybuild-plugin-pyproject set to manually installed. bsdextrautils is already the newest version (2.41.3-4). bsdextrautils set to manually installed. libacl1 is already the newest version (2.3.2-3). python3 is already the newest version (3.13.9-3). python3 set to manually installed. python3-jaraco.context is already the newest version (6.0.1-2). python3-jaraco.context set to manually installed. libpython3-stdlib is already the newest version (3.13.9-3). libpython3-stdlib set to manually installed. gcc is already the newest version (4:15.2.0-5). gcc set to manually installed. python3-pyparsing is already the newest version (3.1.3-1). python3-pyparsing set to manually installed. libgcc-s1 is already the newest version (15.2.0-14). python3-more-itertools is already the newest version (10.8.0-1). python3-more-itertools set to manually installed. python3-tinycss2 is already the newest version (1.5.1-1). python3-tinycss2 set to manually installed. python3-scipy is already the newest version (1.16.3-4). python3-scipy set to manually installed. libpam-modules is already the newest version (1.7.0-5+b1). libngtcp2-16 is already the newest version (1.16.0-1). libngtcp2-16 set to manually installed. coreutils is already the newest version (9.10-1). liblzma5 is already the newest version (5.8.2-2). libsystemd0 is already the newest version (260~rc1-2). python3-soupsieve is already the newest version (2.8.3-1). python3-soupsieve set to manually installed. python3-requests is already the newest version (2.32.5+dfsg-1). python3-requests set to manually installed. libquadmath0 is already the newest version (15.2.0-14). libquadmath0 set to manually installed. binutils-x86-64-linux-gnu is already the newest version (2.46-2). binutils-x86-64-linux-gnu set to manually installed. base-files is already the newest version (14). ncurses-base is already the newest version (6.6+20251231-1). libgfortran5 is already the newest version (15.2.0-14). libgfortran5 set to manually installed. sed is already the newest version (4.9-2). dash is already the newest version (0.5.12-12). gettext-base is already the newest version (0.23.2-1). gettext-base set to manually installed. libbsd0 is already the newest version (0.12.2-2+b1). libbsd0 set to manually installed. python3-numpy is already the newest version (1:2.3.5+ds-3). python3-numpy set to manually installed. libngtcp2-crypto-gnutls8 is already the newest version (1.16.0-1). libngtcp2-crypto-gnutls8 set to manually installed. python3-jinja2 is already the newest version (3.1.6-1). python3-jinja2 set to manually installed. python3-zmq is already the newest version (27.1.0-1+b1). python3-zmq set to manually installed. g++-x86-64-linux-gnu is already the newest version (4:15.2.0-5). g++-x86-64-linux-gnu set to manually installed. python3.13-dev is already the newest version (3.13.12-1). python3.13-dev set to manually installed. libkeyutils1 is already the newest version (1.6.3-6+b1). libkeyutils1 set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libidn2-0 is already the newest version (2.3.8-4+b1). libidn2-0 set to manually installed. python3-jsonschema is already the newest version (4.26.0-1). python3-jsonschema set to manually installed. dh-autoreconf is already the newest version (22). dh-autoreconf set to manually installed. libitm1 is already the newest version (15.2.0-14). libitm1 set to manually installed. libudev1 is already the newest version (260~rc1-2). python3-jaraco.text is already the newest version (4.0.0-1). python3-jaraco.text set to manually installed. libuchardet0 is already the newest version (0.0.8-2+b1). libuchardet0 set to manually installed. python3-pytest-rerunfailures is already the newest version (16.1-1). python3-pytest-rerunfailures set to manually installed. libreadline8t64 is already the newest version (8.3-4). libreadline8t64 set to manually installed. gcc-15-x86-64-linux-gnu is already the newest version (15.2.0-14). gcc-15-x86-64-linux-gnu set to manually installed. fonts-mathjax is already the newest version (2.7.9+dfsg-1). fonts-mathjax set to manually installed. python3-roman-numerals is already the newest version (4.1.0-1). python3-roman-numerals set to manually installed. libpython3.13-minimal is already the newest version (3.13.12-1). libpython3.13-minimal set to manually installed. tzdata is already the newest version (2025c-3). tzdata set to manually installed. libjansson4 is already the newest version (2.14-2+b4). libjansson4 set to manually installed. g++ is already the newest version (4:15.2.0-5). g++ set to manually installed. libpipeline1 is already the newest version (1.5.8-2). libpipeline1 set to manually installed. python-babel-localedata is already the newest version (2.17.0-2). python-babel-localedata set to manually installed. libzmq5 is already the newest version (4.3.5-1+b4). libzmq5 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.18Kx5cUxPH (Reading database ... 35552 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.18Kx5cUxPH I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.18Kx5cUxPH 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.18Kx5cUxPH... I: success in 172.0772 seconds Downloading dependency 256 of 315: debhelper:amd64=13.31 Downloading dependency 257 of 315: libselinux1:amd64=3.9-4+b1 Downloading dependency 258 of 315: libpam-runtime:amd64=1.7.0-5 Downloading dependency 259 of 315: libblkid1:amd64=2.41.3-4 Downloading dependency 260 of 315: xz-utils:amd64=5.8.2-2 Downloading dependency 261 of 315: pybuild-plugin-pyproject:amd64=7.20260125 Downloading dependency 262 of 315: bsdextrautils:amd64=2.41.3-4 Downloading dependency 263 of 315: libacl1:amd64=2.3.2-3 Downloading dependency 264 of 315: python3:amd64=3.13.9-3 Downloading dependency 265 of 315: python3-jaraco.context:amd64=6.0.1-2 Downloading dependency 266 of 315: libpython3-stdlib:amd64=3.13.9-3 Downloading dependency 267 of 315: gcc:amd64=4:15.2.0-5 Downloading dependency 268 of 315: python3-pyparsing:amd64=3.1.3-1 Downloading dependency 269 of 315: libgcc-s1:amd64=15.2.0-14 Downloading dependency 270 of 315: python3-more-itertools:amd64=10.8.0-1 Downloading dependency 271 of 315: python3-tinycss2:amd64=1.5.1-1 Downloading dependency 272 of 315: python3-scipy:amd64=1.16.3-4 Downloading dependency 273 of 315: libpam-modules:amd64=1.7.0-5+b1 Downloading dependency 274 of 315: libngtcp2-16:amd64=1.16.0-1 Downloading dependency 275 of 315: coreutils:amd64=9.10-1 Downloading dependency 276 of 315: liblzma5:amd64=5.8.2-2 Downloading dependency 277 of 315: libsystemd0:amd64=260~rc1-2 Downloading dependency 278 of 315: python3-soupsieve:amd64=2.8.3-1 Downloading dependency 279 of 315: python3-requests:amd64=2.32.5+dfsg-1 Downloading dependency 280 of 315: libquadmath0:amd64=15.2.0-14 Downloading dependency 281 of 315: binutils-x86-64-linux-gnu:amd64=2.46-2 Downloading dependency 282 of 315: base-files:amd64=14 Downloading dependency 283 of 315: ncurses-base:amd64=6.6+20251231-1 Downloading dependency 284 of 315: libgfortran5:amd64=15.2.0-14 Downloading dependency 285 of 315: sed:amd64=4.9-2 Downloading dependency 286 of 315: dash:amd64=0.5.12-12 Downloading dependency 287 of 315: gettext-base:amd64=0.23.2-1 Downloading dependency 288 of 315: libbsd0:amd64=0.12.2-2+b1 Downloading dependency 289 of 315: python3-numpy:amd64=1:2.3.5+ds-3 Downloading dependency 290 of 315: libngtcp2-crypto-gnutls8:amd64=1.16.0-1 Downloading dependency 291 of 315: python3-jinja2:amd64=3.1.6-1 Downloading dependency 292 of 315: python3-zmq:amd64=27.1.0-1+b1 Downloading dependency 293 of 315: g++-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 294 of 315: python3.13-dev:amd64=3.13.12-1 Downloading dependency 295 of 315: libkeyutils1:amd64=1.6.3-6+b1 Downloading dependency 296 of 315: libarchive-zip-perl:amd64=1.68-1 Downloading dependency 297 of 315: libidn2-0:amd64=2.3.8-4+b1 Downloading dependency 298 of 315: python3-jsonschema:amd64=4.26.0-1 Downloading dependency 299 of 315: dh-autoreconf:amd64=22 Downloading dependency 300 of 315: libitm1:amd64=15.2.0-14 Downloading dependency 301 of 315: libudev1:amd64=260~rc1-2 Downloading dependency 302 of 315: python3-jaraco.text:amd64=4.0.0-1 Downloading dependency 303 of 315: libuchardet0:amd64=0.0.8-2+b1 Downloading dependency 304 of 315: python3-pytest-rerunfailures:amd64=16.1-1 Downloading dependency 305 of 315: libreadline8t64:amd64=8.3-4 Downloading dependency 306 of 315: gcc-15-x86-64-linux-gnu:amd64=15.2.0-14 Downloading dependency 307 of 315: fonts-mathjax:amd64=2.7.9+dfsg-1 Downloading dependency 308 of 315: python3-roman-numerals:amd64=4.1.0-1 Downloading dependency 309 of 315: libpython3.13-minimal:amd64=3.13.12-1 Downloading dependency 310 of 315: tzdata:amd64=2025c-3 Downloading dependency 311 of 315: libjansson4:amd64=2.14-2+b4 Downloading dependency 312 of 315: g++:amd64=4:15.2.0-5 Downloading dependency 313 of 315: libpipeline1:amd64=1.5.8-2 Downloading dependency 314 of 315: python-babel-localedata:amd64=2.17.0-2 Downloading dependency 315 of 315: libzmq5:amd64=4.3.5-1+b4 env --chdir=/srv/rebuilderd/tmp/rebuilderd4rQZSi/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1772564708 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildUBhfJ1/debrebuild.sbuildrc.urSzmCkgiV9v sbuild --build=amd64 --host=amd64 --no-source --arch-any --no-arch-all --chroot=/srv/rebuilderd/tmp/debrebuildUBhfJ1/debrebuild.tar.FsDZNMndwADc --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=mdtraj-1.11.1.post1 /srv/rebuilderd/tmp/rebuilderd4rQZSi/inputs/mdtraj_1.11.1.post1-3.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+deb13u4 (28 December 2025) on osuosl41-amd64.novalocal +==============================================================================+ | mdtraj 1.11.1.post1-3 (amd64) Wed, 04 Mar 2026 06:43:22 +0000 | +==============================================================================+ Package: mdtraj Version: 1.11.1.post1-3 Source Version: 1.11.1.post1-3 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuildUBhfJ1/debrebuild.tar.FsDZNMndwADc to /srv/rebuilderd/tmp/tmp.sbuild.5j0cOFB6mB... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Wed, 04 Mar 2026 06:43:27 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderd4rQZSi/inputs/mdtraj_1.11.1.post1-3.dsc exists in /srv/rebuilderd/tmp/rebuilderd4rQZSi/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Wed, 04 Mar 2026 06:43:28 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-sequence-python3, dh-sequence-numpy3, pybuild-plugin-pyproject, cython3, python3-setuptools, python3-all-dev, python3-gsd, python3-numpy (>= 2.0.0~), python3-scipy, python3-nbsphinx, python3-netcdf4, python3-networkx, python3-packaging, python3-pandas, python3-pyparsing, python3-pytest, python3-pytest-rerunfailures, python3-sphinx, python3-tables, python3-versioneer, libjs-mathjax, build-essential Filtered Build-Depends: debhelper-compat (= 13), dh-sequence-python3, dh-sequence-numpy3, pybuild-plugin-pyproject, cython3, python3-setuptools, python3-all-dev, python3-gsd, python3-numpy (>= 2.0.0~), python3-scipy, python3-nbsphinx, python3-netcdf4, python3-networkx, python3-packaging, python3-pandas, python3-pyparsing, python3-pytest, python3-pytest-rerunfailures, python3-sphinx, python3-tables, python3-versioneer, libjs-mathjax, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-Ee5Opz/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Wed, 04 Mar 2026 06:43:31 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any-amd64 arm64 i386 all) +------------------------------------------------------------------------------+ | Build environment Wed, 04 Mar 2026 06:43:31 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.73+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.73-1 (2026-02-17) amd64 (x86_64) Toolchain package versions: binutils_2.46-2 dpkg-dev_1.23.5 g++-15_15.2.0-14 gcc-15_15.2.0-14 libc6-dev_2.42-13 libstdc++-15-dev_15.2.0-14 libstdc++6_15.2.0-14 linux-libc-dev_6.18.15-1 Package versions: autoconf_2.72-5 automake_1:1.18.1-4 autopoint_0.23.2-1 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python3-charset-normalizer_3.4.4-2 python3-cpuinfo_9.0.0+git20221119-3 python3-dateutil_2.9.0-4 python3-decorator_5.2.1-2 python3-defusedxml_0.7.1-3 python3-dev_3.13.9-3 python3-docutils_0.22.4+dfsg-1 python3-fastjsonschema_2.21.1-1 python3-gsd_4.2.0-1 python3-html5lib_1.2-3 python3-idna_3.11-1 python3-imagesize_1.4.1-1 python3-inflect_7.5.0-1 python3-iniconfig_2.1.0-2 python3-installer_0.7.0+dfsg1-3 python3-jaraco.context_6.0.1-2 python3-jaraco.functools_4.1.0-1 python3-jaraco.text_4.0.0-1 python3-jinja2_3.1.6-1 python3-jsonschema_4.26.0-1 python3-jsonschema-specifications_2023.12.1-4 python3-jupyter-client_8.7.0-1 python3-jupyter-core_5.9.1-1 python3-jupyterlab-pygments_0.2.2-3 python3-markupsafe_3.0.3-1+b1 python3-minimal_3.13.9-3 python3-mistune_3.1.4-1 python3-more-itertools_10.8.0-1 python3-nbclient_0.10.4-1 python3-nbconvert_7.17.0-1 python3-nbformat_5.10.4-1 python3-nbsphinx_0.9.5+ds-1 python3-netcdf4_1.7.4-1 python3-networkx_3.4.2-4 python3-numexpr_2.14.1-1+b1 python3-numpy_1:2.3.5+ds-3 python3-numpy-dev_1:2.3.5+ds-3 python3-packaging_25.0-2 python3-pandas_2.3.3+dfsg-3 python3-pandas-lib_2.3.3+dfsg-3 python3-pandocfilters_1.5.1-1 python3-pkg-resources_78.1.1-0.1 python3-platformdirs_4.9.2-1 python3-pluggy_1.6.0-2 python3-psutil_7.1.0-1 python3-pygments_2.19.2+dfsg-1 python3-pyparsing_3.1.3-1 python3-pyproject-hooks_1.2.0-1 python3-pytest_9.0.2-2 python3-pytest-rerunfailures_16.1-1 python3-pytz_2025.2-5 python3-referencing_0.36.2-2 python3-requests_2.32.5+dfsg-1 python3-roman-numerals_4.1.0-1 python3-rpds-py_0.28.0-1 python3-scipy_1.16.3-4 python3-setuptools_78.1.1-0.1 python3-snowballstemmer_3.0.1-1 python3-soupsieve_2.8.3-1 python3-sphinx_8.2.3-12 python3-tables_3.11.0-3 python3-tables-lib_3.11.0-3 python3-tinycss2_1.5.1-1 python3-tornado_6.5.4-0.1 python3-traitlets_5.14.3+really5.14.3-3 python3-typeguard_4.4.4-2 python3-typing-extensions_4.15.0-2 python3-urllib3_2.6.3-1 python3-versioneer_0.29-2 python3-webencodings_0.5.1-5 python3-wheel_0.46.3-2 python3-zipp_3.23.0-1 python3-zmq_27.1.0-1+b1 python3.13_3.13.12-1 python3.13-dev_3.13.12-1 python3.13-minimal_3.13.12-1 python3.14_3.14.3-1 python3.14-dev_3.14.3-1 python3.14-minimal_3.14.3-1 readline-common_8.3-4 rpcsvc-proto_1.4.3-1 sed_4.9-2 sensible-utils_0.0.26 sgml-base_1.31+nmu1 sphinx-common_8.2.3-12 sysvinit-utils_3.15-6 tar_1.35+dfsg-4 tzdata_2025c-3 util-linux_2.41.3-4 xml-core_0.19 xz-utils_5.8.2-2 zlib1g_1:1.3.dfsg+really1.3.1-3 zlib1g-dev_1:1.3.dfsg+really1.3.1-3 +------------------------------------------------------------------------------+ | Build Wed, 04 Mar 2026 06:43:31 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: mdtraj Binary: python3-mdtraj, python-mdtraj-doc Architecture: any-amd64 arm64 i386 all Version: 1.11.1.post1-3 Maintainer: Debichem Team Uploaders: Drew Parsons Homepage: https://mdtraj.org/ Standards-Version: 4.7.3 Vcs-Browser: https://salsa.debian.org/debichem-team/mdtraj Vcs-Git: https://salsa.debian.org/debichem-team/mdtraj.git Testsuite: autopkgtest Testsuite-Triggers: python3-all, python3-gsd, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbformat, python3-netcdf4, python3-packaging, python3-pandas, python3-pytest, python3-pytest-rerunfailures, python3-sklearn Build-Depends: debhelper-compat (= 13), dh-sequence-python3, dh-sequence-numpy3, pybuild-plugin-pyproject, cython3, python3-setuptools, python3-all-dev, python3-gsd, python3-numpy (>= 2.0.0~), python3-scipy, python3-nbsphinx, python3-netcdf4, python3-networkx, python3-packaging , python3-pandas, python3-pyparsing, python3-pytest , python3-pytest-rerunfailures , python3-sphinx, python3-tables, python3-versioneer, libjs-mathjax Build-Depends-Indep: pandoc, python3-msmb-theme, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbconvert, python3-nbformat, python3-numpydoc, python3-sklearn Package-List: python-mdtraj-doc deb doc optional arch=all python3-mdtraj deb python optional arch=any-amd64,arm64,i386 Checksums-Sha1: 5bd6e2c259d9910cfd9450987fe17042290ababf 22729550 mdtraj_1.11.1.post1.orig.tar.gz 51c7f01c63b8795f4109e8b91136e9bad24af650 301808 mdtraj_1.11.1.post1-3.debian.tar.xz Checksums-Sha256: 8a46153ba6102b851639bc61ab6db5387b4c5d5b46d09a72a519e845b3c1f390 22729550 mdtraj_1.11.1.post1.orig.tar.gz 5379a71153de26c9329136774ae225ba9e1a70ced7e3192397733087177ef578 301808 mdtraj_1.11.1.post1-3.debian.tar.xz Files: 2536c860136d6edee6ef01ec56ab1037 22729550 mdtraj_1.11.1.post1.orig.tar.gz 23b5547e7580a3755c5e6836dac44aff 301808 mdtraj_1.11.1.post1-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmmnPrgACgkQVz7x5L1a Afrakg/+IDLSP2LXHyc2N94NOMtvc58cFMAZb1EnPEkjOeF7B0V1QCU5nLWLNVgh rbu8VmzyUa51t7pAC8jaPTHszbRt6sGHuc76aUSXSSFcW6vFlel74Akyt3NPZHef 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/usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting mdtraj in /build/reproducible-path/mdtraj-1.11.1.post1 dpkg-source: info: unpacking mdtraj_1.11.1.post1.orig.tar.gz dpkg-source: info: unpacking mdtraj_1.11.1.post1-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying docs_use_local_mathjax.patch dpkg-source: info: applying build_dir_pybuild.patch dpkg-source: info: applying python_hashbang.patch dpkg-source: info: applying 32bit_skip_image_molecule.patch dpkg-source: info: applying test_relax_tol.patch dpkg-source: info: applying rename-mdconvert-mdtraj.patch dpkg-source: info: applying drop_notebook_in_docs.patch dpkg-source: info: applying test_increase_timeout.patch dpkg-source: info: applying openmm_version_skip.patch dpkg-source: warning: diff '/build/reproducible-path/mdtraj-1.11.1.post1/debian/patches/fix_netcdf_PR2143.patch' patches file /build/reproducible-path/mdtraj-1.11.1.post1/mdtraj/formats/netcdf.py more than once dpkg-source: info: applying fix_netcdf_PR2143.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=1772564708 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package mdtraj dpkg-buildpackage: info: source version 1.11.1.post1-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from mdtraj-1.11.1.post1/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean -i python{version} -p "3.14 3.13" rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdtraj-1.11.1.post1' for f in mdtraj/formats/binpos/binpos.c \ mdtraj/formats/dcd/dcd.c \ mdtraj/formats/dtr/dtr.cpp \ mdtraj/formats/tng/tng.c \ mdtraj/formats/xtc/trr.c \ mdtraj/formats/xtc/xtc.c \ mdtraj/geometry/drid.cpp \ mdtraj/geometry/neighborlist.cpp \ mdtraj/geometry/neighbors.cpp \ mdtraj/geometry/src/_geometry.cpp \ mdtraj/rmsd/_lprmsd.cpp \ mdtraj/rmsd/_rmsd.cpp \ mdtraj/version.py; \ do rm -f $f; done rm -rf mdtraj/core/lib rm -rf docs/api/generated rm -rf __pycache__ .pybuild find . -name "lib*.a" -delete make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.11.1.post1' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-mdtraj.substvars debian/python-mdtraj-doc.substvars debian/files rm -fr -- debian/python3-mdtraj/ debian/tmp/ debian/python-mdtraj-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild pybuild --configure -i python{version} -p "3.14 3.13" dh_auto_build -a -O--buildsystem=pybuild pybuild --build -i python{version} -p "3.14 3.13" I: pybuild plugin_pyproject:142: Building wheel for python3.14 with "build" module I: pybuild base:384: python3.14 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdtraj-1.11.1.post1/.pybuild/cpython3_3.14_mdtraj * Building wheel... Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/15/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 15.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-15/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust,cobol,algol68 --prefix=/usr --with-gcc-major-version-only --program-suffix=-15 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-15-15.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-15-15.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 15.2.0 (Debian 15.2.0-14) warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running bdist_wheel running build running build_py creating build/lib.linux-x86_64-cpython-314/mdtraj copying mdtraj/_version.py -> build/lib.linux-x86_64-cpython-314/mdtraj copying mdtraj/io.py -> build/lib.linux-x86_64-cpython-314/mdtraj copying mdtraj/__init__.py -> build/lib.linux-x86_64-cpython-314/mdtraj creating build/lib.linux-x86_64-cpython-314/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> build/lib.linux-x86_64-cpython-314/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> build/lib.linux-x86_64-cpython-314/mdtraj/scripts copying mdtraj/scripts/__init__.py -> build/lib.linux-x86_64-cpython-314/mdtraj/scripts creating build/lib.linux-x86_64-cpython-314/mdtraj/utils copying mdtraj/utils/validation.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils copying mdtraj/utils/rotation.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils copying mdtraj/utils/singleton.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils copying mdtraj/utils/unitcell.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils copying mdtraj/utils/delay_import.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils copying mdtraj/utils/zipped.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils copying mdtraj/utils/__init__.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils creating build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/gro.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/amberrst.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/registry.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/prmtop.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/lh5.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/openmmxml.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/xyzfile.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/arc.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/hdf5.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/mol2.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/netcdf.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/psf.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/__init__.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/gsd.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/mdcrd.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats creating build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/sasa.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/dssp.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/rg.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/distance.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/shape.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/alignment.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/order.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/pi_stacking.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/contact.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/internal.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/angle.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/hbond.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/rdf.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/__init__.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry creating build/lib.linux-x86_64-cpython-314/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-x86_64-cpython-314/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-x86_64-cpython-314/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-x86_64-cpython-314/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> build/lib.linux-x86_64-cpython-314/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-x86_64-cpython-314/mdtraj/reporters copying mdtraj/reporters/__init__.py -> build/lib.linux-x86_64-cpython-314/mdtraj/reporters creating build/lib.linux-x86_64-cpython-314/mdtraj/core copying mdtraj/core/trajectory.py -> build/lib.linux-x86_64-cpython-314/mdtraj/core copying mdtraj/core/topology.py -> build/lib.linux-x86_64-cpython-314/mdtraj/core copying mdtraj/core/residue_names.py -> build/lib.linux-x86_64-cpython-314/mdtraj/core copying mdtraj/core/element.py -> build/lib.linux-x86_64-cpython-314/mdtraj/core copying mdtraj/core/__init__.py -> build/lib.linux-x86_64-cpython-314/mdtraj/core copying mdtraj/core/selection.py -> build/lib.linux-x86_64-cpython-314/mdtraj/core creating build/lib.linux-x86_64-cpython-314/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-x86_64-cpython-314/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-x86_64-cpython-314/mdtraj/nmr copying mdtraj/nmr/__init__.py -> build/lib.linux-x86_64-cpython-314/mdtraj/nmr creating build/lib.linux-x86_64-cpython-314/mdtraj/testing copying mdtraj/testing/testing.py -> build/lib.linux-x86_64-cpython-314/mdtraj/testing copying mdtraj/testing/docscrape.py -> build/lib.linux-x86_64-cpython-314/mdtraj/testing copying mdtraj/testing/docstrings.py -> build/lib.linux-x86_64-cpython-314/mdtraj/testing copying mdtraj/testing/__init__.py -> build/lib.linux-x86_64-cpython-314/mdtraj/testing creating build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit creating build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdb creating build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/PdbxContainers.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/pdbxfile.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/PdbxReader.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/__init__.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/pdbx.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdbx creating build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdb/data UPDATING build/lib.linux-x86_64-cpython-314/mdtraj/_version.py set build/lib.linux-x86_64-cpython-314/mdtraj/_version.py to '1.11.1.post1' running build_ext building 'mdtraj.formats.trr' extension creating build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src building 'mdtraj.formats.xtc' extension building 'mdtraj.formats.dcd' extension building 'mdtraj.formats.dtr' extension creating build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src building 'mdtraj._rmsd' extension creating build/temp.linux-x86_64-cpython-314/mdtraj/rmsd x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating build/temp.linux-x86_64-cpython-314/mdtraj/formats/dtr building 'mdtraj._lprmsd' extension creating build/temp.linux-x86_64-cpython-314/mdtraj/formats/dcd creating build/temp.linux-x86_64-cpython-314/mdtraj/formats/dtr/src x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating build/temp.linux-x86_64-cpython-314/mdtraj/formats/dcd/src x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-x86_64-cpython-314/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-x86_64-cpython-314/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-x86_64-cpython-314/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const std::string&)’: mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/mdtraj/formats/dcd/dcd.o build/temp.linux-x86_64-cpython-314/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-314/mdtraj/formats/dcd.cpython-314-x86_64-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc-ar rcs build/lib.linux-x86_64-cpython-314/mdtraj/core/lib/libtheobald.a build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const std::string&, mode_t, int, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void DDmkdir(const std::string&, mode_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const std::string&, mode_t, int, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void DDmkdir(const std::string&, mode_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/_lprmsd.o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/Munkres.o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/fancy_index.o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/x86_64-linux-gnu -lgomp -o build/lib.linux-x86_64-cpython-314/mdtraj/_lprmsd.cpython-314-x86_64-linux-gnu.so mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘std::string DDreldir(const std::string&, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function ‘std::string DDreldir(const std::string&, int, int)’, inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘std::string DDreldir(const std::string&, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ building 'mdtraj.geometry.drid' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/drid.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/xtc.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-314/mdtraj/formats/xtc.cpython-314-x86_64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/trr.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-314/mdtraj/formats/trr.cpython-314-x86_64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/mdtraj/formats/dtr/dtr.o build/temp.linux-x86_64-cpython-314/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-314/mdtraj/formats/dtr.cpython-314-x86_64-linux-gnu.so x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/_rmsd.o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-cpython-314/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/x86_64-linux-gnu -lgomp -o build/lib.linux-x86_64-cpython-314/mdtraj/_rmsd.cpython-314-x86_64-linux-gnu.so x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/mdtraj/geometry/drid.o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/dridkernels.o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/moments.o -L/usr/lib/x86_64-linux-gnu -lgomp -o build/lib.linux-x86_64-cpython-314/mdtraj/geometry/drid.cpython-314-x86_64-linux-gnu.so x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/mdtraj/geometry/neighbors.o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/neighbors.o -L/usr/lib/x86_64-linux-gnu -lgomp -o build/lib.linux-x86_64-cpython-314/mdtraj/geometry/neighbors.cpython-314-x86_64-linux-gnu.so x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/mdtraj/geometry/neighborlist.o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/neighborlist.o -L/usr/lib/x86_64-linux-gnu -lgomp -o build/lib.linux-x86_64-cpython-314/mdtraj/geometry/neighborlist.cpython-314-x86_64-linux-gnu.so x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/_geometry.o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/dssp.o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/geometry.o build/temp.linux-x86_64-cpython-314/mdtraj/geometry/src/sasa.o -L/usr/lib/x86_64-linux-gnu -lgomp -o build/lib.linux-x86_64-cpython-314/mdtraj/geometry/_geometry.cpython-314-x86_64-linux-gnu.so installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/mdtraj creating build/bdist.linux-x86_64/wheel/mdtraj/scripts copying build/lib.linux-x86_64-cpython-314/mdtraj/scripts/mdinspect.py -> build/bdist.linux-x86_64/wheel/./mdtraj/scripts copying build/lib.linux-x86_64-cpython-314/mdtraj/scripts/mdconvert.py -> build/bdist.linux-x86_64/wheel/./mdtraj/scripts copying build/lib.linux-x86_64-cpython-314/mdtraj/scripts/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/scripts copying build/lib.linux-x86_64-cpython-314/mdtraj/_version.py -> build/bdist.linux-x86_64/wheel/./mdtraj creating build/bdist.linux-x86_64/wheel/mdtraj/utils copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/validation.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/rotation.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils creating build/bdist.linux-x86_64/wheel/mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit/doctests.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit/quantity.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit/constants.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit/prefix.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit/unit.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/singleton.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/unitcell.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/delay_import.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/zipped.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/contextmanagers.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils creating build/bdist.linux-x86_64/wheel/mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/gro.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/amberrst.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/registry.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/prmtop.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/lh5.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/dcd.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/openmmxml.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/xyzfile.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/dtr.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/arc.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/hdf5.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/mol2.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/hoomdxml.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/netcdf.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats creating build/bdist.linux-x86_64/wheel/mdtraj/formats/pdb copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdb copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdb creating build/bdist.linux-x86_64/wheel/mdtraj/formats/pdb/data copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdb/data copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdb/data copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdb copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/psf.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/xtc.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats creating build/bdist.linux-x86_64/wheel/mdtraj/formats/pdbx copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdbx/PdbxContainers.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdbx/pdbxfile.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdbx/PdbxReader.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdbx/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdbx/pdbx.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/gsd.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/trr.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/mdcrd.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-314/mdtraj/formats/lammpstrj.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats creating build/bdist.linux-x86_64/wheel/mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/sasa.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/dssp.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/dihedral.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/rg.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/distance.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/shape.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/alignment.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/order.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/pi_stacking.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/contact.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/internal.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/drid.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/neighbors.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/neighborlist.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/angle.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/hbond.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/_geometry.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/rdf.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/geometry/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-314/mdtraj/_rmsd.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj creating build/bdist.linux-x86_64/wheel/mdtraj/reporters copying build/lib.linux-x86_64-cpython-314/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters copying build/lib.linux-x86_64-cpython-314/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters copying build/lib.linux-x86_64-cpython-314/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters copying build/lib.linux-x86_64-cpython-314/mdtraj/reporters/basereporter.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters copying build/lib.linux-x86_64-cpython-314/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters copying build/lib.linux-x86_64-cpython-314/mdtraj/reporters/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters creating build/bdist.linux-x86_64/wheel/mdtraj/core creating build/bdist.linux-x86_64/wheel/mdtraj/core/lib copying build/lib.linux-x86_64-cpython-314/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-x86_64/wheel/./mdtraj/core/lib copying build/lib.linux-x86_64-cpython-314/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-x86_64/wheel/./mdtraj/core/lib copying build/lib.linux-x86_64-cpython-314/mdtraj/core/lib/center.h -> build/bdist.linux-x86_64/wheel/./mdtraj/core/lib copying build/lib.linux-x86_64-cpython-314/mdtraj/core/trajectory.py -> build/bdist.linux-x86_64/wheel/./mdtraj/core copying build/lib.linux-x86_64-cpython-314/mdtraj/core/topology.py -> build/bdist.linux-x86_64/wheel/./mdtraj/core copying build/lib.linux-x86_64-cpython-314/mdtraj/core/residue_names.py -> build/bdist.linux-x86_64/wheel/./mdtraj/core copying build/lib.linux-x86_64-cpython-314/mdtraj/core/element.py -> build/bdist.linux-x86_64/wheel/./mdtraj/core copying build/lib.linux-x86_64-cpython-314/mdtraj/core/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/core copying build/lib.linux-x86_64-cpython-314/mdtraj/core/selection.py -> build/bdist.linux-x86_64/wheel/./mdtraj/core copying build/lib.linux-x86_64-cpython-314/mdtraj/io.py -> build/bdist.linux-x86_64/wheel/./mdtraj creating build/bdist.linux-x86_64/wheel/mdtraj/nmr copying build/lib.linux-x86_64-cpython-314/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-x86_64/wheel/./mdtraj/nmr copying build/lib.linux-x86_64-cpython-314/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-x86_64/wheel/./mdtraj/nmr copying build/lib.linux-x86_64-cpython-314/mdtraj/nmr/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/nmr copying build/lib.linux-x86_64-cpython-314/mdtraj/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj copying build/lib.linux-x86_64-cpython-314/mdtraj/_lprmsd.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj creating build/bdist.linux-x86_64/wheel/mdtraj/testing copying build/lib.linux-x86_64-cpython-314/mdtraj/testing/testing.py -> build/bdist.linux-x86_64/wheel/./mdtraj/testing copying build/lib.linux-x86_64-cpython-314/mdtraj/testing/docscrape.py -> build/bdist.linux-x86_64/wheel/./mdtraj/testing copying build/lib.linux-x86_64-cpython-314/mdtraj/testing/docstrings.py -> build/bdist.linux-x86_64/wheel/./mdtraj/testing copying build/lib.linux-x86_64-cpython-314/mdtraj/testing/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/testing running install_egg_info running egg_info creating mdtraj.egg-info writing mdtraj.egg-info/PKG-INFO writing dependency_links to mdtraj.egg-info/dependency_links.txt writing entry points to mdtraj.egg-info/entry_points.txt writing requirements to mdtraj.egg-info/requires.txt writing top-level names to mdtraj.egg-info/top_level.txt writing manifest file 'mdtraj.egg-info/SOURCES.txt' dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching '__pycache__' no previously-included directories found matching '*.pyc' adding license file 'LICENSE' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to build/bdist.linux-x86_64/wheel/./mdtraj-1.11.1.post1.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/mdtraj-1.11.1.post1.dist-info/WHEEL creating '/build/reproducible-path/mdtraj-1.11.1.post1/.pybuild/cpython3_3.14_mdtraj/.tmp-p31wexs4/mdtraj-1.11.1.post1-cp314-cp314-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'mdtraj/__init__.py' adding 'mdtraj/_lprmsd.cpython-314-x86_64-linux-gnu.so' adding 'mdtraj/_rmsd.cpython-314-x86_64-linux-gnu.so' adding 'mdtraj/_version.py' adding 'mdtraj/io.py' adding 'mdtraj/core/__init__.py' adding 'mdtraj/core/element.py' adding 'mdtraj/core/residue_names.py' adding 'mdtraj/core/selection.py' adding 'mdtraj/core/topology.py' adding 'mdtraj/core/trajectory.py' adding 'mdtraj/core/lib/center.h' adding 'mdtraj/core/lib/libtheobald.a' adding 'mdtraj/core/lib/theobald_rmsd.h' adding 'mdtraj/formats/__init__.py' adding 'mdtraj/formats/amberrst.py' adding 'mdtraj/formats/arc.py' adding 'mdtraj/formats/dcd.cpython-314-x86_64-linux-gnu.so' adding 'mdtraj/formats/dtr.cpython-314-x86_64-linux-gnu.so' adding 'mdtraj/formats/gro.py' adding 'mdtraj/formats/gsd.py' adding 'mdtraj/formats/hdf5.py' adding 'mdtraj/formats/hoomdxml.py' adding 'mdtraj/formats/lammpstrj.py' adding 'mdtraj/formats/lh5.py' adding 'mdtraj/formats/mdcrd.py' adding 'mdtraj/formats/mol2.py' adding 'mdtraj/formats/netcdf.py' adding 'mdtraj/formats/openmmxml.py' adding 'mdtraj/formats/prmtop.py' adding 'mdtraj/formats/psf.py' adding 'mdtraj/formats/registry.py' adding 'mdtraj/formats/trr.cpython-314-x86_64-linux-gnu.so' adding 'mdtraj/formats/xtc.cpython-314-x86_64-linux-gnu.so' adding 'mdtraj/formats/xyzfile.py' adding 'mdtraj/formats/pdb/__init__.py' adding 'mdtraj/formats/pdb/pdbfile.py' adding 'mdtraj/formats/pdb/pdbstructure.py' adding 'mdtraj/formats/pdb/data/pdbNames.xml' adding 'mdtraj/formats/pdb/data/residues.xml' adding 'mdtraj/formats/pdbx/PdbxContainers.py' adding 'mdtraj/formats/pdbx/PdbxReader.py' adding 'mdtraj/formats/pdbx/__init__.py' adding 'mdtraj/formats/pdbx/pdbx.py' adding 'mdtraj/formats/pdbx/pdbxfile.py' adding 'mdtraj/geometry/__init__.py' adding 'mdtraj/geometry/_geometry.cpython-314-x86_64-linux-gnu.so' adding 'mdtraj/geometry/alignment.py' adding 'mdtraj/geometry/angle.py' adding 'mdtraj/geometry/contact.py' adding 'mdtraj/geometry/dihedral.py' adding 'mdtraj/geometry/distance.py' adding 'mdtraj/geometry/drid.cpython-314-x86_64-linux-gnu.so' adding 'mdtraj/geometry/dssp.py' adding 'mdtraj/geometry/hbond.py' adding 'mdtraj/geometry/internal.py' adding 'mdtraj/geometry/neighborlist.cpython-314-x86_64-linux-gnu.so' adding 'mdtraj/geometry/neighbors.cpython-314-x86_64-linux-gnu.so' adding 'mdtraj/geometry/order.py' adding 'mdtraj/geometry/pi_stacking.py' adding 'mdtraj/geometry/rdf.py' adding 'mdtraj/geometry/rg.py' adding 'mdtraj/geometry/sasa.py' adding 'mdtraj/geometry/shape.py' adding 'mdtraj/geometry/thermodynamic_properties.py' adding 'mdtraj/nmr/__init__.py' adding 'mdtraj/nmr/scalar_couplings.py' adding 'mdtraj/nmr/shift_wrappers.py' adding 'mdtraj/reporters/__init__.py' adding 'mdtraj/reporters/basereporter.py' adding 'mdtraj/reporters/dcdreporter.py' adding 'mdtraj/reporters/hdf5reporter.py' adding 'mdtraj/reporters/netcdfreporter.py' adding 'mdtraj/reporters/xtcreporter.py' adding 'mdtraj/scripts/__init__.py' adding 'mdtraj/scripts/mdconvert.py' adding 'mdtraj/scripts/mdinspect.py' adding 'mdtraj/testing/__init__.py' adding 'mdtraj/testing/docscrape.py' adding 'mdtraj/testing/docstrings.py' adding 'mdtraj/testing/testing.py' adding 'mdtraj/utils/__init__.py' adding 'mdtraj/utils/contextmanagers.py' adding 'mdtraj/utils/delay_import.py' adding 'mdtraj/utils/rotation.py' adding 'mdtraj/utils/singleton.py' adding 'mdtraj/utils/unitcell.py' adding 'mdtraj/utils/validation.py' adding 'mdtraj/utils/zipped.py' adding 'mdtraj/utils/unit/__init__.py' adding 'mdtraj/utils/unit/basedimension.py' adding 'mdtraj/utils/unit/baseunit.py' adding 'mdtraj/utils/unit/constants.py' adding 'mdtraj/utils/unit/doctests.py' adding 'mdtraj/utils/unit/mymatrix.py' adding 'mdtraj/utils/unit/prefix.py' adding 'mdtraj/utils/unit/quantity.py' adding 'mdtraj/utils/unit/standard_dimensions.py' adding 'mdtraj/utils/unit/unit.py' adding 'mdtraj/utils/unit/unit_definitions.py' adding 'mdtraj/utils/unit/unit_math.py' adding 'mdtraj/utils/unit/unit_operators.py' adding 'mdtraj-1.11.1.post1.dist-info/licenses/LICENSE' adding 'mdtraj-1.11.1.post1.dist-info/METADATA' adding 'mdtraj-1.11.1.post1.dist-info/WHEEL' adding 'mdtraj-1.11.1.post1.dist-info/entry_points.txt' adding 'mdtraj-1.11.1.post1.dist-info/top_level.txt' adding 'mdtraj-1.11.1.post1.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built mdtraj-1.11.1.post1-cp314-cp314-linux_x86_64.whl I: pybuild plugin_pyproject:168: Unpacking wheel built for python3.14 with "installer" module I: pybuild plugin_pyproject:142: Building wheel for python3.13 with "build" module I: pybuild base:384: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdtraj-1.11.1.post1/.pybuild/cpython3_3.13_mdtraj * Building wheel... Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/15/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 15.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-15/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust,cobol,algol68 --prefix=/usr --with-gcc-major-version-only --program-suffix=-15 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-15-15.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-15-15.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 15.2.0 (Debian 15.2.0-14) warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running bdist_wheel running build running build_py creating build/lib.linux-x86_64-cpython-313/mdtraj copying mdtraj/_version.py -> build/lib.linux-x86_64-cpython-313/mdtraj copying mdtraj/io.py -> build/lib.linux-x86_64-cpython-313/mdtraj copying mdtraj/__init__.py -> build/lib.linux-x86_64-cpython-313/mdtraj creating build/lib.linux-x86_64-cpython-313/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> build/lib.linux-x86_64-cpython-313/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> build/lib.linux-x86_64-cpython-313/mdtraj/scripts copying mdtraj/scripts/__init__.py -> build/lib.linux-x86_64-cpython-313/mdtraj/scripts creating build/lib.linux-x86_64-cpython-313/mdtraj/utils copying mdtraj/utils/validation.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils copying mdtraj/utils/rotation.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils copying mdtraj/utils/singleton.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils copying mdtraj/utils/unitcell.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils copying mdtraj/utils/delay_import.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils copying mdtraj/utils/zipped.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils copying mdtraj/utils/__init__.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils creating build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/gro.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/amberrst.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/registry.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/prmtop.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/lh5.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/openmmxml.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/xyzfile.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/arc.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/hdf5.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/mol2.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/netcdf.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/psf.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/__init__.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/gsd.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/mdcrd.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats creating build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/sasa.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/dssp.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/rg.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/distance.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/shape.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/alignment.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/order.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/pi_stacking.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/contact.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/internal.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/angle.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/hbond.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/rdf.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/__init__.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry creating build/lib.linux-x86_64-cpython-313/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-x86_64-cpython-313/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-x86_64-cpython-313/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-x86_64-cpython-313/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> build/lib.linux-x86_64-cpython-313/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-x86_64-cpython-313/mdtraj/reporters copying mdtraj/reporters/__init__.py -> build/lib.linux-x86_64-cpython-313/mdtraj/reporters creating build/lib.linux-x86_64-cpython-313/mdtraj/core copying mdtraj/core/trajectory.py -> build/lib.linux-x86_64-cpython-313/mdtraj/core copying mdtraj/core/topology.py -> build/lib.linux-x86_64-cpython-313/mdtraj/core copying mdtraj/core/residue_names.py -> build/lib.linux-x86_64-cpython-313/mdtraj/core copying mdtraj/core/element.py -> build/lib.linux-x86_64-cpython-313/mdtraj/core copying mdtraj/core/__init__.py -> build/lib.linux-x86_64-cpython-313/mdtraj/core copying mdtraj/core/selection.py -> build/lib.linux-x86_64-cpython-313/mdtraj/core creating build/lib.linux-x86_64-cpython-313/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-x86_64-cpython-313/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-x86_64-cpython-313/mdtraj/nmr copying mdtraj/nmr/__init__.py -> build/lib.linux-x86_64-cpython-313/mdtraj/nmr creating build/lib.linux-x86_64-cpython-313/mdtraj/testing copying mdtraj/testing/testing.py -> build/lib.linux-x86_64-cpython-313/mdtraj/testing copying mdtraj/testing/docscrape.py -> build/lib.linux-x86_64-cpython-313/mdtraj/testing copying mdtraj/testing/docstrings.py -> build/lib.linux-x86_64-cpython-313/mdtraj/testing copying mdtraj/testing/__init__.py -> build/lib.linux-x86_64-cpython-313/mdtraj/testing creating build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit creating build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdb creating build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/PdbxContainers.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/pdbxfile.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/PdbxReader.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/__init__.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/pdbx.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdbx creating build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdb/data UPDATING build/lib.linux-x86_64-cpython-313/mdtraj/_version.py set build/lib.linux-x86_64-cpython-313/mdtraj/_version.py to '1.11.1.post1' running build_ext building 'mdtraj.formats.xtc' extension building 'mdtraj.formats.trr' extension creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src building 'mdtraj.formats.dtr' extension building 'mdtraj.formats.dcd' extension creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src building 'mdtraj._rmsd' extension building 'mdtraj._lprmsd' extension creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr creating build/temp.linux-x86_64-cpython-313/mdtraj/rmsd x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating build/temp.linux-x86_64-cpython-313/mdtraj/rmsd creating build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr/src x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/src x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const std::string&)’: mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/dcd.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 x86_64-linux-gnu-gcc-ar rcs build/lib.linux-x86_64-cpython-313/mdtraj/core/lib/libtheobald.a build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const std::string&, mode_t, int, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void DDmkdir(const std::string&, mode_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const std::string&, mode_t, int, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void DDmkdir(const std::string&, mode_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘std::string DDreldir(const std::string&, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function ‘std::string DDreldir(const std::string&, int, int)’, inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘std::string DDreldir(const std::string&, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr/dtr.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare building 'mdtraj.geometry.drid' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/drid.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/_lprmsd.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/Munkres.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/fancy_index.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/x86_64-linux-gnu -lgomp -o build/lib.linux-x86_64-cpython-313/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/xtc.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare building 'mdtraj.geometry.neighborlist' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/trr.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/_rmsd.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/x86_64-linux-gnu -lgomp -o build/lib.linux-x86_64-cpython-313/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/geometry/neighbors.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/neighbors.o -L/usr/lib/x86_64-linux-gnu -lgomp -o build/lib.linux-x86_64-cpython-313/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/geometry/drid.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/dridkernels.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/moments.o -L/usr/lib/x86_64-linux-gnu -lgomp -o build/lib.linux-x86_64-cpython-313/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/geometry/neighborlist.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/neighborlist.o -L/usr/lib/x86_64-linux-gnu -lgomp -o build/lib.linux-x86_64-cpython-313/mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.1.post1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/_geometry.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/dssp.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/geometry.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/sasa.o -L/usr/lib/x86_64-linux-gnu -lgomp -o build/lib.linux-x86_64-cpython-313/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/mdtraj creating build/bdist.linux-x86_64/wheel/mdtraj/scripts copying build/lib.linux-x86_64-cpython-313/mdtraj/scripts/mdinspect.py -> build/bdist.linux-x86_64/wheel/./mdtraj/scripts copying build/lib.linux-x86_64-cpython-313/mdtraj/scripts/mdconvert.py -> build/bdist.linux-x86_64/wheel/./mdtraj/scripts copying build/lib.linux-x86_64-cpython-313/mdtraj/scripts/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/scripts copying build/lib.linux-x86_64-cpython-313/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj copying build/lib.linux-x86_64-cpython-313/mdtraj/_version.py -> build/bdist.linux-x86_64/wheel/./mdtraj creating build/bdist.linux-x86_64/wheel/mdtraj/utils copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/validation.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/rotation.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils creating build/bdist.linux-x86_64/wheel/mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit/doctests.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit/quantity.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit/constants.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit/prefix.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit/unit.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/singleton.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/unitcell.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/delay_import.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/zipped.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils copying build/lib.linux-x86_64-cpython-313/mdtraj/utils/contextmanagers.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils creating build/bdist.linux-x86_64/wheel/mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/gro.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/amberrst.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/registry.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/prmtop.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/lh5.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/openmmxml.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/xyzfile.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/arc.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/hdf5.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/mol2.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/hoomdxml.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/netcdf.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/formats creating build/bdist.linux-x86_64/wheel/mdtraj/formats/pdb copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdb copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdb creating build/bdist.linux-x86_64/wheel/mdtraj/formats/pdb/data copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdb/data copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdb/data copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdb copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/psf.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats creating build/bdist.linux-x86_64/wheel/mdtraj/formats/pdbx copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdbx/PdbxContainers.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdbx/pdbxfile.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdbx/PdbxReader.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdbx/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdbx/pdbx.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/gsd.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/mdcrd.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/lammpstrj.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats creating build/bdist.linux-x86_64/wheel/mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/sasa.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/dssp.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/dihedral.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/rg.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/distance.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/shape.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/alignment.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/order.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/pi_stacking.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/contact.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/internal.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/angle.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/hbond.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/rdf.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry copying build/lib.linux-x86_64-cpython-313/mdtraj/geometry/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry creating build/bdist.linux-x86_64/wheel/mdtraj/reporters copying build/lib.linux-x86_64-cpython-313/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters copying build/lib.linux-x86_64-cpython-313/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters copying build/lib.linux-x86_64-cpython-313/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters copying build/lib.linux-x86_64-cpython-313/mdtraj/reporters/basereporter.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters copying build/lib.linux-x86_64-cpython-313/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters copying build/lib.linux-x86_64-cpython-313/mdtraj/reporters/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters creating build/bdist.linux-x86_64/wheel/mdtraj/core creating build/bdist.linux-x86_64/wheel/mdtraj/core/lib copying build/lib.linux-x86_64-cpython-313/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-x86_64/wheel/./mdtraj/core/lib copying build/lib.linux-x86_64-cpython-313/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-x86_64/wheel/./mdtraj/core/lib copying build/lib.linux-x86_64-cpython-313/mdtraj/core/lib/center.h -> build/bdist.linux-x86_64/wheel/./mdtraj/core/lib copying build/lib.linux-x86_64-cpython-313/mdtraj/core/trajectory.py -> build/bdist.linux-x86_64/wheel/./mdtraj/core copying build/lib.linux-x86_64-cpython-313/mdtraj/core/topology.py -> build/bdist.linux-x86_64/wheel/./mdtraj/core copying build/lib.linux-x86_64-cpython-313/mdtraj/core/residue_names.py -> build/bdist.linux-x86_64/wheel/./mdtraj/core copying build/lib.linux-x86_64-cpython-313/mdtraj/core/element.py -> build/bdist.linux-x86_64/wheel/./mdtraj/core copying build/lib.linux-x86_64-cpython-313/mdtraj/core/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/core copying build/lib.linux-x86_64-cpython-313/mdtraj/core/selection.py -> build/bdist.linux-x86_64/wheel/./mdtraj/core copying build/lib.linux-x86_64-cpython-313/mdtraj/io.py -> build/bdist.linux-x86_64/wheel/./mdtraj creating build/bdist.linux-x86_64/wheel/mdtraj/nmr copying build/lib.linux-x86_64-cpython-313/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-x86_64/wheel/./mdtraj/nmr copying build/lib.linux-x86_64-cpython-313/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-x86_64/wheel/./mdtraj/nmr copying build/lib.linux-x86_64-cpython-313/mdtraj/nmr/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/nmr copying build/lib.linux-x86_64-cpython-313/mdtraj/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj creating build/bdist.linux-x86_64/wheel/mdtraj/testing copying build/lib.linux-x86_64-cpython-313/mdtraj/testing/testing.py -> build/bdist.linux-x86_64/wheel/./mdtraj/testing copying build/lib.linux-x86_64-cpython-313/mdtraj/testing/docscrape.py -> build/bdist.linux-x86_64/wheel/./mdtraj/testing copying build/lib.linux-x86_64-cpython-313/mdtraj/testing/docstrings.py -> build/bdist.linux-x86_64/wheel/./mdtraj/testing copying build/lib.linux-x86_64-cpython-313/mdtraj/testing/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj/testing copying build/lib.linux-x86_64-cpython-313/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj running install_egg_info running egg_info writing mdtraj.egg-info/PKG-INFO writing dependency_links to mdtraj.egg-info/dependency_links.txt writing entry points to mdtraj.egg-info/entry_points.txt writing requirements to mdtraj.egg-info/requires.txt writing top-level names to mdtraj.egg-info/top_level.txt dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching '__pycache__' no previously-included directories found matching '*.pyc' adding license file 'LICENSE' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to build/bdist.linux-x86_64/wheel/./mdtraj-1.11.1.post1.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/mdtraj-1.11.1.post1.dist-info/WHEEL creating '/build/reproducible-path/mdtraj-1.11.1.post1/.pybuild/cpython3_3.13_mdtraj/.tmp-6_gfwkr3/mdtraj-1.11.1.post1-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'mdtraj/__init__.py' adding 'mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so' adding 'mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so' adding 'mdtraj/_version.py' adding 'mdtraj/io.py' adding 'mdtraj/core/__init__.py' adding 'mdtraj/core/element.py' adding 'mdtraj/core/residue_names.py' adding 'mdtraj/core/selection.py' adding 'mdtraj/core/topology.py' adding 'mdtraj/core/trajectory.py' adding 'mdtraj/core/lib/center.h' adding 'mdtraj/core/lib/libtheobald.a' adding 'mdtraj/core/lib/theobald_rmsd.h' adding 'mdtraj/formats/__init__.py' adding 'mdtraj/formats/amberrst.py' adding 'mdtraj/formats/arc.py' adding 'mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so' adding 'mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so' adding 'mdtraj/formats/gro.py' adding 'mdtraj/formats/gsd.py' adding 'mdtraj/formats/hdf5.py' adding 'mdtraj/formats/hoomdxml.py' adding 'mdtraj/formats/lammpstrj.py' adding 'mdtraj/formats/lh5.py' adding 'mdtraj/formats/mdcrd.py' adding 'mdtraj/formats/mol2.py' adding 'mdtraj/formats/netcdf.py' adding 'mdtraj/formats/openmmxml.py' adding 'mdtraj/formats/prmtop.py' adding 'mdtraj/formats/psf.py' adding 'mdtraj/formats/registry.py' adding 'mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so' adding 'mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so' adding 'mdtraj/formats/xyzfile.py' adding 'mdtraj/formats/pdb/__init__.py' adding 'mdtraj/formats/pdb/pdbfile.py' adding 'mdtraj/formats/pdb/pdbstructure.py' adding 'mdtraj/formats/pdb/data/pdbNames.xml' adding 'mdtraj/formats/pdb/data/residues.xml' adding 'mdtraj/formats/pdbx/PdbxContainers.py' adding 'mdtraj/formats/pdbx/PdbxReader.py' adding 'mdtraj/formats/pdbx/__init__.py' adding 'mdtraj/formats/pdbx/pdbx.py' adding 'mdtraj/formats/pdbx/pdbxfile.py' adding 'mdtraj/geometry/__init__.py' adding 'mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so' adding 'mdtraj/geometry/alignment.py' adding 'mdtraj/geometry/angle.py' adding 'mdtraj/geometry/contact.py' adding 'mdtraj/geometry/dihedral.py' adding 'mdtraj/geometry/distance.py' adding 'mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so' adding 'mdtraj/geometry/dssp.py' adding 'mdtraj/geometry/hbond.py' adding 'mdtraj/geometry/internal.py' adding 'mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so' adding 'mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so' adding 'mdtraj/geometry/order.py' adding 'mdtraj/geometry/pi_stacking.py' adding 'mdtraj/geometry/rdf.py' adding 'mdtraj/geometry/rg.py' adding 'mdtraj/geometry/sasa.py' adding 'mdtraj/geometry/shape.py' adding 'mdtraj/geometry/thermodynamic_properties.py' adding 'mdtraj/nmr/__init__.py' adding 'mdtraj/nmr/scalar_couplings.py' adding 'mdtraj/nmr/shift_wrappers.py' adding 'mdtraj/reporters/__init__.py' adding 'mdtraj/reporters/basereporter.py' adding 'mdtraj/reporters/dcdreporter.py' adding 'mdtraj/reporters/hdf5reporter.py' adding 'mdtraj/reporters/netcdfreporter.py' adding 'mdtraj/reporters/xtcreporter.py' adding 'mdtraj/scripts/__init__.py' adding 'mdtraj/scripts/mdconvert.py' adding 'mdtraj/scripts/mdinspect.py' adding 'mdtraj/testing/__init__.py' adding 'mdtraj/testing/docscrape.py' adding 'mdtraj/testing/docstrings.py' adding 'mdtraj/testing/testing.py' adding 'mdtraj/utils/__init__.py' adding 'mdtraj/utils/contextmanagers.py' adding 'mdtraj/utils/delay_import.py' adding 'mdtraj/utils/rotation.py' adding 'mdtraj/utils/singleton.py' adding 'mdtraj/utils/unitcell.py' adding 'mdtraj/utils/validation.py' adding 'mdtraj/utils/zipped.py' adding 'mdtraj/utils/unit/__init__.py' adding 'mdtraj/utils/unit/basedimension.py' adding 'mdtraj/utils/unit/baseunit.py' adding 'mdtraj/utils/unit/constants.py' adding 'mdtraj/utils/unit/doctests.py' adding 'mdtraj/utils/unit/mymatrix.py' adding 'mdtraj/utils/unit/prefix.py' adding 'mdtraj/utils/unit/quantity.py' adding 'mdtraj/utils/unit/standard_dimensions.py' adding 'mdtraj/utils/unit/unit.py' adding 'mdtraj/utils/unit/unit_definitions.py' adding 'mdtraj/utils/unit/unit_math.py' adding 'mdtraj/utils/unit/unit_operators.py' adding 'mdtraj-1.11.1.post1.dist-info/licenses/LICENSE' adding 'mdtraj-1.11.1.post1.dist-info/METADATA' adding 'mdtraj-1.11.1.post1.dist-info/WHEEL' adding 'mdtraj-1.11.1.post1.dist-info/entry_points.txt' adding 'mdtraj-1.11.1.post1.dist-info/top_level.txt' adding 'mdtraj-1.11.1.post1.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built mdtraj-1.11.1.post1-cp313-cp313-linux_x86_64.whl I: pybuild plugin_pyproject:168: Unpacking wheel built for python3.13 with "installer" module dh_auto_test -a -O--buildsystem=pybuild pybuild --test --test-pytest -i python{version} -p "3.14 3.13" I: pybuild base:384: cd /build/reproducible-path/mdtraj-1.11.1.post1/.pybuild/cpython3_3.14_mdtraj/build; python3.14 -m pytest -k 'not ( mdconvert or pi_stacking.ipynb or nmr.ipynb or test_image_molecules or test_3 or from_url or test_1vii_url_and_gz or test_1vii_load_from_mixture )' ============================= test session starts ============================== platform linux -- Python 3.14.3, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.14 cachedir: .pytest_cache rootdir: /build/reproducible-path/mdtraj-1.11.1.post1/.pybuild/cpython3_3.14_mdtraj/build configfile: pyproject.toml testpaths: tests, examples plugins: rerunfailures-16.1, typeguard-4.4.4 collecting ... collected 1175 items / 24 deselected / 1151 selected tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] tests/test_alignment.py::test_transform PASSED [ 0%] tests/test_alignment.py::test_transform2 PASSED [ 0%] tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] tests/test_angles.py::test_generator PASSED [ 0%] tests/test_angles.py::test_angle_180[True] PASSED [ 0%] tests/test_angles.py::test_angle_180[False] PASSED [ 0%] tests/test_arc.py::test_read_0 PASSED [ 0%] tests/test_arc.py::test_read_arctraj PASSED [ 0%] tests/test_arc.py::test_read_arctraj_top PASSED [ 0%] tests/test_arc.py::test_read_pbc PASSED [ 1%] tests/test_capi.py::test_1 PASSED [ 1%] tests/test_contact.py::test_contact_0 PASSED [ 1%] tests/test_contact.py::test_contact_1 PASSED [ 1%] tests/test_contact.py::test_contact_2 PASSED [ 1%] tests/test_contact.py::test_contact_3 PASSED [ 1%] tests/test_contact.py::test_contact_4 PASSED [ 1%] tests/test_crd.py::test_prmtop_with_overflow_mdcrd PASSED [ 1%] tests/test_dcd.py::test_read PASSED [ 1%] tests/test_dcd.py::test_read_2 PASSED [ 1%] tests/test_dcd.py::test_read_stride PASSED [ 1%] tests/test_dcd.py::test_read_stride_2 PASSED [ 1%] tests/test_dcd.py::test_read_3 PASSED [ 2%] tests/test_dcd.py::test_read_4 PASSED [ 2%] tests/test_dcd.py::test_read_5 PASSED [ 2%] tests/test_dcd.py::test_read_6 PASSED [ 2%] 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[ 3%] tests/test_dihedral.py::test_compute_omega PASSED [ 3%] tests/test_dihedral.py::test_shape_when_none PASSED [ 3%] tests/test_dihedral.py::test_dihedral_1 SKIPPED (pymol executable no...) [ 3%] tests/test_dihedral.py::test_dihedral_2chains PASSED [ 4%] tests/test_dihedral.py::test_generator PASSED [ 4%] tests/test_distance.py::Test_Distance::test_generator PASSED [ 4%] tests/test_distance.py::Test_Distance::test_0 PASSED [ 4%] tests/test_distance.py::Test_Distance::test_compute_distances_core_nonperiodic PASSED [ 4%] tests/test_distance.py::Test_Distance::test_compute_distances_core_periodic PASSED [ 4%] tests/test_distance.py::Test_Distance::test_1 PASSED [ 4%] tests/test_distance.py::Test_Distance::test_2 PASSED [ 4%] tests/test_distance.py::Test_Distance::test_0p PASSED [ 4%] tests/test_distance.py::Test_Distance::test_1p PASSED [ 4%] tests/test_distance.py::Test_Distance::test_2p PASSED [ 4%] tests/test_distance.py::Test_Distance::test_4 PASSED [ 5%] tests/test_distance.py::Test_Distance::test_5 PASSED [ 5%] tests/test_distance.py::Test_Distance::test_6 PASSED [ 5%] tests/test_distance.py::Test_Distance::test_7 PASSED [ 5%] tests/test_distance.py::Test_Distance::test_closest_contact PASSED [ 5%] tests/test_distance.py::Test_Distance::test_distance_nan PASSED [ 5%] tests/test_distance.py::Test_Distance::test_closest_contact_nan_pos PASSED [ 5%] tests/test_distance.py::Test_Distance::test_distance_t_inputs PASSED [ 5%] tests/test_distance.py::Test_Distance::test_distances_t PASSED [ 5%] tests/test_distance.py::Test_Distance::test_distances_t_at_0 PASSED [ 5%] tests/test_distance.py::Test_Distance::test_amber_t PASSED [ 5%] tests/test_docstrings.py::test_docstrings[mdtraj._lprmsd] PASSED [ 5%] tests/test_docstrings.py::test_docstrings[mdtraj._rmsd] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj._version] SKIPPED (...) [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.core.element] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.core.residue_names] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.core.selection] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.core.topology] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.core.trajectory] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.amberrst] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.arc] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.dcd] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.dtr] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.gro] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.gsd] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.hdf5] SKIPPED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.hoomdxml] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.lammpstrj] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.lh5] SKIPPED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.mdcrd] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.mol2] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.netcdf] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.openmmxml] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbfile] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbstructure] SKIPPED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx.PdbxContainers] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx.PdbxReader] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx.pdbx] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx.pdbxfile] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.prmtop] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.psf] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.registry] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.trr] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.xtc] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.xyzfile] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry._geometry] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.alignment] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.angle] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.contact] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dihedral] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.distance] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.drid] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dssp] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.hbond] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.internal] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighborlist] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighbors] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.order] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.pi_stacking] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rdf] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rg] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.sasa] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.shape] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.thermodynamic_properties] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.io] SKIPPED (Skip c...) [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.nmr.scalar_couplings] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.nmr.shift_wrappers] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.reporters.basereporter] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.reporters.dcdreporter] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.reporters.hdf5reporter] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.reporters.netcdfreporter] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.reporters.xtcreporter] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdinspect] SKIPPED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.testing.docscrape] SKIPPED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.testing.docstrings] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.testing.testing] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.contextmanagers] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.delay_import] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.rotation] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.singleton] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.basedimension] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.baseunit] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.constants] PASSED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.mymatrix] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.prefix] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.quantity] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.standard_dimensions] PASSED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_definitions] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_math] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_operators] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unitcell] PASSED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.validation] PASSED [ 13%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.zipped] PASSED [ 13%] tests/test_drid.py::test_drid_1 PASSED [ 13%] tests/test_drid.py::test_drid_2 PASSED [ 13%] tests/test_dssp.py::test_1[1bpi.pdb] PASSED [ 13%] tests/test_dssp.py::test_1[1vii.pdb] PASSED [ 13%] tests/test_dssp.py::test_1[4ZUO.pdb] PASSED [ 13%] tests/test_dssp.py::test_1[1am7_protein.pdb] PASSED [ 13%] tests/test_dssp.py::test_2[2EQQ.pdb] PASSED [ 13%] tests/test_dssp.py::test_4 PASSED [ 13%] tests/test_dssp.py::test_5 PASSED [ 13%] tests/test_dssp.py::test_7 PASSED [ 13%] tests/test_dtr.py::test_read PASSED [ 14%] tests/test_dtr.py::test_read_1 PASSED [ 14%] tests/test_dtr.py::test_read_2 PASSED [ 14%] tests/test_dtr.py::test_read_3 PASSED [ 14%] tests/test_dtr.py::test_read_stride PASSED [ 14%] tests/test_dtr.py::test_read_4 PASSED [ 14%] tests/test_dtr.py::test_read_5 PASSED [ 14%] tests/test_dtr.py::test_read_6 PASSED [ 14%] tests/test_dtr.py::test_read_7 PASSED [ 14%] tests/test_dtr.py::test_read_8 PASSED [ 14%] tests/test_dtr.py::test_write_1 PASSED [ 14%] tests/test_dtr.py::test_write_2 PASSED [ 15%] tests/test_dtr.py::test_write_3 PASSED [ 15%] tests/test_dtr.py::test_write_4 PASSED [ 15%] tests/test_dtr.py::test_seek PASSED [ 15%] tests/test_dtr.py::test_read_closed PASSED [ 15%] tests/test_dtr.py::test_tell PASSED [ 15%] tests/test_element.py::test_immutable PASSED [ 15%] tests/test_element.py::test_element_0 PASSED [ 15%] tests/test_element.py::test_element_pickle PASSED [ 15%] tests/test_geometry.py::test_rg PASSED [ 15%] tests/test_geometry.py::test_distances PASSED [ 15%] tests/test_geometry.py::test_center_of_mass PASSED [ 15%] tests/test_geometry.py::test_center_of_geometry PASSED [ 16%] tests/test_geometry.py::test_dihedral_indices PASSED [ 16%] tests/test_geometry.py::test_dihedral_index_offset_generation PASSED [ 16%] tests/test_geometry.py::test_dihedral_0 PASSED [ 16%] tests/test_geometry.py::test_dihedral_1 PASSED [ 16%] tests/test_geometry.py::test_dihedral_triclinic PASSED [ 16%] tests/test_geometry.py::test_angle_0 PASSED [ 16%] tests/test_geometry.py::test_angle_periodic_0 PASSED [ 16%] tests/test_geometry.py::test_angle_triclinic_0 PASSED [ 16%] tests/test_geometry.py::test_angle_1 PASSED [ 16%] tests/test_geometry.py::test_dihedral_performance SKIPPED (Not doing...) 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tests/test_lammpstrj.py::test_multiread PASSED [ 23%] tests/test_lammpstrj.py::test_seek PASSED [ 23%] tests/test_lammpstrj.py::test_custom PASSED [ 23%] tests/test_lh5.py::test_write_coordinates PASSED [ 23%] tests/test_lh5.py::test_write_coordinates_reshape PASSED [ 23%] tests/test_lh5.py::test_write_multiple PASSED [ 23%] tests/test_lh5.py::test_topology PASSED [ 23%] tests/test_lh5.py::test_read_slice_0 PASSED [ 24%] tests/test_lh5.py::test_vsite_elements PASSED [ 24%] tests/test_lh5.py::test_do_overwrite_0 PASSED [ 24%] tests/test_lh5.py::test_do_overwrite_1 PASSED [ 24%] tests/test_load.py::test_load_single PASSED [ 24%] tests/test_load.py::test_load_single_top_none PASSED [ 24%] tests/test_load.py::test_load_single_list PASSED [ 24%] tests/test_load.py::test_load_many_list PASSED [ 24%] tests/test_load.py::test_load_atom_indices_multiple_files PASSED [ 24%] tests/test_lprmsd.py::test_munkres_0 PASSED [ 24%] tests/test_lprmsd.py::test_lprmsd_null PASSED [ 24%] 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tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 28%] tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_after_close PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_shape PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_1 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_2 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_3 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_1 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_2 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_1 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_2 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_25 PASSED [ 29%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_write_3 PASSED [ 29%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_n_atoms PASSED [ 29%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_overwrite PASSED [ 29%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_not_overwrite PASSED [ 29%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_trajectory_save_load PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_read_after_close PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_shape PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_1 PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_2 PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_3 PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_read_write_1 PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_read_write_2 PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_ragged_1 PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_ragged_2 PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_read_write_25 PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_write_3 PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_n_atoms PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_do_overwrite PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_do_not_overwrite PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_trajectory_save_load PASSED [ 30%] tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 30%] tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 30%] tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 31%] tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 31%] tests/test_nmr.py::test_2_scalar_couplings PASSED [ 31%] tests/test_order.py::test_nematic_order PASSED [ 31%] tests/test_order.py::test_director PASSED [ 31%] tests/test_order.py::test_inertia PASSED [ 31%] tests/test_order.py::test_nematic_order_args PASSED [ 31%] tests/test_order.py::test_order_from_traj PASSED [ 31%] tests/test_order.py::test_directors_angle_from_traj PASSED [ 31%] tests/test_pdb.py::test_pdbread PASSED [ 31%] tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 31%] tests/test_pdb.py::test_pdbwrite PASSED [ 31%] tests/test_pdb.py::test_load_multiframe PASSED [ 32%] tests/test_pdb.py::test_4ZUO PASSED [ 32%] tests/test_pdb.py::test_2EQQ_0 PASSED [ 32%] tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 32%] tests/test_pdb.py::test_write_large PASSED [ 32%] tests/test_pdb.py::test_write_large_2 PASSED [ 32%] tests/test_pdb.py::test_pdbstructure_0 PASSED [ 32%] tests/test_pdb.py::test_pdbstructure_1 PASSED [ 32%] tests/test_pdb.py::test_pdbstructure_2 PASSED [ 32%] tests/test_pdb.py::test_pdbstructure_3 PASSED [ 32%] tests/test_pdb.py::test_1ncw PASSED [ 32%] tests/test_pdb.py::test_segment_id PASSED [ 33%] tests/test_pdb.py::test_bfactors PASSED [ 33%] tests/test_pdb.py::test_hex PASSED [ 33%] tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 33%] tests/test_pdb.py::test_multichain_load_cycle PASSED [ 33%] tests/test_pdb.py::test_multichain_load_cycle_noter PASSED [ 33%] tests/test_pdb.py::test_load_pdb_input_top PASSED [ 33%] tests/test_pdb.py::test_chimera_indexing PASSED [ 33%] tests/test_pdb.py::test_chimera_indexing_skip PASSED [ 33%] tests/test_pdb.py::test_vmd_indexing PASSED [ 33%] tests/test_pdb.py::test_overflow_indexing PASSED [ 33%] tests/test_pdb.py::test_blank_indexing PASSED [ 33%] tests/test_pdb.py::test_pdb_charge_read PASSED [ 34%] tests/test_pdb.py::test_pdb_charge_write PASSED [ 34%] tests/test_pdb.py::test_ala3_bond_order_read[bond_orders=False] PASSED [ 34%] tests/test_pdb.py::test_ala3_bond_order_read[bond_orders=True] PASSED [ 34%] tests/test_pdb.py::test_bnz_bond_order_conect_write[omit_write_bond_order] PASSED [ 34%] tests/test_pdb.py::test_bnz_bond_order_conect_write[write_bond_order] PASSED [ 34%] tests/test_pdb.py::test_bond_order_conect_priority[ignore repeated bonds] PASSED [ 34%] tests/test_pdb.py::test_bond_order_conect_priority[read repeated bonds] PASSED [ 34%] tests/test_pdbx.py::test_convert PASSED [ 34%] tests/test_pdbx.py::test_load_pdbx_file PASSED [ 34%] tests/test_pdbx.py::test_write_and_read_pdbx PASSED [ 34%] tests/test_pdbx.py::test_write_and_read_pdbx_4py5 PASSED [ 35%] tests/test_pdbx.py::test_write_and_read_pdbx_from_dcd_with_bonds_and_keepids PASSED [ 35%] tests/test_pdbx.py::test_residue_selection_from_cif PASSED [ 35%] tests/test_pi_stacking.py::test_pi_stacking PASSED [ 35%] tests/test_pi_stacking.py::test_t_stacking_more_relaxed_radius PASSED [ 35%] tests/test_pi_stacking.py::test_t_stacking_default_settings PASSED [ 35%] tests/test_prmtop.py::test_load_prmtop PASSED [ 35%] tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 35%] tests/test_psf.py::test_load_psf PASSED [ 35%] tests/test_psf.py::test_multichain_psf PASSED [ 35%] tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 35%] tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 35%] tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 36%] tests/test_quaternion.py::test_quaternion_0 PASSED [ 36%] tests/test_quaternion.py::test_quaternion_1 PASSED [ 36%] tests/test_quaternion.py::test_quaternion_2 PASSED [ 36%] tests/test_rdf.py::test_rdf_norm PASSED [ 36%] tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 36%] tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 36%] tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 36%] tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 36%] tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 36%] tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 36%] tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 37%] tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 37%] tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 37%] tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 37%] tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 37%] tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 37%] tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 37%] tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 37%] tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 37%] tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 37%] tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 37%] tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 37%] tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 38%] tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 38%] tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 38%] tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 38%] tests/test_restart.py::test_read_after_close PASSED [ 38%] tests/test_restart.py::test_shape PASSED [ 38%] tests/test_restart.py::test_shape_2 PASSED [ 38%] tests/test_restart.py::test_read_write_1 PASSED [ 38%] tests/test_restart.py::test_read_write_2 PASSED [ 38%] tests/test_restart.py::test_read_write_3 PASSED [ 38%] tests/test_restart.py::test_read_write_4 PASSED [ 38%] tests/test_rmsd.py::test_trajectory_rmsd[superpose-parallel] PASSED [ 39%] tests/test_rmsd.py::test_trajectory_rmsd[superpose-serial] PASSED [ 39%] tests/test_rmsd.py::test_trajectory_rmsd[qcp-parallel] PASSED [ 39%] tests/test_rmsd.py::test_trajectory_rmsd[qcp-serial] PASSED [ 39%] tests/test_rmsd.py::test_precentered_1 PASSED [ 39%] tests/test_rmsd.py::test_precentered_2 PASSED [ 39%] tests/test_rmsd.py::test_superpose_0 PASSED [ 39%] tests/test_rmsd.py::test_superpose_1 PASSED [ 39%] tests/test_rmsd.py::test_superpose_2 PASSED [ 39%] tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] tests/test_rmsd.py::test_rmsd_ref_ainds_superpose[superpose] PASSED [ 39%] tests/test_rmsd.py::test_rmsd_ref_ainds_superpose[qcp] PASSED [ 40%] tests/test_rmsd.py::test_average_structure PASSED [ 40%] tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 40%] tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 40%] tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 40%] tests/test_rmsd_memmap.py::test_1 PASSED [ 40%] tests/test_rmsd_memmap.py::test_2 PASSED [ 40%] tests/test_sasa.py::test_sasa_0 PASSED [ 40%] tests/test_sasa.py::test_sasa_1 PASSED [ 40%] tests/test_sasa.py::test_sasa_2 PASSED [ 40%] tests/test_sasa.py::test_sasa_3 PASSED [ 40%] tests/test_sasa.py::test_sasa_4 PASSED [ 41%] tests/test_sasa.py::test_sasa_5 PASSED [ 41%] tests/test_sasa.py::test_sasa_6 PASSED [ 41%] tests/test_sasa.py::test_sasa_7 PASSED [ 41%] tests/test_selection.py::test_range PASSED [ 41%] tests/test_selection.py::test_unary_2 PASSED [ 41%] tests/test_selection.py::test_unary_3 PASSED [ 41%] tests/test_selection.py::test_binary_1 PASSED [ 41%] tests/test_selection.py::test_binary_2 PASSED [ 41%] tests/test_selection.py::test_simple PASSED [ 41%] tests/test_selection.py::test_alias PASSED [ 41%] tests/test_selection.py::test_unary_1 PASSED [ 41%] tests/test_selection.py::test_binary_selection_operator PASSED [ 42%] tests/test_selection.py::test_raises PASSED [ 42%] tests/test_selection.py::test_raises2 PASSED [ 42%] tests/test_selection.py::test_bool PASSED [ 42%] tests/test_selection.py::test_nested_bool PASSED [ 42%] tests/test_selection.py::test_values PASSED [ 42%] tests/test_selection.py::test_element PASSED [ 42%] tests/test_selection.py::test_not PASSED [ 42%] tests/test_selection.py::test_re PASSED [ 42%] tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] tests/test_selection.py::test_quotes PASSED [ 42%] tests/test_selection.py::test_top PASSED [ 43%] tests/test_selection.py::test_top_2 PASSED [ 43%] tests/test_selection.py::test_backbone PASSED [ 43%] tests/test_selection.py::test_sidechain PASSED [ 43%] tests/test_selection.py::test_literal PASSED [ 43%] tests/test_selection.py::test_in PASSED [ 43%] tests/test_shape.py::test_gyration PASSED [ 43%] tests/test_shape.py::test_principal_moments PASSED [ 43%] tests/test_shape.py::test_asphericity PASSED [ 43%] tests/test_shape.py::test_shape_metrics PASSED [ 43%] tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 44%] tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 44%] tests/test_thermodynamic_properties.py::test_kappa PASSED [ 44%] tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 44%] tests/test_topology.py::test_topology_amber_nonstandard_names PASSED [ 44%] tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 44%] tests/test_topology.py::test_topology_openmm_preserve_chain_id_when_specified SKIPPED [ 44%] tests/test_topology.py::test_topology_openmm_roundtrip_chain_id SKIPPED [ 44%] tests/test_topology.py::test_topology_openmm_preserve_chain_id_even_when_empty SKIPPED [ 44%] tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 44%] tests/test_topology.py::test_topology_openmm_formal_charges SKIPPED [ 44%] tests/test_topology.py::test_topology_dataframe_formal_charges PASSED [ 45%] tests/test_topology.py::test_topology_pandas PASSED [ 45%] tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 45%] tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 45%] tests/test_topology.py::test_topology_numbers PASSED [ 45%] tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 45%] tests/test_topology.py::test_chain PASSED [ 45%] tests/test_topology.py::test_residue PASSED [ 45%] tests/test_topology.py::test_segment_id PASSED [ 45%] tests/test_topology.py::test_nonconsective_resSeq PASSED [ 45%] tests/test_topology.py::test_pickle PASSED [ 45%] tests/test_topology.py::test_atoms_by_name PASSED [ 45%] tests/test_topology.py::test_select_atom_indices PASSED [ 46%] tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 46%] tests/test_topology.py::test_n_bonds PASSED [ 46%] tests/test_topology.py::test_load_unknown_topology PASSED [ 46%] tests/test_topology.py::test_unique_pairs PASSED [ 46%] tests/test_topology.py::test_select_pairs PASSED [ 46%] tests/test_topology.py::test_to_fasta PASSED [ 46%] tests/test_topology.py::test_subset PASSED [ 46%] tests/test_topology.py::test_subset_re_index_residues PASSED [ 46%] tests/test_topology.py::test_molecules PASSED [ 46%] tests/test_topology.py::test_copy_and_hash PASSED [ 46%] tests/test_topology.py::test_copy[traj.h5] PASSED [ 47%] tests/test_topology.py::test_copy[1ply_charge.pdb] PASSED [ 47%] tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 47%] tests/test_topology.py::test_topology_join PASSED [ 47%] tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 47%] tests/test_topology.py::test_topology_join_formal_charge PASSED [ 47%] tests/test_topology.py::test_delete_atom_by_index PASSED [ 47%] tests/test_trajectory.py::test_mismatch PASSED [ 47%] tests/test_trajectory.py::test_box PASSED [ 47%] tests/test_trajectory.py::test_load_pdb_box PASSED [ 47%] tests/test_trajectory.py::test_load_pdb_gz PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 48%] tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 48%] tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 48%] tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 48%] tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 49%] tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 49%] tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 49%] tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 49%] tests/test_trajectory.py::test_slice PASSED [ 49%] tests/test_trajectory.py::test_slice2 PASSED [ 49%] tests/test_trajectory.py::test_read_path[nc] PASSED [ 49%] tests/test_trajectory.py::test_read_path[h5] PASSED [ 49%] tests/test_trajectory.py::test_read_path[xtc] PASSED [ 49%] tests/test_trajectory.py::test_read_path[trr] PASSED [ 49%] tests/test_trajectory.py::test_read_path[dcd] PASSED [ 49%] tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 49%] tests/test_trajectory.py::test_read_path[dtr] PASSED [ 50%] tests/test_trajectory.py::test_read_path[xyz] PASSED [ 50%] tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 50%] tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 50%] tests/test_trajectory.py::test_read_path[lh5] PASSED [ 50%] tests/test_trajectory.py::test_read_path[pdb] PASSED [ 50%] tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 50%] tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 50%] tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 50%] tests/test_trajectory.py::test_read_path[gro] PASSED [ 50%] tests/test_trajectory.py::test_write_path[nc] PASSED [ 50%] tests/test_trajectory.py::test_write_path[h5] PASSED [ 50%] tests/test_trajectory.py::test_write_path[xtc] PASSED [ 51%] tests/test_trajectory.py::test_write_path[trr] PASSED [ 51%] tests/test_trajectory.py::test_write_path[dcd] PASSED [ 51%] tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 51%] tests/test_trajectory.py::test_write_path[dtr] PASSED [ 51%] tests/test_trajectory.py::test_write_path[xyz] PASSED [ 51%] tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 51%] tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 51%] tests/test_trajectory.py::test_write_path[lh5] PASSED [ 51%] tests/test_trajectory.py::test_write_path[pdb] PASSED [ 51%] tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 51%] tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 52%] tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 52%] tests/test_trajectory.py::test_write_path[gro] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 52%] tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 53%] tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 53%] tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 53%] tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 53%] tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 53%] tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 53%] tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 54%] tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 54%] tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 54%] tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 55%] tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 56%] tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 56%] tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 56%] tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 56%] tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 56%] tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 57%] tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 57%] tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 57%] tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 57%] tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 57%] tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 57%] tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 57%] tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 57%] tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 58%] tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 58%] tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 59%] tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 60%] tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 60%] tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 60%] tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 60%] tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 60%] tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 60%] tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 61%] tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 61%] tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 61%] tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 63%] tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 63%] tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 66%] tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 66%] tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 66%] tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 66%] tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 67%] tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 67%] tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 67%] tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 67%] tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 67%] tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 68%] tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 68%] tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 68%] tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 70%] tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 70%] tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 70%] tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 70%] tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 73%] tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 73%] tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 74%] tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 74%] tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 74%] tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 74%] tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 74%] tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 74%] tests/test_trajectory.py::test_load[nc] PASSED [ 74%] tests/test_trajectory.py::test_load[h5] PASSED [ 74%] tests/test_trajectory.py::test_load[xtc] PASSED [ 74%] tests/test_trajectory.py::test_load[trr] PASSED [ 74%] tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] tests/test_trajectory.py::test_load[dtr] PASSED [ 75%] tests/test_trajectory.py::test_load[xyz] PASSED [ 75%] tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 75%] tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 75%] tests/test_trajectory.py::test_load[lh5] PASSED [ 75%] tests/test_trajectory.py::test_load[pdb] PASSED [ 75%] tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 75%] tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 75%] tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 75%] tests/test_trajectory.py::test_load[gro] PASSED [ 75%] tests/test_trajectory.py::test_hdf5 PASSED [ 75%] tests/test_trajectory.py::test_center PASSED [ 76%] tests/test_trajectory.py::test_center_aind PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 77%] tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 77%] tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 77%] tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 77%] tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 77%] tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 77%] tests/test_trajectory.py::test_restrict_atoms PASSED [ 77%] tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 77%] tests/test_trajectory.py::test_array_vs_matrix PASSED [ 77%] tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] tests/test_trajectory.py::test_load_combination[h5] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[trr] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 79%] tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 79%] tests/test_trajectory.py::test_load_combination[gro] PASSED [ 79%] tests/test_trajectory.py::test_no_topology PASSED [ 79%] tests/test_trajectory.py::test_join PASSED [ 79%] tests/test_trajectory.py::test_md_join PASSED [ 79%] tests/test_trajectory.py::test_stack_1 PASSED [ 79%] tests/test_trajectory.py::test_stack_2 PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 81%] tests/test_trajectory.py::test_load_frame[nc] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[h5] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[trr] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 81%] tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 82%] tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 82%] tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 82%] tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 82%] tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 82%] tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 82%] tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 82%] tests/test_trajectory.py::test_iterload[nc] PASSED [ 82%] tests/test_trajectory.py::test_iterload[h5] PASSED [ 82%] tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 83%] tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 83%] tests/test_trajectory.py::test_iterload[xyz] PASSED [ 83%] tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 83%] tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 83%] tests/test_trajectory.py::test_iterload[lh5] PASSED [ 83%] tests/test_trajectory.py::test_iterload[pdb] PASSED [ 83%] tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 83%] tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 85%] tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 85%] tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 85%] tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 85%] tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 85%] tests/test_trajectory.py::test_save_load[nc] PASSED [ 85%] tests/test_trajectory.py::test_save_load[h5] PASSED [ 85%] tests/test_trajectory.py::test_save_load[xtc] PASSED [ 85%] tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] tests/test_trajectory.py::test_save_load[dtr] PASSED [ 86%] tests/test_trajectory.py::test_save_load[xyz] PASSED [ 86%] tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 86%] tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 86%] tests/test_trajectory.py::test_save_load[lh5] PASSED [ 86%] tests/test_trajectory.py::test_save_load[pdb] PASSED [ 86%] tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 86%] tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 86%] tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 87%] tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 88%] tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 88%] tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 89%] tests/test_trajectory.py::test_open_and_load PASSED [ 89%] tests/test_trajectory.py::test_length PASSED [ 89%] tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[trr] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 90%] tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 91%] tests/test_trajectory.py::test_unitcell[gro] PASSED [ 91%] tests/test_trajectory.py::test_chunk0_iterload PASSED [ 91%] tests/test_trajectory.py::test_hashing PASSED [ 91%] tests/test_trajectory.py::test_smooth PASSED [ 91%] tests/test_trajectory.py::test_make_whole PASSED [ 91%] tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 91%] tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 91%] tests/test_trajectory.py::test_atom_slicing PASSED [ 91%] tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] tests/test_trr.py::test_1 PASSED [ 92%] tests/test_trr.py::test_read_stride PASSED [ 92%] tests/test_trr.py::test_read_stride_n_frames PASSED [ 92%] tests/test_trr.py::test_read_stride_offsets PASSED [ 92%] tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 92%] tests/test_trr.py::test_read_stride_switching PASSED [ 92%] tests/test_trr.py::test_write_read PASSED [ 92%] tests/test_trr.py::test_read_atomindices_1 PASSED [ 92%] tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] tests/test_trr.py::test_deficient_shape PASSED [ 92%] tests/test_trr.py::test_ragged_1 PASSED [ 92%] tests/test_trr.py::test_ragged_2 PASSED [ 92%] tests/test_trr.py::test_malformed PASSED [ 93%] tests/test_trr.py::test_tell PASSED [ 93%] tests/test_trr.py::test_seek PASSED [ 93%] tests/test_trr.py::test_get_velocities PASSED [ 93%] tests/test_trr.py::test_get_forces PASSED [ 93%] tests/test_trr.py::test_get_velocities_and_forces PASSED [ 93%] tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 93%] tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] tests/test_unitcell.py::Test_Unitcell::test_valid[orthogonal] PASSED [ 93%] tests/test_unitcell.py::Test_Unitcell::test_valid[triclinic] PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_invalid_over360[over360] PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_invalid_over360[close] PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_valid_array PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_invalid_over360_array PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_invalid_angles_close_array PASSED [ 94%] tests/test_utils.py::test_unitcell_0 PASSED [ 94%] tests/test_utils.py::test_unitcell_1 PASSED [ 94%] tests/test_utils.py::test_ensure_type_1 PASSED [ 94%] tests/test_utils.py::test_ensure_type_2 PASSED [ 94%] tests/test_utils.py::test_ensure_type_25 PASSED [ 94%] tests/test_utils.py::test_ensure_type_3 PASSED [ 94%] tests/test_utils.py::test_ensure_type_4 PASSED [ 95%] tests/test_utils.py::test_ensure_type_5 PASSED [ 95%] tests/test_utils.py::test_ensure_type_6 PASSED [ 95%] tests/test_utils.py::test_ensure_type_7 PASSED [ 95%] tests/test_utils.py::test_ensure_type_8 PASSED [ 95%] tests/test_utils.py::test_ensure_type_9 PASSED [ 95%] tests/test_utils.py::test_ensure_type_10 PASSED [ 95%] tests/test_utils.py::test_ensure_type_11 PASSED [ 95%] tests/test_utils.py::test_ensure_type_12 PASSED [ 95%] tests/test_utils.py::test_ensure_type_13 PASSED [ 95%] tests/test_utils.py::test_ensure_type_14 PASSED [ 95%] tests/test_utils.py::test_ensure_type_15 PASSED [ 96%] tests/test_utils.py::test_delay_import_fail_1 PASSED [ 96%] tests/test_utils.py::test_delay_import PASSED [ 96%] tests/test_utils.py::test_unit_0 PASSED [ 96%] tests/test_utils.py::test_unit_1 PASSED [ 96%] tests/test_utils.py::test_unit_2 PASSED [ 96%] tests/test_utils.py::test_unit_3 PASSED [ 96%] tests/test_xml.py::test_xml PASSED [ 96%] tests/test_xtc.py::test_read_chunk1 PASSED [ 96%] tests/test_xtc.py::test_read_stride PASSED [ 96%] tests/test_xtc.py::test_read_stride_n_frames PASSED [ 96%] tests/test_xtc.py::test_read_stride_offsets PASSED [ 96%] tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 97%] tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 97%] tests/test_xtc.py::test_read_atomindices_1 PASSED [ 97%] tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 97%] tests/test_xtc.py::test_read_atomindices_2 PASSED [ 97%] tests/test_xtc.py::test_read_chunk2 PASSED [ 97%] tests/test_xtc.py::test_read_chunk3 PASSED [ 97%] tests/test_xtc.py::test_write_0 PASSED [ 97%] tests/test_xtc.py::test_write_1 PASSED [ 97%] tests/test_xtc.py::test_write_2 PASSED [ 97%] tests/test_xtc.py::test_read_error_0 PASSED [ 97%] tests/test_xtc.py::test_write_error_0 PASSED [ 98%] tests/test_xtc.py::test_read_error_1 PASSED [ 98%] tests/test_xtc.py::test_read_error_2 PASSED [ 98%] tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 98%] tests/test_xtc.py::test_tell PASSED [ 98%] tests/test_xtc.py::test_seek PASSED [ 98%] tests/test_xtc.py::test_seek_natoms9 PASSED [ 98%] tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 98%] tests/test_xtc.py::test_ragged_1 PASSED [ 98%] tests/test_xtc.py::test_ragged_2 PASSED [ 98%] tests/test_xtc.py::test_short_traj PASSED [ 98%] tests/test_xtc.py::test_flush PASSED [ 98%] tests/test_xyz.py::test_read_0 PASSED [ 99%] tests/test_xyz.py::test_read_1 PASSED [ 99%] tests/test_xyz.py::test_read_gz PASSED [ 99%] tests/test_xyz.py::test_read_write PASSED [ 99%] tests/test_xyz.py::test_mdwrite PASSED [ 99%] tests/test_xyz.py::test_multiread PASSED [ 99%] tests/test_xyz.py::test_seek PASSED [ 99%] tests/test_xyz.py::test_len PASSED [ 99%] tests/test_zipped.py::test_read_gz PASSED [ 99%] tests/test_zipped.py::test_write_gz PASSED [ 99%] tests/test_zipped.py::test_read_bz2 PASSED [ 99%] tests/test_zipped.py::test_write_bz2 PASSED [100%] =============================== warnings summary =============================== tests/test_distance.py::Test_Distance::test_6 :491: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found SKIPPED [15] tests/test_docstrings.py:38: Skip checking certain modules' docstrings SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing SKIPPED [1] tests/test_hdf5.py:105: requires openmm.units SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units SKIPPED [1] tests/test_mol2.py:65: Requires obabel SKIPPED [1] tests/test_netcdf.py:274: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found SKIPPED [1] tests/test_nmr.py:26: PPM binary not found SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. SKIPPED [1] tests/test_selection.py:267: failed to parse selection SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. SKIPPED [1] tests/test_topology.py:66: needs OpenMM SKIPPED [1] tests/test_topology.py:83: needs OpenMM SKIPPED [1] tests/test_topology.py:93: needs OpenMM SKIPPED [1] tests/test_topology.py:102: needs OpenMM SKIPPED [1] tests/test_topology.py:112: needs OpenMM SKIPPED [1] tests/test_topology.py:119: requires openmm >= 8.2 SKIPPED [1] tests/test_topology.py:295: needs OpenMM SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information SKIPPED [1] tests/test_trajectory.py:225: mdcrd can only store rectilinear boxes SKIPPED [1] tests/test_trajectory.py:223: ncrst can only store 1 frame per file SKIPPED [1] tests/test_trajectory.py:223: rst7 can only store 1 frame per file SKIPPED [14] tests/test_trajectory.py:247: mdcrd can only store rectilinear boxes SKIPPED [14] tests/test_trajectory.py:245: ncrst can only store 1 frame per file SKIPPED [14] tests/test_trajectory.py:245: rst7 can only store 1 frame per file SKIPPED [4] tests/test_trajectory.py:255: dtr needs to write unitcells SKIPPED [4] tests/test_trajectory.py:255: lammpstrj needs to write unitcells SKIPPED [2] tests/test_trajectory.py:641: Only 1 frame per file format XFAIL tests/test_trajectory.py::test_read_path[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_path[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load_combination[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - This is broken XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - PDB Files don't support seeking XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - PDB Files don't support seeking XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - This is broken XFAIL tests/test_trajectory.py::test_load_frame[dtr] - DTR doesn't load a single frame properly XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load_frame[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load_frame[gro] - Gro doesn't implement seek XFAIL tests/test_trajectory.py::test_iterload[dtr] - This is broken with dtr XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - PDB Iterloads an extra frame!! XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - PDB Iterloads an extra frame!! XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - Not implemented for some reason XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - This is broken with dtr XFAIL tests/test_trajectory.py::test_unitcell[dtr] - dtr seems to need unit vectors XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - lammpstrj seems to need unit vectors XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - ncrst seems to need unit vectors XFAIL tests/test_trajectory.py::test_unitcell[rst7] - rst7 seems to need unit vectors = 987 passed, 103 skipped, 24 deselected, 61 xfailed, 1 warning in 289.25s (0:04:49) = lugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) I: pybuild base:384: cd /build/reproducible-path/mdtraj-1.11.1.post1/.pybuild/cpython3_3.13_mdtraj/build; python3.13 -m pytest -k 'not ( mdconvert or pi_stacking.ipynb or nmr.ipynb or test_image_molecules or test_3 or from_url or test_1vii_url_and_gz or test_1vii_load_from_mixture )' ============================= test session starts ============================== platform linux -- Python 3.13.12, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.13 cachedir: .pytest_cache rootdir: /build/reproducible-path/mdtraj-1.11.1.post1/.pybuild/cpython3_3.13_mdtraj/build configfile: pyproject.toml testpaths: tests, examples plugins: rerunfailures-16.1, typeguard-4.4.4 collecting ... collected 1175 items / 24 deselected / 1151 selected tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] tests/test_alignment.py::test_transform PASSED [ 0%] tests/test_alignment.py::test_transform2 PASSED [ 0%] tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] tests/test_angles.py::test_generator PASSED [ 0%] tests/test_angles.py::test_angle_180[True] PASSED [ 0%] tests/test_angles.py::test_angle_180[False] PASSED [ 0%] tests/test_arc.py::test_read_0 PASSED [ 0%] tests/test_arc.py::test_read_arctraj PASSED [ 0%] tests/test_arc.py::test_read_arctraj_top PASSED [ 0%] tests/test_arc.py::test_read_pbc PASSED [ 1%] tests/test_capi.py::test_1 PASSED [ 1%] tests/test_contact.py::test_contact_0 PASSED [ 1%] tests/test_contact.py::test_contact_1 PASSED [ 1%] tests/test_contact.py::test_contact_2 PASSED [ 1%] tests/test_contact.py::test_contact_3 PASSED [ 1%] tests/test_contact.py::test_contact_4 PASSED [ 1%] tests/test_crd.py::test_prmtop_with_overflow_mdcrd PASSED [ 1%] tests/test_dcd.py::test_read PASSED [ 1%] tests/test_dcd.py::test_read_2 PASSED [ 1%] tests/test_dcd.py::test_read_stride PASSED [ 1%] tests/test_dcd.py::test_read_stride_2 PASSED [ 1%] tests/test_dcd.py::test_read_3 PASSED [ 2%] tests/test_dcd.py::test_read_4 PASSED [ 2%] tests/test_dcd.py::test_read_5 PASSED [ 2%] tests/test_dcd.py::test_read_6 PASSED [ 2%] tests/test_dcd.py::test_write_0 PASSED [ 2%] tests/test_dcd.py::test_write_1 PASSED [ 2%] tests/test_dcd.py::test_write_2 PASSED [ 2%] tests/test_dcd.py::test_write_3 PASSED [ 2%] tests/test_dcd.py::test_write_4 PASSED [ 2%] tests/test_dcd.py::test_do_overwrite PASSED [ 2%] tests/test_dcd.py::test_dont_overwrite PASSED [ 2%] tests/test_dcd.py::test_read_closed PASSED [ 3%] tests/test_dcd.py::test_write_closed PASSED [ 3%] tests/test_dcd.py::test_tell PASSED [ 3%] tests/test_dcd.py::test_seek PASSED [ 3%] tests/test_dcd.py::test_ragged_1 PASSED [ 3%] tests/test_dcd.py::test_ragged_2 PASSED [ 3%] tests/test_dihedral.py::test_compute_phi PASSED [ 3%] tests/test_dihedral.py::test_compute_psi PASSED [ 3%] tests/test_dihedral.py::test_compute_chi SKIPPED (pymol executable n...) [ 3%] tests/test_dihedral.py::test_compute_omega PASSED [ 3%] tests/test_dihedral.py::test_shape_when_none PASSED [ 3%] tests/test_dihedral.py::test_dihedral_1 SKIPPED (pymol executable no...) [ 3%] tests/test_dihedral.py::test_dihedral_2chains PASSED [ 4%] tests/test_dihedral.py::test_generator PASSED [ 4%] tests/test_distance.py::Test_Distance::test_generator PASSED [ 4%] tests/test_distance.py::Test_Distance::test_0 PASSED [ 4%] tests/test_distance.py::Test_Distance::test_compute_distances_core_nonperiodic PASSED [ 4%] tests/test_distance.py::Test_Distance::test_compute_distances_core_periodic PASSED [ 4%] tests/test_distance.py::Test_Distance::test_1 PASSED [ 4%] tests/test_distance.py::Test_Distance::test_2 PASSED [ 4%] tests/test_distance.py::Test_Distance::test_0p PASSED [ 4%] tests/test_distance.py::Test_Distance::test_1p PASSED [ 4%] tests/test_distance.py::Test_Distance::test_2p PASSED [ 4%] tests/test_distance.py::Test_Distance::test_4 PASSED [ 5%] tests/test_distance.py::Test_Distance::test_5 PASSED [ 5%] tests/test_distance.py::Test_Distance::test_6 PASSED [ 5%] tests/test_distance.py::Test_Distance::test_7 PASSED [ 5%] tests/test_distance.py::Test_Distance::test_closest_contact PASSED [ 5%] tests/test_distance.py::Test_Distance::test_distance_nan PASSED [ 5%] tests/test_distance.py::Test_Distance::test_closest_contact_nan_pos PASSED [ 5%] tests/test_distance.py::Test_Distance::test_distance_t_inputs PASSED [ 5%] tests/test_distance.py::Test_Distance::test_distances_t PASSED [ 5%] tests/test_distance.py::Test_Distance::test_distances_t_at_0 PASSED [ 5%] tests/test_distance.py::Test_Distance::test_amber_t PASSED [ 5%] tests/test_docstrings.py::test_docstrings[mdtraj._lprmsd] PASSED [ 5%] tests/test_docstrings.py::test_docstrings[mdtraj._rmsd] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj._version] SKIPPED (...) [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.core.element] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.core.residue_names] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.core.selection] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.core.topology] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.core.trajectory] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.amberrst] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.arc] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.dcd] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.dtr] PASSED [ 6%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.gro] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.gsd] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.hdf5] SKIPPED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.hoomdxml] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.lammpstrj] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.lh5] SKIPPED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.mdcrd] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.mol2] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.netcdf] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.openmmxml] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbfile] PASSED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbstructure] SKIPPED [ 7%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx.PdbxContainers] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx.PdbxReader] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx.pdbx] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx.pdbxfile] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.prmtop] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.psf] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.registry] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.trr] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.xtc] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.formats.xyzfile] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry._geometry] PASSED [ 8%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.alignment] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.angle] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.contact] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dihedral] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.distance] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.drid] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dssp] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.hbond] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.internal] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighborlist] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighbors] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.order] PASSED [ 9%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.pi_stacking] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rdf] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rg] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.sasa] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.shape] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.thermodynamic_properties] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.io] SKIPPED (Skip c...) [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.nmr.scalar_couplings] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.nmr.shift_wrappers] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.reporters.basereporter] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.reporters.dcdreporter] PASSED [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.reporters.hdf5reporter] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.reporters.netcdfreporter] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.reporters.xtcreporter] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdinspect] SKIPPED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.testing.docscrape] SKIPPED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.testing.docstrings] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.testing.testing] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.contextmanagers] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.delay_import] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.rotation] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.singleton] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.basedimension] PASSED [ 11%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.baseunit] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.constants] PASSED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.mymatrix] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.prefix] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.quantity] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.standard_dimensions] PASSED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_definitions] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_math] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_operators] SKIPPED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unitcell] PASSED [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.validation] PASSED [ 13%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.zipped] PASSED [ 13%] tests/test_drid.py::test_drid_1 PASSED [ 13%] tests/test_drid.py::test_drid_2 PASSED [ 13%] tests/test_dssp.py::test_1[1bpi.pdb] PASSED [ 13%] tests/test_dssp.py::test_1[1vii.pdb] PASSED [ 13%] tests/test_dssp.py::test_1[4ZUO.pdb] PASSED [ 13%] tests/test_dssp.py::test_1[1am7_protein.pdb] PASSED [ 13%] tests/test_dssp.py::test_2[2EQQ.pdb] PASSED [ 13%] tests/test_dssp.py::test_4 PASSED [ 13%] tests/test_dssp.py::test_5 PASSED [ 13%] tests/test_dssp.py::test_7 PASSED [ 13%] tests/test_dtr.py::test_read PASSED [ 14%] tests/test_dtr.py::test_read_1 PASSED [ 14%] tests/test_dtr.py::test_read_2 PASSED [ 14%] tests/test_dtr.py::test_read_3 PASSED [ 14%] tests/test_dtr.py::test_read_stride PASSED [ 14%] tests/test_dtr.py::test_read_4 PASSED [ 14%] tests/test_dtr.py::test_read_5 PASSED [ 14%] tests/test_dtr.py::test_read_6 PASSED [ 14%] tests/test_dtr.py::test_read_7 PASSED [ 14%] tests/test_dtr.py::test_read_8 PASSED [ 14%] tests/test_dtr.py::test_write_1 PASSED [ 14%] tests/test_dtr.py::test_write_2 PASSED [ 15%] tests/test_dtr.py::test_write_3 PASSED [ 15%] tests/test_dtr.py::test_write_4 PASSED [ 15%] tests/test_dtr.py::test_seek PASSED [ 15%] tests/test_dtr.py::test_read_closed PASSED [ 15%] tests/test_dtr.py::test_tell PASSED [ 15%] tests/test_element.py::test_immutable PASSED [ 15%] tests/test_element.py::test_element_0 PASSED [ 15%] tests/test_element.py::test_element_pickle PASSED [ 15%] tests/test_geometry.py::test_rg PASSED [ 15%] tests/test_geometry.py::test_distances PASSED [ 15%] tests/test_geometry.py::test_center_of_mass PASSED [ 15%] tests/test_geometry.py::test_center_of_geometry PASSED [ 16%] tests/test_geometry.py::test_dihedral_indices PASSED [ 16%] tests/test_geometry.py::test_dihedral_index_offset_generation PASSED [ 16%] tests/test_geometry.py::test_dihedral_0 PASSED [ 16%] tests/test_geometry.py::test_dihedral_1 PASSED [ 16%] tests/test_geometry.py::test_dihedral_triclinic PASSED [ 16%] tests/test_geometry.py::test_angle_0 PASSED [ 16%] tests/test_geometry.py::test_angle_periodic_0 PASSED [ 16%] tests/test_geometry.py::test_angle_triclinic_0 PASSED [ 16%] tests/test_geometry.py::test_angle_1 PASSED [ 16%] tests/test_geometry.py::test_dihedral_performance SKIPPED (Not doing...) 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tests/test_lammpstrj.py::test_multiread PASSED [ 23%] tests/test_lammpstrj.py::test_seek PASSED [ 23%] tests/test_lammpstrj.py::test_custom PASSED [ 23%] tests/test_lh5.py::test_write_coordinates PASSED [ 23%] tests/test_lh5.py::test_write_coordinates_reshape PASSED [ 23%] tests/test_lh5.py::test_write_multiple PASSED [ 23%] tests/test_lh5.py::test_topology PASSED [ 23%] tests/test_lh5.py::test_read_slice_0 PASSED [ 24%] tests/test_lh5.py::test_vsite_elements PASSED [ 24%] tests/test_lh5.py::test_do_overwrite_0 PASSED [ 24%] tests/test_lh5.py::test_do_overwrite_1 PASSED [ 24%] tests/test_load.py::test_load_single PASSED [ 24%] tests/test_load.py::test_load_single_top_none PASSED [ 24%] tests/test_load.py::test_load_single_list PASSED [ 24%] tests/test_load.py::test_load_many_list PASSED [ 24%] tests/test_load.py::test_load_atom_indices_multiple_files PASSED [ 24%] tests/test_lprmsd.py::test_munkres_0 PASSED [ 24%] tests/test_lprmsd.py::test_lprmsd_null PASSED [ 24%] 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tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 28%] tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_after_close PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_shape PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_1 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_2 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_3 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_1 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_2 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_1 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_2 PASSED [ 28%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_25 PASSED [ 29%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_write_3 PASSED [ 29%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_n_atoms PASSED [ 29%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_overwrite PASSED [ 29%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_not_overwrite PASSED [ 29%] tests/test_netcdf.py::TestNetCDFNetCDF4::test_trajectory_save_load PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_read_after_close PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_shape PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_1 PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_2 PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_3 PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_read_write_1 PASSED [ 29%] tests/test_netcdf.py::TestNetCDFScipy::test_read_write_2 PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_ragged_1 PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_ragged_2 PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_read_write_25 PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_write_3 PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_n_atoms PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_do_overwrite PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_do_not_overwrite PASSED [ 30%] tests/test_netcdf.py::TestNetCDFScipy::test_trajectory_save_load PASSED [ 30%] tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 30%] tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 30%] tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 31%] tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 31%] tests/test_nmr.py::test_2_scalar_couplings PASSED [ 31%] tests/test_order.py::test_nematic_order PASSED [ 31%] tests/test_order.py::test_director PASSED [ 31%] tests/test_order.py::test_inertia PASSED [ 31%] tests/test_order.py::test_nematic_order_args PASSED [ 31%] tests/test_order.py::test_order_from_traj PASSED [ 31%] tests/test_order.py::test_directors_angle_from_traj PASSED [ 31%] tests/test_pdb.py::test_pdbread PASSED [ 31%] tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 31%] tests/test_pdb.py::test_pdbwrite PASSED [ 31%] tests/test_pdb.py::test_load_multiframe PASSED [ 32%] tests/test_pdb.py::test_4ZUO PASSED [ 32%] tests/test_pdb.py::test_2EQQ_0 PASSED [ 32%] tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 32%] tests/test_pdb.py::test_write_large PASSED [ 32%] tests/test_pdb.py::test_write_large_2 PASSED [ 32%] tests/test_pdb.py::test_pdbstructure_0 PASSED [ 32%] tests/test_pdb.py::test_pdbstructure_1 PASSED [ 32%] tests/test_pdb.py::test_pdbstructure_2 PASSED [ 32%] tests/test_pdb.py::test_pdbstructure_3 PASSED [ 32%] tests/test_pdb.py::test_1ncw PASSED [ 32%] tests/test_pdb.py::test_segment_id PASSED [ 33%] tests/test_pdb.py::test_bfactors PASSED [ 33%] tests/test_pdb.py::test_hex PASSED [ 33%] tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 33%] tests/test_pdb.py::test_multichain_load_cycle PASSED [ 33%] tests/test_pdb.py::test_multichain_load_cycle_noter PASSED [ 33%] tests/test_pdb.py::test_load_pdb_input_top PASSED [ 33%] tests/test_pdb.py::test_chimera_indexing PASSED [ 33%] tests/test_pdb.py::test_chimera_indexing_skip PASSED [ 33%] tests/test_pdb.py::test_vmd_indexing PASSED [ 33%] tests/test_pdb.py::test_overflow_indexing PASSED [ 33%] tests/test_pdb.py::test_blank_indexing PASSED [ 33%] tests/test_pdb.py::test_pdb_charge_read PASSED [ 34%] tests/test_pdb.py::test_pdb_charge_write PASSED [ 34%] tests/test_pdb.py::test_ala3_bond_order_read[bond_orders=False] PASSED [ 34%] tests/test_pdb.py::test_ala3_bond_order_read[bond_orders=True] PASSED [ 34%] tests/test_pdb.py::test_bnz_bond_order_conect_write[omit_write_bond_order] PASSED [ 34%] tests/test_pdb.py::test_bnz_bond_order_conect_write[write_bond_order] PASSED [ 34%] tests/test_pdb.py::test_bond_order_conect_priority[ignore repeated bonds] PASSED [ 34%] tests/test_pdb.py::test_bond_order_conect_priority[read repeated bonds] PASSED [ 34%] tests/test_pdbx.py::test_convert PASSED [ 34%] tests/test_pdbx.py::test_load_pdbx_file PASSED [ 34%] tests/test_pdbx.py::test_write_and_read_pdbx PASSED [ 34%] tests/test_pdbx.py::test_write_and_read_pdbx_4py5 PASSED [ 35%] tests/test_pdbx.py::test_write_and_read_pdbx_from_dcd_with_bonds_and_keepids PASSED [ 35%] tests/test_pdbx.py::test_residue_selection_from_cif PASSED [ 35%] tests/test_pi_stacking.py::test_pi_stacking PASSED [ 35%] tests/test_pi_stacking.py::test_t_stacking_more_relaxed_radius PASSED [ 35%] tests/test_pi_stacking.py::test_t_stacking_default_settings PASSED [ 35%] tests/test_prmtop.py::test_load_prmtop PASSED [ 35%] tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 35%] tests/test_psf.py::test_load_psf PASSED [ 35%] tests/test_psf.py::test_multichain_psf PASSED [ 35%] tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 35%] tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 35%] tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 36%] tests/test_quaternion.py::test_quaternion_0 PASSED [ 36%] tests/test_quaternion.py::test_quaternion_1 PASSED [ 36%] tests/test_quaternion.py::test_quaternion_2 PASSED [ 36%] tests/test_rdf.py::test_rdf_norm PASSED [ 36%] tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 36%] tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 36%] tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 36%] tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 36%] tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 36%] tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 36%] tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 37%] tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 37%] tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 37%] tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 37%] tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 37%] tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 37%] tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 37%] tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 37%] tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 37%] tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 37%] tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 37%] tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 37%] tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 38%] tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 38%] tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 38%] tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 38%] tests/test_restart.py::test_read_after_close PASSED [ 38%] tests/test_restart.py::test_shape PASSED [ 38%] tests/test_restart.py::test_shape_2 PASSED [ 38%] tests/test_restart.py::test_read_write_1 PASSED [ 38%] tests/test_restart.py::test_read_write_2 PASSED [ 38%] tests/test_restart.py::test_read_write_3 PASSED [ 38%] tests/test_restart.py::test_read_write_4 PASSED [ 38%] tests/test_rmsd.py::test_trajectory_rmsd[superpose-parallel] PASSED [ 39%] tests/test_rmsd.py::test_trajectory_rmsd[superpose-serial] PASSED [ 39%] tests/test_rmsd.py::test_trajectory_rmsd[qcp-parallel] PASSED [ 39%] tests/test_rmsd.py::test_trajectory_rmsd[qcp-serial] PASSED [ 39%] tests/test_rmsd.py::test_precentered_1 PASSED [ 39%] tests/test_rmsd.py::test_precentered_2 PASSED [ 39%] tests/test_rmsd.py::test_superpose_0 PASSED [ 39%] tests/test_rmsd.py::test_superpose_1 PASSED [ 39%] tests/test_rmsd.py::test_superpose_2 PASSED [ 39%] tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] tests/test_rmsd.py::test_rmsd_ref_ainds_superpose[superpose] PASSED [ 39%] tests/test_rmsd.py::test_rmsd_ref_ainds_superpose[qcp] PASSED [ 40%] tests/test_rmsd.py::test_average_structure PASSED [ 40%] tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 40%] tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 40%] tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 40%] tests/test_rmsd_memmap.py::test_1 PASSED [ 40%] tests/test_rmsd_memmap.py::test_2 PASSED [ 40%] tests/test_sasa.py::test_sasa_0 PASSED [ 40%] tests/test_sasa.py::test_sasa_1 PASSED [ 40%] tests/test_sasa.py::test_sasa_2 PASSED [ 40%] tests/test_sasa.py::test_sasa_3 PASSED [ 40%] tests/test_sasa.py::test_sasa_4 PASSED [ 41%] tests/test_sasa.py::test_sasa_5 PASSED [ 41%] tests/test_sasa.py::test_sasa_6 PASSED [ 41%] tests/test_sasa.py::test_sasa_7 PASSED [ 41%] tests/test_selection.py::test_range PASSED [ 41%] tests/test_selection.py::test_unary_2 PASSED [ 41%] tests/test_selection.py::test_unary_3 PASSED [ 41%] tests/test_selection.py::test_binary_1 PASSED [ 41%] tests/test_selection.py::test_binary_2 PASSED [ 41%] tests/test_selection.py::test_simple PASSED [ 41%] tests/test_selection.py::test_alias PASSED [ 41%] tests/test_selection.py::test_unary_1 PASSED [ 41%] tests/test_selection.py::test_binary_selection_operator PASSED [ 42%] tests/test_selection.py::test_raises PASSED [ 42%] tests/test_selection.py::test_raises2 PASSED [ 42%] tests/test_selection.py::test_bool PASSED [ 42%] tests/test_selection.py::test_nested_bool PASSED [ 42%] tests/test_selection.py::test_values PASSED [ 42%] tests/test_selection.py::test_element PASSED [ 42%] tests/test_selection.py::test_not PASSED [ 42%] tests/test_selection.py::test_re PASSED [ 42%] tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] tests/test_selection.py::test_quotes PASSED [ 42%] tests/test_selection.py::test_top PASSED [ 43%] tests/test_selection.py::test_top_2 PASSED [ 43%] tests/test_selection.py::test_backbone PASSED [ 43%] tests/test_selection.py::test_sidechain PASSED [ 43%] tests/test_selection.py::test_literal PASSED [ 43%] tests/test_selection.py::test_in PASSED [ 43%] tests/test_shape.py::test_gyration PASSED [ 43%] tests/test_shape.py::test_principal_moments PASSED [ 43%] tests/test_shape.py::test_asphericity PASSED [ 43%] tests/test_shape.py::test_shape_metrics PASSED [ 43%] tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 44%] tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 44%] tests/test_thermodynamic_properties.py::test_kappa PASSED [ 44%] tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 44%] tests/test_topology.py::test_topology_amber_nonstandard_names PASSED [ 44%] tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 44%] tests/test_topology.py::test_topology_openmm_preserve_chain_id_when_specified SKIPPED [ 44%] tests/test_topology.py::test_topology_openmm_roundtrip_chain_id SKIPPED [ 44%] tests/test_topology.py::test_topology_openmm_preserve_chain_id_even_when_empty SKIPPED [ 44%] tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 44%] tests/test_topology.py::test_topology_openmm_formal_charges SKIPPED [ 44%] tests/test_topology.py::test_topology_dataframe_formal_charges PASSED [ 45%] tests/test_topology.py::test_topology_pandas PASSED [ 45%] tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 45%] tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 45%] tests/test_topology.py::test_topology_numbers PASSED [ 45%] tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 45%] tests/test_topology.py::test_chain PASSED [ 45%] tests/test_topology.py::test_residue PASSED [ 45%] tests/test_topology.py::test_segment_id PASSED [ 45%] tests/test_topology.py::test_nonconsective_resSeq PASSED [ 45%] tests/test_topology.py::test_pickle PASSED [ 45%] tests/test_topology.py::test_atoms_by_name PASSED [ 45%] tests/test_topology.py::test_select_atom_indices PASSED [ 46%] tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 46%] tests/test_topology.py::test_n_bonds PASSED [ 46%] tests/test_topology.py::test_load_unknown_topology PASSED [ 46%] tests/test_topology.py::test_unique_pairs PASSED [ 46%] tests/test_topology.py::test_select_pairs PASSED [ 46%] tests/test_topology.py::test_to_fasta PASSED [ 46%] tests/test_topology.py::test_subset PASSED [ 46%] tests/test_topology.py::test_subset_re_index_residues PASSED [ 46%] tests/test_topology.py::test_molecules PASSED [ 46%] tests/test_topology.py::test_copy_and_hash PASSED [ 46%] tests/test_topology.py::test_copy[traj.h5] PASSED [ 47%] tests/test_topology.py::test_copy[1ply_charge.pdb] PASSED [ 47%] tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 47%] tests/test_topology.py::test_topology_join PASSED [ 47%] tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 47%] tests/test_topology.py::test_topology_join_formal_charge PASSED [ 47%] tests/test_topology.py::test_delete_atom_by_index PASSED [ 47%] tests/test_trajectory.py::test_mismatch PASSED [ 47%] tests/test_trajectory.py::test_box PASSED [ 47%] tests/test_trajectory.py::test_load_pdb_box PASSED [ 47%] tests/test_trajectory.py::test_load_pdb_gz PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 48%] tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 48%] tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 48%] tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 48%] tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 49%] tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 49%] tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 49%] tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 49%] tests/test_trajectory.py::test_slice PASSED [ 49%] tests/test_trajectory.py::test_slice2 PASSED [ 49%] tests/test_trajectory.py::test_read_path[nc] PASSED [ 49%] tests/test_trajectory.py::test_read_path[h5] PASSED [ 49%] tests/test_trajectory.py::test_read_path[xtc] PASSED [ 49%] tests/test_trajectory.py::test_read_path[trr] PASSED [ 49%] tests/test_trajectory.py::test_read_path[dcd] PASSED [ 49%] tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 49%] tests/test_trajectory.py::test_read_path[dtr] PASSED [ 50%] tests/test_trajectory.py::test_read_path[xyz] PASSED [ 50%] tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 50%] tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 50%] tests/test_trajectory.py::test_read_path[lh5] PASSED [ 50%] tests/test_trajectory.py::test_read_path[pdb] PASSED [ 50%] tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 50%] tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 50%] tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 50%] tests/test_trajectory.py::test_read_path[gro] PASSED [ 50%] tests/test_trajectory.py::test_write_path[nc] PASSED [ 50%] tests/test_trajectory.py::test_write_path[h5] PASSED [ 50%] tests/test_trajectory.py::test_write_path[xtc] PASSED [ 51%] tests/test_trajectory.py::test_write_path[trr] PASSED [ 51%] tests/test_trajectory.py::test_write_path[dcd] PASSED [ 51%] tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 51%] tests/test_trajectory.py::test_write_path[dtr] PASSED [ 51%] tests/test_trajectory.py::test_write_path[xyz] PASSED [ 51%] tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 51%] tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 51%] tests/test_trajectory.py::test_write_path[lh5] PASSED [ 51%] tests/test_trajectory.py::test_write_path[pdb] PASSED [ 51%] tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 51%] tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 52%] tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 52%] tests/test_trajectory.py::test_write_path[gro] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 52%] tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 53%] tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 53%] tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 53%] tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 53%] tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 53%] tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 53%] tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 54%] tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 54%] tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 54%] tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 55%] tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 56%] tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 56%] tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 56%] tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 56%] tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 56%] tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 57%] tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 57%] tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 57%] tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 57%] tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 57%] tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 57%] tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 57%] tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 57%] tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 58%] tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 58%] tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 59%] tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 60%] tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 60%] tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 60%] tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 60%] tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 60%] tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 60%] tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 61%] tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 61%] tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 61%] tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 63%] tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 63%] tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 66%] tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 66%] tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 66%] tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 66%] tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 67%] tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 67%] tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 67%] tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 67%] tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 67%] tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 68%] tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 68%] tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 68%] tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 70%] tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 70%] tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 70%] tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 70%] tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 73%] tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 73%] tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 74%] tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 74%] tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 74%] tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 74%] tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 74%] tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 74%] tests/test_trajectory.py::test_load[nc] PASSED [ 74%] tests/test_trajectory.py::test_load[h5] PASSED [ 74%] tests/test_trajectory.py::test_load[xtc] PASSED [ 74%] tests/test_trajectory.py::test_load[trr] PASSED [ 74%] tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] tests/test_trajectory.py::test_load[dtr] PASSED [ 75%] tests/test_trajectory.py::test_load[xyz] PASSED [ 75%] tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 75%] tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 75%] tests/test_trajectory.py::test_load[lh5] PASSED [ 75%] tests/test_trajectory.py::test_load[pdb] PASSED [ 75%] tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 75%] tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 75%] tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 75%] tests/test_trajectory.py::test_load[gro] PASSED [ 75%] tests/test_trajectory.py::test_hdf5 PASSED [ 75%] tests/test_trajectory.py::test_center PASSED [ 76%] tests/test_trajectory.py::test_center_aind PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 77%] tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 77%] tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 77%] tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 77%] tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 77%] tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 77%] tests/test_trajectory.py::test_restrict_atoms PASSED [ 77%] tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 77%] tests/test_trajectory.py::test_array_vs_matrix PASSED [ 77%] tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] tests/test_trajectory.py::test_load_combination[h5] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[trr] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 79%] tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 79%] tests/test_trajectory.py::test_load_combination[gro] PASSED [ 79%] tests/test_trajectory.py::test_no_topology PASSED [ 79%] tests/test_trajectory.py::test_join PASSED [ 79%] tests/test_trajectory.py::test_md_join PASSED [ 79%] tests/test_trajectory.py::test_stack_1 PASSED [ 79%] tests/test_trajectory.py::test_stack_2 PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 81%] tests/test_trajectory.py::test_load_frame[nc] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[h5] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[trr] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 81%] tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 82%] tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 82%] tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 82%] tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 82%] tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 82%] tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 82%] tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 82%] tests/test_trajectory.py::test_iterload[nc] PASSED [ 82%] tests/test_trajectory.py::test_iterload[h5] PASSED [ 82%] tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 83%] tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 83%] tests/test_trajectory.py::test_iterload[xyz] PASSED [ 83%] tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 83%] tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 83%] tests/test_trajectory.py::test_iterload[lh5] PASSED [ 83%] tests/test_trajectory.py::test_iterload[pdb] PASSED [ 83%] tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 83%] tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 85%] tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 85%] tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 85%] tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 85%] tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 85%] tests/test_trajectory.py::test_save_load[nc] PASSED [ 85%] tests/test_trajectory.py::test_save_load[h5] PASSED [ 85%] tests/test_trajectory.py::test_save_load[xtc] PASSED [ 85%] tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] tests/test_trajectory.py::test_save_load[dtr] PASSED [ 86%] tests/test_trajectory.py::test_save_load[xyz] PASSED [ 86%] tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 86%] tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 86%] tests/test_trajectory.py::test_save_load[lh5] PASSED [ 86%] tests/test_trajectory.py::test_save_load[pdb] PASSED [ 86%] tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 86%] tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 86%] tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 87%] tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 88%] tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 88%] tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 89%] tests/test_trajectory.py::test_open_and_load PASSED [ 89%] tests/test_trajectory.py::test_length PASSED [ 89%] tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[trr] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 90%] tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 91%] tests/test_trajectory.py::test_unitcell[gro] PASSED [ 91%] tests/test_trajectory.py::test_chunk0_iterload PASSED [ 91%] tests/test_trajectory.py::test_hashing PASSED [ 91%] tests/test_trajectory.py::test_smooth PASSED [ 91%] tests/test_trajectory.py::test_make_whole PASSED [ 91%] tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 91%] tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 91%] tests/test_trajectory.py::test_atom_slicing PASSED [ 91%] tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] tests/test_trr.py::test_1 PASSED [ 92%] tests/test_trr.py::test_read_stride PASSED [ 92%] tests/test_trr.py::test_read_stride_n_frames PASSED [ 92%] tests/test_trr.py::test_read_stride_offsets PASSED [ 92%] tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 92%] tests/test_trr.py::test_read_stride_switching PASSED [ 92%] tests/test_trr.py::test_write_read PASSED [ 92%] tests/test_trr.py::test_read_atomindices_1 PASSED [ 92%] tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] tests/test_trr.py::test_deficient_shape PASSED [ 92%] tests/test_trr.py::test_ragged_1 PASSED [ 92%] tests/test_trr.py::test_ragged_2 PASSED [ 92%] tests/test_trr.py::test_malformed PASSED [ 93%] tests/test_trr.py::test_tell PASSED [ 93%] tests/test_trr.py::test_seek PASSED [ 93%] tests/test_trr.py::test_get_velocities PASSED [ 93%] tests/test_trr.py::test_get_forces PASSED [ 93%] tests/test_trr.py::test_get_velocities_and_forces PASSED [ 93%] tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 93%] tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] tests/test_unitcell.py::Test_Unitcell::test_valid[orthogonal] PASSED [ 93%] tests/test_unitcell.py::Test_Unitcell::test_valid[triclinic] PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_invalid_over360[over360] PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_invalid_over360[close] PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_valid_array PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_invalid_over360_array PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_invalid_angles_close_array PASSED [ 94%] tests/test_utils.py::test_unitcell_0 PASSED [ 94%] tests/test_utils.py::test_unitcell_1 PASSED [ 94%] tests/test_utils.py::test_ensure_type_1 PASSED [ 94%] tests/test_utils.py::test_ensure_type_2 PASSED [ 94%] tests/test_utils.py::test_ensure_type_25 PASSED [ 94%] tests/test_utils.py::test_ensure_type_3 PASSED [ 94%] tests/test_utils.py::test_ensure_type_4 PASSED [ 95%] tests/test_utils.py::test_ensure_type_5 PASSED [ 95%] tests/test_utils.py::test_ensure_type_6 PASSED [ 95%] tests/test_utils.py::test_ensure_type_7 PASSED [ 95%] tests/test_utils.py::test_ensure_type_8 PASSED [ 95%] tests/test_utils.py::test_ensure_type_9 PASSED [ 95%] tests/test_utils.py::test_ensure_type_10 PASSED [ 95%] tests/test_utils.py::test_ensure_type_11 PASSED [ 95%] tests/test_utils.py::test_ensure_type_12 PASSED [ 95%] tests/test_utils.py::test_ensure_type_13 PASSED [ 95%] tests/test_utils.py::test_ensure_type_14 PASSED [ 95%] tests/test_utils.py::test_ensure_type_15 PASSED [ 96%] tests/test_utils.py::test_delay_import_fail_1 PASSED [ 96%] tests/test_utils.py::test_delay_import PASSED [ 96%] tests/test_utils.py::test_unit_0 PASSED [ 96%] tests/test_utils.py::test_unit_1 PASSED [ 96%] tests/test_utils.py::test_unit_2 PASSED [ 96%] tests/test_utils.py::test_unit_3 PASSED [ 96%] tests/test_xml.py::test_xml PASSED [ 96%] tests/test_xtc.py::test_read_chunk1 PASSED [ 96%] tests/test_xtc.py::test_read_stride PASSED [ 96%] tests/test_xtc.py::test_read_stride_n_frames PASSED [ 96%] tests/test_xtc.py::test_read_stride_offsets PASSED [ 96%] tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 97%] tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 97%] tests/test_xtc.py::test_read_atomindices_1 PASSED [ 97%] tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 97%] tests/test_xtc.py::test_read_atomindices_2 PASSED [ 97%] tests/test_xtc.py::test_read_chunk2 PASSED [ 97%] tests/test_xtc.py::test_read_chunk3 PASSED [ 97%] tests/test_xtc.py::test_write_0 PASSED [ 97%] tests/test_xtc.py::test_write_1 PASSED [ 97%] tests/test_xtc.py::test_write_2 PASSED [ 97%] tests/test_xtc.py::test_read_error_0 PASSED [ 97%] tests/test_xtc.py::test_write_error_0 PASSED [ 98%] tests/test_xtc.py::test_read_error_1 PASSED [ 98%] tests/test_xtc.py::test_read_error_2 PASSED [ 98%] tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 98%] tests/test_xtc.py::test_tell PASSED [ 98%] tests/test_xtc.py::test_seek PASSED [ 98%] tests/test_xtc.py::test_seek_natoms9 PASSED [ 98%] tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 98%] tests/test_xtc.py::test_ragged_1 PASSED [ 98%] tests/test_xtc.py::test_ragged_2 PASSED [ 98%] tests/test_xtc.py::test_short_traj PASSED [ 98%] tests/test_xtc.py::test_flush PASSED [ 98%] tests/test_xyz.py::test_read_0 PASSED [ 99%] tests/test_xyz.py::test_read_1 PASSED [ 99%] tests/test_xyz.py::test_read_gz PASSED [ 99%] tests/test_xyz.py::test_read_write PASSED [ 99%] tests/test_xyz.py::test_mdwrite PASSED [ 99%] tests/test_xyz.py::test_multiread PASSED [ 99%] tests/test_xyz.py::test_seek PASSED [ 99%] tests/test_xyz.py::test_len PASSED [ 99%] tests/test_zipped.py::test_read_gz PASSED [ 99%] tests/test_zipped.py::test_write_gz PASSED [ 99%] tests/test_zipped.py::test_read_bz2 PASSED [ 99%] tests/test_zipped.py::test_write_bz2 PASSED [100%] =============================== warnings summary =============================== tests/test_distance.py::Test_Distance::test_6 :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found SKIPPED [15] tests/test_docstrings.py:38: Skip checking certain modules' docstrings SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing SKIPPED [1] tests/test_hdf5.py:105: requires openmm.units SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units SKIPPED [1] tests/test_mol2.py:65: Requires obabel SKIPPED [1] tests/test_netcdf.py:274: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found SKIPPED [1] tests/test_nmr.py:26: PPM binary not found SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. SKIPPED [1] tests/test_selection.py:267: failed to parse selection SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. SKIPPED [1] tests/test_topology.py:66: needs OpenMM SKIPPED [1] tests/test_topology.py:83: needs OpenMM SKIPPED [1] tests/test_topology.py:93: needs OpenMM SKIPPED [1] tests/test_topology.py:102: needs OpenMM SKIPPED [1] tests/test_topology.py:112: needs OpenMM SKIPPED [1] tests/test_topology.py:119: requires openmm >= 8.2 SKIPPED [1] tests/test_topology.py:295: needs OpenMM SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information SKIPPED [1] tests/test_trajectory.py:225: mdcrd can only store rectilinear boxes SKIPPED [1] tests/test_trajectory.py:223: ncrst can only store 1 frame per file SKIPPED [1] tests/test_trajectory.py:223: rst7 can only store 1 frame per file SKIPPED [14] tests/test_trajectory.py:247: mdcrd can only store rectilinear boxes SKIPPED [14] tests/test_trajectory.py:245: ncrst can only store 1 frame per file SKIPPED [14] tests/test_trajectory.py:245: rst7 can only store 1 frame per file SKIPPED [4] tests/test_trajectory.py:255: dtr needs to write unitcells SKIPPED [4] tests/test_trajectory.py:255: lammpstrj needs to write unitcells SKIPPED [2] tests/test_trajectory.py:641: Only 1 frame per file format XFAIL tests/test_trajectory.py::test_read_path[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_path[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load_combination[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - This is broken XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - PDB Files don't support seeking XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - PDB Files don't support seeking XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - This is broken XFAIL tests/test_trajectory.py::test_load_frame[dtr] - DTR doesn't load a single frame properly XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load_frame[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load_frame[gro] - Gro doesn't implement seek XFAIL tests/test_trajectory.py::test_iterload[dtr] - This is broken with dtr XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - PDB Iterloads an extra frame!! XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - PDB Iterloads an extra frame!! XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - These reference files don't exist yet XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - Not implemented for some reason XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - This is broken with dtr XFAIL tests/test_trajectory.py::test_unitcell[dtr] - dtr seems to need unit vectors XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - lammpstrj seems to need unit vectors XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - ncrst seems to need unit vectors XFAIL tests/test_trajectory.py::test_unitcell[rst7] - rst7 seems to need unit vectors = 987 passed, 103 skipped, 24 deselected, 61 xfailed, 1 warning in 388.46s (0:06:28) = lugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) rm -fr -- /tmp/dh-xdg-rundir-gj7Fh6od create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild rm -f -- debian/python3-mdtraj.substvars rm -fr -- debian/.debhelper/generated/python3-mdtraj/ debian/python3-mdtraj/ debian/tmp/ dh_auto_install -a -O--buildsystem=pybuild install -m0755 -d /build/reproducible-path/mdtraj-1.11.1.post1/debian/tmp pybuild --install -i python{version} -p "3.14 3.13" I: pybuild plugin_pyproject:199: Copying package built for python3.14 to destdir I: pybuild plugin_pyproject:199: Copying package built for python3.13 to destdir dh_install -a -O--buildsystem=pybuild dh_installdocs -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/share/doc/python3-mdtraj install -p -m0644 debian/copyright debian/python3-mdtraj/usr/share/doc/python3-mdtraj/copyright dh_sphinxdoc -a -O--buildsystem=pybuild dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/share/doc/python3-mdtraj install -p -m0644 debian/.debhelper/generated/python3-mdtraj/dh_installchangelogs.dch.trimmed debian/python3-mdtraj/usr/share/doc/python3-mdtraj/changelog.Debian dh_installexamples -a -O--buildsystem=pybuild dh_installman -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/ install -p -m0644 ./debian/mdconvert-mdtraj.1 debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/ install -p -m0644 ./debian/mdinspect.1 debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 mv debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 chmod 0644 -- debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 mv debian/python3-mdtraj/usr/share/man/man1/mdinspect.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 chmod 0644 -- debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 dh_python3 -a -O--buildsystem=pybuild D: dh_python3 dh_python3:87: version: 7.20260125 D: dh_python3 dh_python3:88: argv: ['/usr/bin/dh_python3', '-a', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:89: options: DHPythonOptions(O=['--buildsystem=pybuild'], accept_upstream_versions=False, arch=True, clean_dbg_pkg=True, compile_all=False, depends=[], depends_section=[], guess_deps=True, ignore_shebangs=False, no_ext_rename=False, no_package=[], no_shebang_rewrite=False, package=[], private_dir=None, recommends=[], recommends_section=[], regexpr=[], remaining_packages=False, requires=[], shebang=None, skip_private=False, suggests=[], suggests_section=[], verbose=True, vrange=None, write_log=False) D: dh_python3 dh_python3:90: supported Python versions: 3.13,3.14 (default=3.13) D: dh_python3 debhelper:224: source=mdtraj, binary packages=['python3-mdtraj'] D: dh_python3 dh_python3:117: processing package python3-mdtraj... D: dh_python3 fs:60: moving files from debian/python3-mdtraj/usr/lib/python3.13/dist-packages to debian/python3-mdtraj/usr/lib/python3/dist-packages/ D: dh_python3 fs:60: moving files from debian/python3-mdtraj/usr/lib/python3.14/dist-packages to debian/python3-mdtraj/usr/lib/python3/dist-packages/ I: dh_python3 tools:128: replacing shebang in debian/python3-mdtraj/usr/bin/mdinspect I: dh_python3 tools:128: replacing shebang in debian/python3-mdtraj/usr/bin/mdconvert-mdtraj D: dh_python3 fs:303: removing dist-packages/.pytest_cache D: dh_python3 fs:196: Writing INSTALLER in debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.11.1.post1.dist-info D: dh_python3 fs:207: Deleting RECORD in debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.11.1.post1.dist-info D: dh_python3 fs:411: package python3-mdtraj details = {'requires.txt': set(), 'egg-info': set(), 'dist-info': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.11.1.post1.dist-info/METADATA'}, 'nsp.txt': set(), 'shebangs': {/usr/bin/python3, /usr/bin/python3}, 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.14'), Version('3.13')}, 'ext_stableabi': set(), 'ext_no_version': set()} D: dh_python3 depends:148: generating dependencies for package python3-mdtraj D: dh_python3 pydist:237: trying to find dependency for numpy~=2.0 (python=None) D: dh_python3 pydist:281: dependency: module numpy is known to pydist: [PyDist(name='numpy', versions={Version('3.14'), Version('3.13')}, dependency='python3-numpy', standard=None, rules=[])] D: dh_python3 pydist:358: dependency: included in build-deps with limits D: dh_python3 pydist:237: trying to find dependency for scipy (python=None) D: dh_python3 pydist:281: dependency: module scipy is known to pydist: [PyDist(name='scipy', versions={Version('3.14'), Version('3.13')}, dependency='python3-scipy', standard=None, rules=[])] D: dh_python3 pydist:365: dependency: included in build-deps D: dh_python3 pydist:237: trying to find dependency for pyparsing (python=None) D: dh_python3 pydist:281: dependency: module pyparsing is known to pydist: [PyDist(name='pyparsing', versions={Version('3.14'), Version('3.13')}, dependency='python3-pyparsing', standard=None, rules=[])] D: dh_python3 pydist:365: dependency: included in build-deps D: dh_python3 pydist:237: trying to find dependency for packaging (python=None) D: dh_python3 pydist:281: dependency: module packaging is known to pydist: [PyDist(name='packaging', versions={Version('3.14'), Version('3.13')}, dependency='python3-packaging', standard=None, rules=[])] D: dh_python3 pydist:365: dependency: included in build-deps D: dh_python3 depends:330: D={'python3-pyparsing', 'python3:any', 'python3-packaging', 'python3 (<< 3.15)', 'python3 (>= 3.13~)', 'python3-scipy', 'python3-numpy (>= 2.0.0~)'}; R=[]; S=[]; E=[], B=[]; RT=[] debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/mdtraj-1.11.1.post1' # setup.py builds the static lib libtheobald.a for each python version # but dh_python3 can't tell the difference between the different builds, # since py3.11 compiles libtheobald.o with -fwrapv, where py3.12 uses -fno-strict-overflow # So clean up manually (assume the binary difference is not an issue) rm -f debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib/libtheobald.a for d in debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib; do if [-d $d]; then rmdir -p --ignore-fail-on-non-empty $d; fi; done /bin/sh: 1: [-d: not found make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.11.1.post1' dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild cd debian/python3-mdtraj chmod a-x usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1 gzip -9nf usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1 cd '/build/reproducible-path/mdtraj-1.11.1.post1' dh_fixperms -a -O--buildsystem=pybuild find debian/python3-mdtraj ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-mdtraj/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-mdtraj/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-mdtraj/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/python3-mdtraj/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/python3-mdtraj/usr/lib/debug/.dwz/x86_64-linux-gnu/python3-mdtraj.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/python3-mdtraj.debug -- debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-314-x86_64-linux-gnu.so objcopy --compress-debug-sections debian/python3-mdtraj/usr/lib/debug/.dwz/x86_64-linux-gnu/python3-mdtraj.debug chmod 0644 -- debian/python3-mdtraj/usr/lib/debug/.dwz/x86_64-linux-gnu/python3-mdtraj.debug dh_strip -a -O--buildsystem=pybuild install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ad objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ad/7b294e9fbdb0635af351a546ae105273f5b714.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ad/7b294e9fbdb0635af351a546ae105273f5b714.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ad/7b294e9fbdb0635af351a546ae105273f5b714.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/0b objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-314-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/0b/fe6b85d5de862da60c40e3591933371df6f0e1.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/0b/fe6b85d5de862da60c40e3591933371df6f0e1.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-314-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/0b/fe6b85d5de862da60c40e3591933371df6f0e1.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-314-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/90 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-314-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/90/d4376a6f75e5fb0d9c1c7e3ba7063d4d991688.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/90/d4376a6f75e5fb0d9c1c7e3ba7063d4d991688.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-314-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/90/d4376a6f75e5fb0d9c1c7e3ba7063d4d991688.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-314-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f0 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f0/e2d330e4f12d44cdd5b36ff80ae824c72ff394.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f0/e2d330e4f12d44cdd5b36ff80ae824c72ff394.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f0/e2d330e4f12d44cdd5b36ff80ae824c72ff394.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/de objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/de/95146ea8fb94fae03ece0f83722dbd63de2e94.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/de/95146ea8fb94fae03ece0f83722dbd63de2e94.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/de/95146ea8fb94fae03ece0f83722dbd63de2e94.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/be objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-314-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/be/56e4a32d5c6b05e5ea198769e9ded3d61559e9.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/be/56e4a32d5c6b05e5ea198769e9ded3d61559e9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-314-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/be/56e4a32d5c6b05e5ea198769e9ded3d61559e9.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-314-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/31 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-314-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/31/290458aad72180a24e684f8183225b56779f15.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/31/290458aad72180a24e684f8183225b56779f15.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-314-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/31/290458aad72180a24e684f8183225b56779f15.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-314-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a8 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a8/26b8cb61c824550bb7c89d5d718f1cbfaa3c38.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a8/26b8cb61c824550bb7c89d5d718f1cbfaa3c38.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a8/26b8cb61c824550bb7c89d5d718f1cbfaa3c38.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f4 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f4/397b552058a95ca3757db1b202a5a5f03d2131.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f4/397b552058a95ca3757db1b202a5a5f03d2131.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f4/397b552058a95ca3757db1b202a5a5f03d2131.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d2 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d2/ab0cd4eb20255ce525ffe0b04376ef93a86d6d.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d2/ab0cd4eb20255ce525ffe0b04376ef93a86d6d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d2/ab0cd4eb20255ce525ffe0b04376ef93a86d6d.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d4 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-314-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d4/a893325756bc7930cf2843058ddf6197ede7a5.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d4/a893325756bc7930cf2843058ddf6197ede7a5.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-314-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d4/a893325756bc7930cf2843058ddf6197ede7a5.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-314-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/92 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-314-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/92/668cd79f7ffa4d9c96a0daf02f63e3bcc26d57.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/92/668cd79f7ffa4d9c96a0daf02f63e3bcc26d57.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-314-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/92/668cd79f7ffa4d9c96a0daf02f63e3bcc26d57.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-314-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/40 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/40/deac29c306367b334d551d472b5e6349aca554.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/40/deac29c306367b334d551d472b5e6349aca554.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/40/deac29c306367b334d551d472b5e6349aca554.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a6 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a6/0b0cc07a65a56aa44c21f6d1ac9108e43f9649.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a6/0b0cc07a65a56aa44c21f6d1ac9108e43f9649.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a6/0b0cc07a65a56aa44c21f6d1ac9108e43f9649.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/78 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/78/0fdad99e900cd3f6d0e0777bc5e813ef178a2a.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/78/0fdad99e900cd3f6d0e0777bc5e813ef178a2a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/78/0fdad99e900cd3f6d0e0777bc5e813ef178a2a.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e6 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-314-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e6/24750036df274c9cc050c2cd8557165ff9851e.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e6/24750036df274c9cc050c2cd8557165ff9851e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-314-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e6/24750036df274c9cc050c2cd8557165ff9851e.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-314-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/8f objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-314-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/8f/567e639ff49f976c92b4ebc5cc445ba95c0515.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/8f/567e639ff49f976c92b4ebc5cc445ba95c0515.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-314-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/8f/567e639ff49f976c92b4ebc5cc445ba95c0515.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-314-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4c objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-314-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4c/2cba60df405f375138e85451fcdb775e04fe32.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4c/2cba60df405f375138e85451fcdb775e04fe32.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-314-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4c/2cba60df405f375138e85451fcdb775e04fe32.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-314-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a1 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a1/5abd2e35049a5ab4b9931128cff33edde70c52.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a1/5abd2e35049a5ab4b9931128cff33edde70c52.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a1/5abd2e35049a5ab4b9931128cff33edde70c52.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/57 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-314-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/57/cbcdd7e8c0d0cb321faae1bc2c1f2ce2f2018b.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/57/cbcdd7e8c0d0cb321faae1bc2c1f2ce2f2018b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-314-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/57/cbcdd7e8c0d0cb321faae1bc2c1f2ce2f2018b.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-314-x86_64-linux-gnu.so strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/core/lib/libtheobald.a install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/python3-mdtraj/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/python3-mdtraj/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/python3-mdtraj/usr/lib/debug install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc ln -s python3-mdtraj debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc/python3-mdtraj-dbgsym install -m0755 -d debian/.debhelper/python3-mdtraj dh_makeshlibs -a -O--buildsystem=pybuild rm -f debian/python3-mdtraj/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN dpkg-shlibdeps -Tdebian/python3-mdtraj.substvars debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-314-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-314-x86_64-linux-gnu.so dh_installdeb -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/postinst cat debian/python3-mdtraj.postinst.debhelper >> debian/python3-mdtraj/DEBIAN/postinst chmod 0755 -- debian/python3-mdtraj/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/prerm cat debian/python3-mdtraj.prerm.debhelper >> debian/python3-mdtraj/DEBIAN/prerm chmod 0755 -- debian/python3-mdtraj/DEBIAN/prerm dh_numpy3 -a -O--buildsystem=pybuild mv debian/python3-mdtraj.substvars.new debian/python3-mdtraj.substvars dh_gencontrol -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN echo misc:Depends= >> debian/python3-mdtraj.substvars echo misc:Pre-Depends= >> debian/python3-mdtraj.substvars install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/.debhelper/python3-mdtraj/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=python3-mdtraj-dbgsym -DDepends="python3-mdtraj (= \${binary:Version})" -DDescription="debug symbols for python3-mdtraj" -DBuild-Ids="0bfe6b85d5de862da60c40e3591933371df6f0e1 31290458aad72180a24e684f8183225b56779f15 40deac29c306367b334d551d472b5e6349aca554 4c2cba60df405f375138e85451fcdb775e04fe32 57cbcdd7e8c0d0cb321faae1bc2c1f2ce2f2018b 780fdad99e900cd3f6d0e0777bc5e813ef178a2a 8f567e639ff49f976c92b4ebc5cc445ba95c0515 90d4376a6f75e5fb0d9c1c7e3ba7063d4d991688 92668cd79f7ffa4d9c96a0daf02f63e3bcc26d57 a15abd2e35049a5ab4b9931128cff33edde70c52 a60b0cc07a65a56aa44c21f6d1ac9108e43f9649 a826b8cb61c824550bb7c89d5d718f1cbfaa3c38 ad7b294e9fbdb0635af351a546ae105273f5b714 be56e4a32d5c6b05e5ea198769e9ded3d61559e9 d2ab0cd4eb20255ce525ffe0b04376ef93a86d6d d4a893325756bc7930cf2843058ddf6197ede7a5 de95146ea8fb94fae03ece0f83722dbd63de2e94 e624750036df274c9cc050c2cd8557165ff9851e f0e2d330e4f12d44cdd5b36ff80ae824c72ff394 f4397b552058a95ca3757db1b202a5a5f03d2131" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/python3-mdtraj chmod 0644 -- debian/python3-mdtraj/DEBIAN/control dh_md5sums -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN cd debian/python3-mdtraj >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python3-mdtraj/DEBIAN/md5sums install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN cd debian/.debhelper/python3-mdtraj/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/md5sums dh_builddeb -a -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/python3-mdtraj .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-mdtraj/dbgsym-root .. dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.11.1.post1-3_amd64.deb'. dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.11.1.post1-3_amd64.deb'. dpkg-genbuildinfo --build=any -O../mdtraj_1.11.1.post1-3_amd64.buildinfo dpkg-genchanges --build=any -O../mdtraj_1.11.1.post1-3_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-source: info: using options from mdtraj-1.11.1.post1/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2026-03-04T06:56:30Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Wed, 04 Mar 2026 06:56:30 +0000 | +------------------------------------------------------------------------------+ mdtraj_1.11.1.post1-3_amd64.changes: ------------------------------------ Format: 1.8 Date: Tue, 03 Mar 2026 20:05:08 +0100 Source: mdtraj Binary: python3-mdtraj python3-mdtraj-dbgsym Architecture: amd64 Version: 1.11.1.post1-3 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Drew Parsons Description: python3-mdtraj - Read, write and analyze MD trajectories in Python Closes: 1129346 Changes: mdtraj (1.11.1.post1-3) unstable; urgency=medium . * debian patch fix_netcdf_PR2143.patch applies upstream PR#2143 to fix use of libnetcdf when handling of netcdf files. Reenable test_iterload[nc]. Closes: #1129346 Checksums-Sha1: f23e6275491129da653d4f31adbd59efcf37fca5 10464 mdtraj_1.11.1.post1-3_amd64.buildinfo 65246c8c8a928aa9dd9b3acbb33086b1d8d3180d 11742916 python3-mdtraj-dbgsym_1.11.1.post1-3_amd64.deb eca5c953e0f39f2b81013e8324a3939e6593cf8b 1426148 python3-mdtraj_1.11.1.post1-3_amd64.deb Checksums-Sha256: 2aa1f733c8f81aff6e5db589e80b737763ce94d174452053405b82fa2f0edd3b 10464 mdtraj_1.11.1.post1-3_amd64.buildinfo deec870f0a9a4df14024ae8f4c7a9b4934cd7569562135ec5c83bd5529f4c322 11742916 python3-mdtraj-dbgsym_1.11.1.post1-3_amd64.deb 839f34a0e9f183987a5b13519bfda473a9c0e9112af98bf0fb601de408fb4a2e 1426148 python3-mdtraj_1.11.1.post1-3_amd64.deb Files: 18741c8291bc203028816eb783e7c851 10464 python optional mdtraj_1.11.1.post1-3_amd64.buildinfo d74e524a2a909c0ecca063c346d4952d 11742916 debug optional python3-mdtraj-dbgsym_1.11.1.post1-3_amd64.deb 521bc2bfcf5b8c3fed676e2bbbfc9132 1426148 python optional python3-mdtraj_1.11.1.post1-3_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Wed, 04 Mar 2026 06:56:31 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: mdtraj Binary: python3-mdtraj python3-mdtraj-dbgsym Architecture: amd64 Version: 1.11.1.post1-3 Checksums-Md5: d74e524a2a909c0ecca063c346d4952d 11742916 python3-mdtraj-dbgsym_1.11.1.post1-3_amd64.deb 521bc2bfcf5b8c3fed676e2bbbfc9132 1426148 python3-mdtraj_1.11.1.post1-3_amd64.deb Checksums-Sha1: 65246c8c8a928aa9dd9b3acbb33086b1d8d3180d 11742916 python3-mdtraj-dbgsym_1.11.1.post1-3_amd64.deb eca5c953e0f39f2b81013e8324a3939e6593cf8b 1426148 python3-mdtraj_1.11.1.post1-3_amd64.deb Checksums-Sha256: deec870f0a9a4df14024ae8f4c7a9b4934cd7569562135ec5c83bd5529f4c322 11742916 python3-mdtraj-dbgsym_1.11.1.post1-3_amd64.deb 839f34a0e9f183987a5b13519bfda473a9c0e9112af98bf0fb601de408fb4a2e 1426148 python3-mdtraj_1.11.1.post1-3_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 04 Mar 2026 06:56:29 +0000 Build-Path: /build/reproducible-path/mdtraj-1.11.1.post1 Installed-Build-Depends: autoconf (= 2.72-5), automake (= 1:1.18.1-4), autopoint (= 0.23.2-1), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.8), bash (= 5.3-2), binutils (= 2.46-2), binutils-common (= 2.46-2), binutils-x86-64-linux-gnu (= 2.46-2), bsdextrautils (= 2.41.3-4), build-essential (= 12.12), bzip2 (= 1.0.8-6+b1), ca-certificates (= 20260223), coreutils (= 9.10-1), cpp (= 4:15.2.0-5), cpp-15 (= 15.2.0-14), cpp-15-x86-64-linux-gnu (= 15.2.0-14), cpp-x86-64-linux-gnu (= 4:15.2.0-5), cython3 (= 3.1.6+dfsg-2+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 13.31), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-python (= 7.20260125), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), docutils-common (= 0.22.4+dfsg-1), dpkg (= 1.23.5), dpkg-dev (= 1.23.5), dwz (= 0.16-2), file (= 1:5.46-5+b1), findutils (= 4.10.0-3), fonts-mathjax (= 2.7.9+dfsg-1), g++ (= 4:15.2.0-5), g++-15 (= 15.2.0-14), g++-15-x86-64-linux-gnu (= 15.2.0-14), g++-x86-64-linux-gnu (= 4:15.2.0-5), gcc (= 4:15.2.0-5), gcc-15 (= 15.2.0-14), gcc-15-base (= 15.2.0-14), gcc-15-x86-64-linux-gnu (= 15.2.0-14), gcc-x86-64-linux-gnu (= 4:15.2.0-5), gettext (= 0.23.2-1), gettext-base (= 0.23.2-1), grep (= 3.12-1), groff-base (= 1.23.0-10), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-14), libatomic1 (= 15.2.0-14), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46-2), libblas3 (= 3.12.1-7+b1), libblkid1 (= 2.41.3-4), libblosc1 (= 1.21.5+ds-2+b1), libblosc2-7 (= 2.23.0+ds-1), libbrotli1 (= 1.2.0-3), libbsd0 (= 0.12.2-2+b1), libbz2-1.0 (= 1.0.8-6+b1), libc-bin (= 2.42-13), libc-dev-bin (= 2.42-13), libc-gconv-modules-extra (= 2.42-13), libc6 (= 2.42-13), libc6-dev (= 2.42-13), libcap-ng0 (= 0.9.1-1), libcc1-0 (= 15.2.0-14), libcom-err2 (= 1.47.2-3+b8), libcrypt1 (= 1:4.5.1-1), libctf-nobfd0 (= 2.46-2), libctf0 (= 2.46-2), libcurl3t64-gnutls (= 8.19.0~rc3-1), libcurl4t64 (= 8.19.0~rc3-1), libdb5.3t64 (= 5.3.28+dfsg2-11), libdebconfclient0 (= 0.282+b2), libdebhelper-perl (= 13.31), libdpkg-perl (= 1.23.5), libelf1t64 (= 0.194-1), libexpat1 (= 2.7.4-1), libexpat1-dev (= 2.7.4-1), libffi8 (= 3.5.2-3+b1), libfile-stripnondeterminism-perl (= 1.15.0-1), libgcc-15-dev (= 15.2.0-14), libgcc-s1 (= 15.2.0-14), libgdbm-compat4t64 (= 1.26-1+b1), libgdbm6t64 (= 1.26-1+b1), libgfortran5 (= 15.2.0-14), libgmp10 (= 2:6.3.0+dfsg-5+b1), libgnutls30t64 (= 3.8.12-3), libgomp1 (= 15.2.0-14), libgprofng0 (= 2.46-2), libgssapi-krb5-2 (= 1.22.1-2), libhdf5-310 (= 1.14.6+repack-2), libhdf5-hl-310 (= 1.14.6+repack-2), libhogweed6t64 (= 3.10.2-1), libhwasan0 (= 15.2.0-14), libidn2-0 (= 2.3.8-4+b1), libisl23 (= 0.27-1+b1), libitm1 (= 15.2.0-14), 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2025.2-5), python3-referencing (= 0.36.2-2), python3-requests (= 2.32.5+dfsg-1), python3-roman-numerals (= 4.1.0-1), python3-rpds-py (= 0.28.0-1), python3-scipy (= 1.16.3-4), python3-setuptools (= 78.1.1-0.1), python3-snowballstemmer (= 3.0.1-1), python3-soupsieve (= 2.8.3-1), python3-sphinx (= 8.2.3-12), python3-tables (= 3.11.0-3), python3-tables-lib (= 3.11.0-3), python3-tinycss2 (= 1.5.1-1), python3-tornado (= 6.5.4-0.1), python3-traitlets (= 5.14.3+really5.14.3-3), python3-typeguard (= 4.4.4-2), python3-typing-extensions (= 4.15.0-2), python3-urllib3 (= 2.6.3-1), python3-versioneer (= 0.29-2), python3-webencodings (= 0.5.1-5), python3-wheel (= 0.46.3-2), python3-zipp (= 3.23.0-1), python3-zmq (= 27.1.0-1+b1), python3.13 (= 3.13.12-1), python3.13-dev (= 3.13.12-1), python3.13-minimal (= 3.13.12-1), python3.14 (= 3.14.3-1), python3.14-dev (= 3.14.3-1), python3.14-minimal (= 3.14.3-1), readline-common (= 8.3-4), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.26), 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./usr/lib/debug/.build-id/f4/397b552058a95ca3757db1b202a5a5f03d2131.debug drwxr-xr-x root/root 0 2026-03-03 19:05 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-03-03 19:05 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 356880 2026-03-03 19:05 ./usr/lib/debug/.dwz/x86_64-linux-gnu/python3-mdtraj.debug drwxr-xr-x root/root 0 2026-03-03 19:05 ./usr/share/ drwxr-xr-x root/root 0 2026-03-03 19:05 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-03-03 19:05 ./usr/share/doc/python3-mdtraj-dbgsym -> python3-mdtraj python3-mdtraj_1.11.1.post1-3_amd64.deb --------------------------------------- new Debian package, version 2.0. size 1426148 bytes: control archive=4628 bytes. 1482 bytes, 32 lines control 11733 bytes, 123 lines md5sums 283 bytes, 12 lines * postinst #!/bin/sh 421 bytes, 12 lines * prerm #!/bin/sh Package: python3-mdtraj Source: mdtraj Version: 1.11.1.post1-3 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 7654 Depends: python3 (<< 3.15), python3 (>= 3.13~), python3-numpy (>= 2.0.0~), python3-numpy2-abi0 | python3-numpy-abi9, python3-packaging, python3-pyparsing, python3-scipy, python3:any, libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libstdc++6 (>= 13.1), python3-networkx, python3-pandas, python3-tables Recommends: python3-gsd, python3-netcdf4 Suggests: python-mdtraj-doc Section: python Priority: optional Homepage: https://mdtraj.org/ Description: Read, write and analyze MD trajectories in Python Read, write and analyze MD trajectories with only a few lines of Python code. . MDTraj is a Python library that allows users to manipulate molecular dynamics (MD) trajectories. Features include: * Wide MD format support, including pdb, xtc, trr, dcd, binpos, netcdf, mdcrd, prmtop, and more. * Extremely fast RMSD calculations (4x the speed of the original Theobald QCP). * Extensive analysis functions including those that compute bonds, angles, dihedrals, hydrogen bonds, secondary structure, and NMR observables. * Lightweight, Pythonic API. . MDTraj includes a command-line application, mdconvert-mdtraj, for converting trajectories between formats. . This package installs the library for Python 3, together with the command line utilities mdconvert-mdtraj and mdinspect. drwxr-xr-x root/root 0 2026-03-03 19:05 ./ drwxr-xr-x root/root 0 2026-03-03 19:05 ./usr/ drwxr-xr-x root/root 0 2026-03-03 19:05 ./usr/bin/ -rwxr-xr-x root/root 238 2026-03-03 19:05 ./usr/bin/mdconvert-mdtraj -rwxr-xr-x root/root 238 2026-03-03 19:05 ./usr/bin/mdinspect drwxr-xr-x root/root 0 2026-03-03 19:05 ./usr/lib/ drwxr-xr-x root/root 0 2026-03-03 19:05 ./usr/lib/python3/ drwxr-xr-x root/root 0 2026-03-03 19:05 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2026-03-03 19:05 ./usr/lib/python3/dist-packages/mdtraj-1.11.1.post1.dist-info/ -rw-r--r-- root/root 7 2026-03-03 19:05 ./usr/lib/python3/dist-packages/mdtraj-1.11.1.post1.dist-info/INSTALLER -rw-r--r-- root/root 2571 2026-03-03 19:05 ./usr/lib/python3/dist-packages/mdtraj-1.11.1.post1.dist-info/METADATA -rw-r--r-- root/root 104 2026-03-03 19:05 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/build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Wed, 04 Mar 2026 06:56:34 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 304108 Build-Time: 777 Distribution: unstable Host Architecture: amd64 Install-Time: 3 Job: /srv/rebuilderd/tmp/rebuilderd4rQZSi/inputs/mdtraj_1.11.1.post1-3.dsc Machine Architecture: amd64 Package: mdtraj Package-Time: 788 Source-Version: 1.11.1.post1-3 Space: 304108 Status: successful Version: 1.11.1.post1-3 -------------------------------------------------------------------------------- Finished at 2026-03-04T06:56:30Z Build needed 00:13:08, 304108k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderd4rQZSi/out size differs for python3-mdtraj-dbgsym_1.11.1.post1-3_amd64.deb checking python3-mdtraj-dbgsym_1.11.1.post1-3_amd64.deb: