=============================================================================== 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/rebuilderdr14PJq/inputs/mdtraj_1.11.0-2+b1_amd64.buildinfo Source: mdtraj Version: 1.11.0-2 rebuilderd-worker node: osuosl43-amd64 +------------------------------------------------------------------------------+ | Downloading sources Sat, 27 Dec 2025 15:34:40 +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 [90.7 kB] Get:9 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:10 https://deb.debian.org/debian trixie/non-free-firmware Sources [6,548 B] Get:11 https://deb.debian.org/debian-security trixie-security/non-free-firmware Sources [696 B] Get:12 https://deb.debian.org/debian-security trixie-security/main Sources [116 kB] Get:13 https://deb.debian.org/debian trixie-updates/main Sources [2,788 B] Get:14 https://deb.debian.org/debian trixie-proposed-updates/non-free-firmware Sources [692 B] Get:15 https://deb.debian.org/debian trixie-proposed-updates/main Sources [158 kB] Get:16 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [2,468 B] Get:17 https://deb.debian.org/debian trixie-backports/main Sources [111 kB] Get:18 https://deb.debian.org/debian forky/main Sources [10.6 MB] Get:19 https://deb.debian.org/debian forky/non-free-firmware Sources [7,696 B] Get:20 https://deb.debian.org/debian sid/non-free-firmware Sources [9,692 B] Get:21 https://deb.debian.org/debian sid/main Sources [11.2 MB] Get:22 https://deb.debian.org/debian experimental/main Sources [352 kB] Get:23 https://deb.debian.org/debian experimental/non-free-firmware Sources [3,180 B] Fetched 33.9 MB in 4s (8,019 kB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.11.0-2.dsc' mdtraj_1.11.0-2.dsc 2859 SHA256:1ae819aeb9454931ec54f41bdce2467332867d1e4e87960d606c9fb6eddbf96c 'https://deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.11.0.orig.tar.gz' mdtraj_1.11.0.orig.tar.gz 22723159 SHA256:fefca787f882d0716a7aeb01b4d8e30caddbd2be0b2893acfa7201c31d13c786 'https://deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.11.0-2.debian.tar.xz' mdtraj_1.11.0-2.debian.tar.xz 300368 SHA256:8553fdf5130d41f5881b2c8cc7d509e3b3b2a9c05699998bafdb905550db2a15 fefca787f882d0716a7aeb01b4d8e30caddbd2be0b2893acfa7201c31d13c786 mdtraj_1.11.0.orig.tar.gz 8553fdf5130d41f5881b2c8cc7d509e3b3b2a9c05699998bafdb905550db2a15 mdtraj_1.11.0-2.debian.tar.xz 1ae819aeb9454931ec54f41bdce2467332867d1e4e87960d606c9fb6eddbf96c mdtraj_1.11.0-2.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Sat, 27 Dec 2025 15:34:46 +0000 | +------------------------------------------------------------------------------+ Rebuilding mdtraj=1.11.0-2 in /srv/rebuilderd/tmp/rebuilderdr14PJq/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdr14PJq/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdr14PJq/inputs/mdtraj_1.11.0-2+b1_amd64.buildinfo /srv/rebuilderd/tmp/rebuilderdr14PJq/inputs/mdtraj_1.11.0-2+b1_amd64.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/mdtraj-1.11.0 I: verifying dsc... successful! Get:1 http://deb.debian.org/debian unstable InRelease [187 kB] Get:2 http://snapshot.debian.org/archive/debian/20251207T204132Z sid InRelease [176 kB] Get:3 http://snapshot.debian.org/archive/debian/20251223T083714Z sid InRelease [187 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages [10.2 MB] Get:5 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 Packages [10.2 MB] Get:6 http://snapshot.debian.org/archive/debian/20251223T083714Z sid/main amd64 Packages [10.2 MB] Fetched 31.2 MB in 3s (9278 kB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20251207T204132Z/dists/sid/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted W: http://snapshot.debian.org/archive/debian/20251223T083714Z/dists/sid/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://deb.debian.org/debian unstable/main amd64 cpp amd64 4:15.2.0-4 [1564 B] Fetched 1564 B in 0s (153 kB/s) dpkg-name: info: moved 'cpp_4%3a15.2.0-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp65hwiop6/cpp_15.2.0-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 mawk amd64 1.3.4.20250131-1 [141 kB] Fetched 141 kB in 0s (13.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvb9q_t6v/mawk_1.3.4.20250131-1_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 (465 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp079mpw5j/python3-webencodings_0.5.1-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules amd64 1.7.0-5 [179 kB] Fetched 179 kB in 0s (15.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw6l5v2b_/libpam-modules_1.7.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpc3 amd64 1.3.1-2 [55.8 kB] Fetched 55.8 kB in 0s (3131 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo1jpkg9n/libmpc3_1.3.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Fetched 58.3 kB in 0s (4756 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpskygggwx/librtmp1_2.4+20151223.gitfa8646d.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Fetched 112 kB in 0s (9913 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmq9av0e4/libexpat1_2.7.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-4 [1448 kB] Fetched 1448 kB in 0s (28.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuodplt3t/libhdf5-310_1.14.5+repack-4_amd64.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 (2307 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_sl7croq/sysvinit-utils_3.15-6_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 hostname amd64 3.25 [11.0 kB] Fetched 11.0 kB in 0s (989 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi_4jojfa/hostname_3.25_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.9-2 [1052 B] Fetched 1052 B in 0s (53.2 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf3lkzwtv/python3-all_3.13.9-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Fetched 68.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw7rts8bf/libuchardet0_0.0.8-2_amd64.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 1s (10.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqw9ovdfx/python3-pandas-lib_2.3.3+dfsg-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Fetched 37.1 kB in 0s (2086 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpascuae22/python3-typeguard_4.4.4-1_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 (2772 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_kaupfs9/python3-requests_2.32.5+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.14-minimal amd64 3.14.2-1+b1 [2407 kB] Fetched 2407 kB in 0s (7133 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdkixnj5e/python3.14-minimal_3.14.2-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libsmartcols1 amd64 2.41.2-4 [145 kB] Fetched 145 kB in 0s (12.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjlb8bg_0/libsmartcols1_2.41.2-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 python3-html5lib all 1.2-2 [92.1 kB] Fetched 92.1 kB in 0s (1827 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc5u_51th/python3-html5lib_1.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b1 [88.9 kB] Fetched 88.9 kB in 0s (8829 kB/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp7x5tf3ha/zlib1g_1.3.dfsg+really1.3.1-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-bin amd64 6.5+20251123-1 [445 kB] Fetched 445 kB in 0s (36.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwoodi4ot/ncurses-bin_6.5+20251123-1_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 (5587 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_o7vi9lb/autotools-dev_20240727.1_all.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 (107 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmi7929zf/libperl5.40_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Fetched 245 kB in 0s (12.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphp_tzguw/libssh2-1t64_1.11.1-1_amd64.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/tmpma_lx1cn/dh-strip-nondeterminism_1.15.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Fetched 13.6 kB in 0s (496 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkxc637vf/python3-autocommand_2.2.2-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Fetched 109 kB in 0s (10.3 MB/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.46-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpdgt_cjp4/libmagic1t64_5.46-5_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 (80.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4ayq35x0/perl-base_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-3 [26.1 kB] Fetched 26.1 kB in 0s (1227 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl6idj882/libffi8_3.5.2-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libcap2 amd64 1:2.75-10+b2 [28.7 kB] Fetched 28.7 kB in 0s (889 kB/s) dpkg-name: info: moved 'libcap2_1%3a2.75-10+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmptoeyliv1/libcap2_2.75-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxxhash0 amd64 0.8.3-2 [27.1 kB] Fetched 27.1 kB in 0s (1154 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvil3pzwc/libxxhash0_0.8.3-2_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 (2256 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx473f4rj/python3-more-itertools_10.8.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 tzdata all 2025b-5 [260 kB] Fetched 260 kB in 0s (17.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7c1kdtib/tzdata_2025b-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.2-2 [30.7 kB] Fetched 30.7 kB in 0s (179 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwh00psx6/libsnappy1v5_1.2.2-2_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 (2660 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvgodi3hd/python3-numexpr_2.14.1-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema all 4.25.1-2 [75.7 kB] Fetched 75.7 kB in 0s (2554 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphoo6su7x/python3-jsonschema_4.25.1-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam0g amd64 1.7.0-5 [69.9 kB] Fetched 69.9 kB in 0s (6692 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppimce4yf/libpam0g_1.7.0-5_amd64.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 (1390 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmploqeu5ut/libseccomp2_2.6.0-2+b1_amd64.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 (11.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpolq434lx/groff-base_1.23.0-10_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 (2162 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcj49uh39/python3-pyparsing_3.1.3-1_all.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 (2246 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1dxz594g/python3-snowballstemmer_3.0.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 2.1.0-1 [7432 B] Fetched 7432 B in 0s (247 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzrio_zr0/python3-iniconfig_2.1.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Fetched 2785 kB in 1s (4341 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp49swbhiv/liblapack3_3.12.1-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libtsan2 amd64 15.2.0-10 [2491 kB] Fetched 2491 kB in 0s (24.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdqxlsorm/libtsan2_15.2.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-tinycss2 all 1.4.0-2 [25.0 kB] Fetched 25.0 kB in 0s (1559 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplugr1vo2/python3-tinycss2_1.4.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 make amd64 4.4.1-3 [463 kB] Fetched 463 kB in 0s (36.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3ahlq5dj/make_4.4.1-3_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 (1177 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp7d73uu4/libngtcp2-crypto-gnutls8_1.16.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.14-dev amd64 3.14.2-1+b1 [507 kB] Fetched 507 kB in 0s (7188 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1iw24wwx/python3.14-dev_3.14.2-1+b1_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 (8182 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppb40gsrf/debianutils_5.23.2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5 [574 kB] Fetched 574 kB in 0s (36.3 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpz4wk37i9/libgmp10_6.3.0+dfsg-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libbinutils amd64 2.45.50.20251201-1 [539 kB] Fetched 539 kB in 0s (13.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpljsl3dwz/libbinutils_2.45.50.20251201-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libsystemd0 amd64 259~rc2-1 [470 kB] Fetched 470 kB in 0s (31.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf_s1e3y2/libsystemd0_259~rc2-1_amd64.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 (3403 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkemwe9w_/libselinux1_3.9-4+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debconf all 1.5.91 [121 kB] Fetched 121 kB in 0s (10.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz_3qqdp2/debconf_1.5.91_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libitm1 amd64 15.2.0-10 [26.5 kB] Fetched 26.5 kB in 0s (1203 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyalri2xl/libitm1_15.2.0-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libmount1 amd64 2.41.2-4 [211 kB] Fetched 211 kB in 0s (17.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpperyt8kt/libmount1_2.41.2-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2025.11.12+ds-1 [10.0 kB] Fetched 10.0 kB in 0s (418 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo1z1xfm1/python3-certifi_2025.11.12+ds-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.11-1+b1 [770 kB] Fetched 770 kB in 0s (9033 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpraevuj4e/python3.13_3.13.11-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Fetched 92.4 kB in 0s (2491 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl6kjup59/python3-typing-extensions_4.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Fetched 16.7 kB in 0s (265 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbcpv3u31/python3-platformdirs_4.4.0-1_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 (2220 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_0xxmoch/python3-attr_25.4.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.9-2 [10.5 kB] Fetched 10.5 kB in 0s (339 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpec3_l8_3/libpython3-stdlib_3.13.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libblkid1 amd64 2.41.2-4 [174 kB] Fetched 174 kB in 0s (13.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcswes69y/libblkid1_2.41.2-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-10 [13.1 MB] Fetched 13.1 MB in 0s (37.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2zks7hko/g++-15-x86-64-linux-gnu_15.2.0-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libgcc-s1 amd64 15.2.0-10 [71.5 kB] Fetched 71.5 kB in 0s (1873 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwvdohdre/libgcc-s1_15.2.0-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 binutils-x86-64-linux-gnu amd64 2.45.50.20251201-1 [1058 kB] Fetched 1058 kB in 1s (1382 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1kkp_pia/binutils-x86-64-linux-gnu_2.45.50.20251201-1_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 (525 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpemvlonbw/python3-jaraco.functools_4.1.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bzip2 amd64 1.0.8-6 [40.5 kB] Fetched 40.5 kB in 0s (3440 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpani1h45z/bzip2_1.0.8-6_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 (744 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8bzbq7f5/python3-pytz_2025.2-5_all.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 (3517 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj2m4yqv5/libsasl2-2_2.1.28+dfsg1-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB] Fetched 55.1 kB in 0s (1895 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3tdxbc1p/liblzo2-2_2.10-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libdpkg-perl all 1.22.21 [650 kB] Fetched 650 kB in 0s (44.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkurzxy19/libdpkg-perl_1.22.21_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gzip amd64 1.13-1 [138 kB] Fetched 138 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph_9q_cqy/gzip_1.13-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.11-1+b1 [2254 kB] Fetched 2254 kB in 0s (13.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfs3mzor0/python3.13-minimal_3.13.11-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.14 amd64 3.14.2-1+b1 [829 kB] Fetched 829 kB in 0s (5929 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqscr4j5n/python3.14_3.14.2-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-10 [12.1 MB] Fetched 12.1 MB in 0s (28.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphuv0foqz/cpp-15-x86-64-linux-gnu_15.2.0-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libcurl4t64 amd64 8.17.0-3 [409 kB] Fetched 409 kB in 0s (31.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3vns0sa_/libcurl4t64_8.17.0-3_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 (4132 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpab9mcrc_/libpipeline1_1.5.8-2_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 (737 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp9woowql/python3-pytest-rerunfailures_16.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20250419 [162 kB] Fetched 162 kB in 0s (3268 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3r81zg9u/ca-certificates_20250419_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libgprofng0 amd64 2.45.50.20251201-1 [822 kB] Fetched 822 kB in 0s (6668 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfru5dt9t/libgprofng0_2.45.50.20251201-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 dpkg amd64 1.22.21 [1538 kB] Fetched 1538 kB in 0s (79.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy4l6xlor/dpkg_1.22.21_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Fetched 110 kB in 0s (9235 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv6nhv4ry/libidn2-0_2.3.8-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libcurl3t64-gnutls amd64 8.17.0-3 [401 kB] Fetched 401 kB in 0s (2783 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcni5qzd9/libcurl3t64-gnutls_8.17.0-3_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 (2330 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi1jea0kv/libjson-perl_4.10000-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libblosc2-4 amd64 2.17.1+ds-2 [198 kB] Fetched 198 kB in 0s (4173 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplv6f_x4d/libblosc2-4_2.17.1+ds-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.5.4-1 [1496 kB] Fetched 1496 kB in 0s (13.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpodlk0qea/openssl_3.5.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251223T083714Z sid/main amd64 python3-sphinx all 8.2.3-11 [478 kB] Fetched 478 kB in 0s (5572 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprtykf9_c/python3-sphinx_8.2.3-11_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-tables all 3.10.2-3 [354 kB] Fetched 354 kB in 0s (5115 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsy1o8z29/python3-tables_3.10.2-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 linux-libc-dev all 6.17.10-1 [2560 kB] Fetched 2560 kB in 0s (26.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3ptjc70o/linux-libc-dev_6.17.10-1_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 (1076 kB/s) dpkg-name: info: moved 'libaudit-common_1%3a4.1.2-1_all.deb' to '/srv/rebuilderd/tmp/tmp8bcwktp2/libaudit-common_4.1.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libncursesw6 amd64 6.5+20251123-1 [136 kB] Fetched 136 kB in 0s (11.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpweknhrfy/libncursesw6_6.5+20251123-1_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 (9550 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi3s6_9dk/libxml2-16_2.15.1+dfsg-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 findutils amd64 4.10.0-3 [700 kB] Fetched 700 kB in 0s (38.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpps616vlh/findutils_4.10.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 python3-tables-lib amd64 3.10.2-3+b1 [706 kB] Fetched 706 kB in 0s (5318 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1kdapkc1/python3-tables-lib_3.10.2-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 cpp-15 amd64 15.2.0-10 [1276 B] Fetched 1276 B in 0s (53.6 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuzjlyoss/cpp-15_15.2.0-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libjansson4 amd64 2.14-2+b3 [39.8 kB] Fetched 39.8 kB in 0s (2881 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplifkl4_w/libjansson4_2.14-2+b3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-versioneer all 0.29-1 [43.0 kB] Fetched 43.0 kB in 0s (1404 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9kgajton/python3-versioneer_0.29-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.3-1 [165 kB] Fetched 165 kB in 0s (5195 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprn1rlqh1/libexpat1-dev_2.7.3-1_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 (3343 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwd4tz2zy/python3-chardet_5.2.0+dfsg-2_all.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 (20.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp562h385h/gettext-base_0.23.2-1_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 (4290 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppopa8_29/libnorm1t64_1.5.9+dfsg-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.9-2 [26.0 kB] Fetched 26.0 kB in 0s (1231 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptc95o82e/python3-dev_3.13.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libc6 amd64 2.42-5 [1888 kB] Fetched 1888 kB in 0s (19.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7ybmppoh/libc6_2.42-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.4-2 [8108 B] Fetched 8108 B in 0s (205 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmxjkhrm4/libsz2_1.1.4-2_amd64.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 (1471 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7e11k8w6/python3-cpuinfo_9.0.0+git20221119-3_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/tmps844grfv/netbase_6.5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.9-2 [1072 B] Fetched 1072 B in 0s (27.2 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsnaj059m/python3-all-dev_3.13.9-2_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 (22.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj3vqdebg/perl_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Fetched 8276 B in 0s (293 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpom4gceoy/python3-jaraco.context_6.0.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblosc1 amd64 1.21.5+ds-2 [49.3 kB] Fetched 49.3 kB in 0s (1646 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8xzazqvr/libblosc1_1.21.5+ds-2_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 (4115 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyyur4zc3/rpcsvc-proto_1.4.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 binutils-common amd64 2.45.50.20251201-1 [2543 kB] Fetched 2543 kB in 0s (42.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf1ia63i9/binutils-common_2.45.50.20251201-1_amd64.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 (1861 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpke968ovp/media-types_14.0.0_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.11-3 [1509 kB] Fetched 1509 kB in 0s (73.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9kohfjzh/libgnutls30t64_3.8.11-3_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 (83.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg82jvmd0/fonts-mathjax_2.7.9+dfsg-1_all.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 (302 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqxq7qpzl/python3-zipp_3.23.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Fetched 27.9 kB in 0s (1042 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt19dzgkz/python3-alabaster_0.7.16-0.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-7 [248 kB] Fetched 248 kB in 0s (4473 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4zy4c05w/libqhull-r8.0_2020.2-7_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 (23.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw5eh0zkp/python-babel-localedata_2.17.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 gcc-15 amd64 15.2.0-10 [529 kB] Fetched 529 kB in 0s (9080 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptox5a7ia/gcc-15_15.2.0-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libgfortran5 amd64 15.2.0-10 [862 kB] Fetched 862 kB in 0s (5627 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8f6dr7cs/libgfortran5_15.2.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-netcdf4 amd64 1.7.3-1+b1 [897 kB] Fetched 897 kB in 0s (4901 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjlbl0snt/python3-netcdf4_1.7.3-1+b1_amd64.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 (3086 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuadr35go/python3-pkg-resources_78.1.1-0.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.9-2 [27.5 kB] Fetched 27.5 kB in 0s (1287 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8ya64_j5/python3_3.13.9-2_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 (18.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuo1eegh3/libpam-runtime_1.7.0-5_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 (25.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_skdm3os/libkrb5-3_1.22.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libstdc++-15-dev amd64 15.2.0-10 [2444 kB] Fetched 2444 kB in 0s (9603 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbyb0752v/libstdc++-15-dev_15.2.0-10_amd64.deb' Downloading dependency 1 of 318: cpp:amd64=4:15.2.0-4 Downloading dependency 2 of 318: mawk:amd64=1.3.4.20250131-1 Downloading dependency 3 of 318: python3-webencodings:amd64=0.5.1-5 Downloading dependency 4 of 318: libpam-modules:amd64=1.7.0-5 Downloading dependency 5 of 318: libmpc3:amd64=1.3.1-2 Downloading dependency 6 of 318: librtmp1:amd64=2.4+20151223.gitfa8646d.1-3 Downloading dependency 7 of 318: libexpat1:amd64=2.7.3-1 Downloading dependency 8 of 318: libhdf5-310:amd64=1.14.5+repack-4 Downloading dependency 9 of 318: sysvinit-utils:amd64=3.15-6 Downloading dependency 10 of 318: hostname:amd64=3.25 Downloading dependency 11 of 318: python3-all:amd64=3.13.9-2 Downloading dependency 12 of 318: libuchardet0:amd64=0.0.8-2 Downloading 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Downloading dependency 90 of 318: libaudit-common:amd64=1:4.1.2-1 Downloading dependency 91 of 318: libncursesw6:amd64=6.5+20251123-1 Downloading dependency 92 of 318: libxml2-16:amd64=2.15.1+dfsg-2+b1 Downloading dependency 93 of 318: findutils:amd64=4.10.0-3 Downloading dependency 94 of 318: python3-tables-lib:amd64=3.10.2-3+b1 Downloading dependency 95 of 318: cpp-15:amd64=15.2.0-10 Downloading dependency 96 of 318: libjansson4:amd64=2.14-2+b3 Downloading dependency 97 of 318: python3-versioneer:amd64=0.29-1 Downloading dependency 98 of 318: libexpat1-dev:amd64=2.7.3-1 Downloading dependency 99 of 318: python3-chardet:amd64=5.2.0+dfsg-2 Downloading dependency 100 of 318: gettext-base:amd64=0.23.2-1 Downloading dependency 101 of 318: libnorm1t64:amd64=1.5.9+dfsg-4 Downloading dependency 102 of 318: python3-dev:amd64=3.13.9-2 Downloading dependency 103 of 318: libc6:amd64=2.42-5 Downloading dependency 104 of 318: libsz2:amd64=1.1.4-2 Downloading dependency 105 of 318: python3-cpuinfo:amd64=9.0.0+git20221119-3 Downloading dependency 106 of 318: netbase:amd64=6.5 Downloading dependency 107 of 318: python3-all-dev:amd64=3.13.9-2 Downloading dependency 108 of 318: perl:amd64=5.40.1-7 Downloading dependency 109 of 318: python3-jaraco.context:amd64=6.0.1-1 Downloading dependency 110 of 318: libblosc1:amd64=1.21.5+ds-2 Downloading dependency 111 of 318: rpcsvc-proto:amd64=1.4.3-1 Downloading dependency 112 of 318: binutils-common:amd64=2.45.50.20251201-1 Downloading dependency 113 of 318: media-types:amd64=14.0.0 Downloading dependency 114 of 318: libgnutls30t64:amd64=3.8.11-3 Downloading dependency 115 of 318: fonts-mathjax:amd64=2.7.9+dfsg-1 Downloading dependency 116 of 318: python3-zipp:amd64=3.23.0-1 Downloading dependency 117 of 318: python3-alabaster:amd64=0.7.16-0.1 Downloading dependency 118 of 318: libqhull-r8.0:amd64=2020.2-7 Downloading dependency 119 of 318: python-babel-localedata:amd64=2.17.0-2 Downloading dependency 120 of 318: gcc-15:amd64=15.2.0-10 Downloading dependency 121 of 318: libgfortran5:amd64=15.2.0-10 Downloading dependency 122 of 318: python3-netcdf4:amd64=1.7.3-1+b1 Downloading dependency 123 of 318: python3-pkg-resources:amd64=78.1.1-0.1 Downloading dependency 124 of 318: python3:amd64=3.13.9-2 Downloading dependency 125 of 318: libpam-runtime:amd64=1.7.0-5 Downloading dependency 126 of 318: libkrb5-3:amd64=1.22.1-2 Downloading dependency 127 of 318: libstdc++-15-dev:amd64=15.2.0-10 Downloading dependency 128 of 318: libpython3-all-dev:amd64=3.13.9-2Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.9-2 [1072 B] Fetched 1072 B in 0s (105 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbpy_zv45/libpython3-all-dev_3.13.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libcom-err2 amd64 1.47.2-3+b4 [25.1 kB] Fetched 25.1 kB in 0s (2439 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgkcc1jv6/libcom-err2_1.47.2-3+b4_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 (1493 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdyznc9qj/python3-mistune_3.1.4-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Fetched 92.4 kB in 0s (8712 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkkci_89i/libdebhelper-perl_13.28_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 gcc-15-base amd64 15.2.0-10 [53.8 kB] Fetched 53.8 kB in 0s (1722 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa5nhgzwd/gcc-15-base_15.2.0-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 g++-15 amd64 15.2.0-10 [24.8 kB] Fetched 24.8 kB in 0s (1506 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7vn445qo/g++-15_15.2.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcrypt-dev amd64 1:4.5.1-1 [128 kB] Fetched 128 kB in 0s (11.0 MB/s) dpkg-name: info: moved 'libcrypt-dev_1%3a4.5.1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpflwtg5gv/libcrypt-dev_4.5.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libquadmath0 amd64 15.2.0-10 [145 kB] Fetched 145 kB in 0s (4099 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpppu7post/libquadmath0_15.2.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.2-1 [772 kB] Fetched 772 kB in 0s (45.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl8c3o70c/autopoint_0.23.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.2-1 [1687 kB] Fetched 1687 kB in 0s (81.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl3h2ww7t/gettext_0.23.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Fetched 76.2 kB in 0s (6972 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfkuj8kf3/libnghttp2-14_1.64.0-1.1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnettle8t64 amd64 3.10.2-1 [307 kB] Fetched 307 kB in 0s (24.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp91fzw74z/libnettle8t64_3.10.2-1_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 (2692 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3o3eq9vc/python3-cftime_1.6.5-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.2.2-4 [36.2 kB] Fetched 36.2 kB in 0s (686 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6uc0xn9u/python3-build_1.2.2-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251223T083714Z sid/main amd64 sphinx-common all 8.2.3-11 [619 kB] Fetched 619 kB in 0s (5374 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6cnz2767/sphinx-common_8.2.3-11_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.14-dev amd64 3.14.2-1+b1 [5429 kB] Fetched 5429 kB in 0s (32.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwanrc_bj/libpython3.14-dev_3.14.2-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4 [1436 B] Fetched 1436 B in 0s (0 B/s) dpkg-name: info: moved 'gcc-x86-64-linux-gnu_4%3a15.2.0-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpv2ne_6m7/gcc-x86-64-linux-gnu_15.2.0-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.14 amd64 3.14.2-1+b1 [2374 kB] Fetched 2374 kB in 0s (27.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5t108iam/libpython3.14_3.14.2-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4 [5292 B] Fetched 5292 B in 0s (0 B/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a15.2.0-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp72frsg8w/cpp-x86-64-linux-gnu_15.2.0-4_amd64.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 (3089 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8k385oxn/libkrb5support0_1.22.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpcre2-8-0 amd64 10.46-1 [298 kB] Fetched 298 kB in 0s (25.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi83rumsy/libpcre2-8-0_10.46-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 grep amd64 3.12-1 [443 kB] Fetched 443 kB in 0s (32.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpijfuxu1o/grep_3.12-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 python3-bs4 all 4.14.3-1 [118 kB] Fetched 118 kB in 0s (4346 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1rtulgro/python3-bs4_4.14.3-1_all.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 (12.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4mk6lqnk/libngtcp2-16_1.16.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssl-provider-legacy amd64 3.5.4-1 [308 kB] Fetched 308 kB in 0s (23.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbw_3nq5r/openssl-provider-legacy_3.5.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.4-2 [23.8 kB] Fetched 23.8 kB in 0s (862 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwwd96upv/libaec0_1.1.4-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-tornado amd64 6.5.2-3 [356 kB] Fetched 356 kB in 0s (5191 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp1onhk3h/python3-tornado_6.5.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-2 [131 kB] Fetched 131 kB in 0s (12.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqfct37s_/libbsd0_0.12.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.9-2 [10.7 kB] Fetched 10.7 kB in 0s (136 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4s_q0lnq/libpython3-dev_3.13.9-2_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 (564 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiatyiw9h/python3-markupsafe_3.0.3-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.10-1 [444 kB] Fetched 444 kB in 0s (29.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcleorie8/libp11-kit0_0.25.10-1_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 (6761 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxhwsr_qp/libdb5.3t64_5.3.28+dfsg2-11_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libubsan1 amd64 15.2.0-10 [1108 kB] Fetched 1108 kB in 0s (7044 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm06tej_z/libubsan1_15.2.0-10_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 (6514 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2xw6ss6t/libnghttp3-9_1.12.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libsframe2 amd64 2.45.50.20251201-1 [80.2 kB] Fetched 80.2 kB in 0s (1962 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvpurnq5w/libsframe2_2.45.50.20251201-1_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 (21.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr9ab_qwx/libhogweed6t64_3.10.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.16.3-2 [18.6 MB] Fetched 18.6 MB in 1s (33.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzsbg_za1/python3-scipy_1.16.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-10 [23.4 MB] Fetched 23.4 MB in 1s (31.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpot9__ohi/gcc-15-x86-64-linux-gnu_15.2.0-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 dpkg-dev all 1.22.21 [1338 kB] Fetched 1338 kB in 0s (65.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphf3zr9rv/dpkg-dev_1.22.21_all.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 (7976 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphiwo6fgz/dash_0.5.12-12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm-compat4t64 amd64 1.26-1 [52.8 kB] Fetched 52.8 kB in 0s (4418 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8koexxnc/libgdbm-compat4t64_1.26-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-nbconvert all 7.16.6-1 [160 kB] Fetched 160 kB in 0s (1160 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa7imo862/python3-nbconvert_7.16.6-1_all.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 (1020 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8zxzl96h/python3-gsd_4.2.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtinfo6 amd64 6.5+20251123-1 [353 kB] Fetched 353 kB in 0s (27.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx79o5g4r/libtinfo6_6.5+20251123-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 patch amd64 2.8-2 [134 kB] Fetched 134 kB in 0s (11.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxf9a37gh/patch_2.8-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 liblsan0 amd64 15.2.0-10 [1248 kB] Fetched 1248 kB in 0s (9857 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdrj02psg/liblsan0_15.2.0-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 python3-docutils all 0.22.3+dfsg-1 [432 kB] Fetched 432 kB in 0s (5619 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmxswm6q9/python3-docutils_0.22.3+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 python3-pytest all 8.4.2-1 [266 kB] Fetched 266 kB in 0s (7712 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdxbrsb7z/python3-pytest_8.4.2-1_all.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 (1627 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw4oo6fcl/libfile-stripnondeterminism-perl_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Fetched 215 kB in 0s (4518 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgu_05w39/libblas3_3.12.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-base all 6.5+20251123-1 [277 kB] Fetched 277 kB in 0s (14.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpelbtk6z2/ncurses-base_6.5+20251123-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 coreutils amd64 9.7-3 [3024 kB] Fetched 3024 kB in 0s (103 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp07h9x3s0/coreutils_9.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libgomp1 amd64 15.2.0-10 [140 kB] Fetched 140 kB in 0s (4297 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8j4cslpb/libgomp1_15.2.0-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 dh-python all 6.20251204.1 [114 kB] Fetched 114 kB in 0s (3107 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjm8yeqkh/dh-python_6.20251204.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.10-1 [42.0 kB] Fetched 42.0 kB in 0s (1065 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6jnrwnld/python3-idna_3.10-1_all.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 (3249 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpue00murk/python3-jinja2_3.1.6-1_all.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 (492 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt_8p9qxf/python3-installer_0.7.0+dfsg1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.11-1+b1 [2185 kB] Fetched 2185 kB in 0s (22.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6vus0s9t/libpython3.13_3.13.11-1+b1_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 (122 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc4vq7lkl/libjs-mathjax_2.7.9+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB] Fetched 45.1 kB in 0s (2349 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm_davkav/python3-nbformat_5.9.1-1_all.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 (2602 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9s2pnxtv/sensible-utils_0.0.26_all.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 (563 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1pxbw8gy/xml-core_0.19_all.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 (2366 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt1s9txdu/python3-dateutil_2.9.0-4_all.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 (3865 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4_fr3jti/python3-babel_2.17.0-2_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 (4143 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpel_in4qu/python3-charset-normalizer_3.4.4-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-4 [72.6 kB] Fetched 72.6 kB in 0s (4285 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp239p0pdf/libhdf5-hl-310_1.14.5+repack-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libattr1 amd64 1:2.5.2-3 [22.9 kB] Fetched 22.9 kB in 0s (2003 kB/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpeiuhkh2v/libattr1_2.5.2-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libc-dev-bin amd64 2.42-5 [60.3 kB] Fetched 60.3 kB in 0s (2145 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmgpafqe8/libc-dev-bin_2.42-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.14-stdlib amd64 3.14.2-1+b1 [2258 kB] Fetched 2258 kB in 0s (18.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprv5s6knp/libpython3.14-stdlib_3.14.2-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.11-1+b1 [1968 kB] Fetched 1968 kB in 0s (29.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg4omey82/libpython3.13-stdlib_3.13.11-1+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 (23.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3tqu9e7d/python3-networkx_3.4.2-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-client all 8.6.3-3 [92.4 kB] Fetched 92.4 kB in 0s (3562 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp51iclqy0/python3-jupyter-client_8.6.3-3_all.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 (97.0 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaassbdqv/python3-jsonschema-specifications_2023.12.1-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Fetched 49.9 kB in 0s (4388 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjgorg93j/libtasn1-6_4.20.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.11-1+b1 [5296 kB] Fetched 5296 kB in 1s (9536 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyseu5y5r/libpython3.13-dev_3.13.11-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 debhelper all 13.28 [941 kB] Fetched 941 kB in 0s (60.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuaw54fy1/debhelper_13.28_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-files amd64 14 [72.9 kB] Fetched 72.9 kB in 0s (6036 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa187qkxg/base-files_14_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libc-bin amd64 2.42-5 [674 kB] Fetched 674 kB in 0s (4323 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgbv37oyw/libc-bin_2.42-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.11-1+b1 [504 kB] Fetched 504 kB in 0s (8389 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzkhd_jaf/python3.13-dev_3.13.11-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libctf0 amd64 2.45.50.20251201-1 [92.4 kB] Fetched 92.4 kB in 0s (1675 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphw7evj05/libctf0_2.45.50.20251201-1_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 (5391 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmparupo2xe/python3-rpds-py_0.28.0-1_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 (4794 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqbti1nkk/base-passwd_3.6.8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssl3t64 amd64 3.5.4-1 [2446 kB] Fetched 2446 kB in 0s (85.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmuicl055/libssl3t64_3.5.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbz2-1.0 amd64 1.0.8-6 [37.9 kB] Fetched 37.9 kB in 0s (3179 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6iuu0r2s/libbz2-1.0_1.0.8-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 920 kB in 0s (55.5 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp5hof_li3/zlib1g-dev_1.3.dfsg+really1.3.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libdebconfclient0 amd64 0.282 [10.9 kB] Fetched 10.9 kB in 0s (839 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsibmsn49/libdebconfclient0_0.282_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblz4-1 amd64 1.10.0-6 [70.5 kB] Fetched 70.5 kB in 0s (1692 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp87pe76xe/liblz4-1_1.10.0-6_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 (11.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_a7n3dgz/libgssapi-krb5-2_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 (1921 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmsaukh6k/libsasl2-modules-db_2.1.28+dfsg1-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libasan8 amd64 15.2.0-10 [2779 kB] Fetched 2779 kB in 0s (18.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp40j1j50e/libasan8_15.2.0-10_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 (1880 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp01w_p6bn/python3-defusedxml_0.7.1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++ amd64 4:15.2.0-4 [1344 B] Fetched 1344 B in 0s (0 B/s) dpkg-name: info: moved 'g++_4%3a15.2.0-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp94ud4ki9/g++_15.2.0-4_amd64.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 (9565 kB/s) dpkg-name: info: moved 'libcrypt1_1%3a4.5.1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp8b_1m50i/libcrypt1_4.5.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b9 [304 kB] Fetched 304 kB in 0s (6700 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw3iawwbu/libbrotli1_1.1.0-2+b9_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 0s (341 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph5cr_299/sgml-base_1.31+nmu1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libudev1 amd64 259~rc2-1 [157 kB] Fetched 157 kB in 0s (13.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjdlr2wzq/libudev1_259~rc2-1_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 (6559 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkybprto2/libtool_2.5.4-9_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 xz-utils amd64 5.8.1-2 [660 kB] Fetched 660 kB in 0s (43.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc98x2j9s/xz-utils_5.8.1-2_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 (4506 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2jgpmd8m/libk5crypto3_1.22.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libzstd1 amd64 1.5.7+dfsg-2 [308 kB] Fetched 308 kB in 0s (21.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0ikuaz8s/libzstd1_1.5.7+dfsg-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnetcdf22 amd64 1:4.9.3-1+b1 [517 kB] Fetched 517 kB in 0s (18.2 MB/s) dpkg-name: info: moved 'libnetcdf22_1%3a4.9.3-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpw5wwj0ug/libnetcdf22_4.9.3-1+b1_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 0s (18.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqm51g21w/python3-pandas_2.3.3+dfsg-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsodium23 amd64 1.0.18-1+b2 [165 kB] Fetched 165 kB in 0s (5067 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuhjvn0hk/libsodium23_1.0.18-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 bsdextrautils amd64 2.41.2-4 [98.5 kB] Fetched 98.5 kB in 0s (8602 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6q5jaxy1/bsdextrautils_2.41.2-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 pybuild-plugin-pyproject all 6.20251204.1 [12.3 kB] Fetched 12.3 kB in 0s (402 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplr69tovf/pybuild-plugin-pyproject_6.20251204.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-nbclient all 0.8.0-3 [62.3 kB] Fetched 62.3 kB in 0s (1302 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsdb1lfzs/python3-nbclient_0.8.0-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm6t64 amd64 1.26-1 [78.5 kB] Fetched 78.5 kB in 0s (6423 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbap8r8rl/libgdbm6t64_1.26-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Fetched 494 kB in 0s (38.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpor5sdvjq/autoconf_2.72-3.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Fetched 216 kB in 0s (8772 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpif91gdmd/po-debconf_1.0.22_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libctf-nobfd0 amd64 2.45.50.20251201-1 [160 kB] Fetched 160 kB in 0s (3263 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxycsv5ls/libctf-nobfd0_2.45.50.20251201-1_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 (3204 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9ile_qz_/init-system-helpers_1.69_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 liblzma5 amd64 5.8.1-2 [310 kB] Fetched 310 kB in 0s (26.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4pmt5_x1/liblzma5_5.8.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 python3-roman-numerals all 3.1.0-2 [8740 B] Fetched 8740 B in 0s (288 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp28mbp480/python3-roman-numerals_3.1.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-3 [878 kB] Fetched 878 kB in 0s (56.7 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-3_all.deb' to '/srv/rebuilderd/tmp/tmpugfwe_gs/automake_1.18.1-3_all.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 (79.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp949s9nri/perl-modules-5.40_5.40.1-7_all.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 (1852 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoj3ihp0p/python3-decorator_5.2.1-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Fetched 74.8 kB in 0s (6679 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfjrc8d0q/readline-common_8.3-3_all.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 (322 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqvj7uyyq/python3-imagesize_1.4.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.3.5+ds-2+b1 [7491 kB] Fetched 7491 kB in 1s (13.6 MB/s) dpkg-name: info: moved 'python3-numpy_1%3a2.3.5+ds-2+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpnwdze2vv/python3-numpy_2.3.5+ds-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 tar amd64 1.35+dfsg-3.1 [815 kB] Fetched 815 kB in 0s (50.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkhff1gte/tar_1.35+dfsg-3.1_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 (1094 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmss24k6k/python3-nbsphinx_0.9.5+ds-1_all.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 (562 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp565q24qr/python3-pyproject-hooks_1.2.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc amd64 4:15.2.0-4 [5160 B] Fetched 5160 B in 0s (448 kB/s) dpkg-name: info: moved 'gcc_4%3a15.2.0-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp5fxm0b73/gcc_15.2.0-4_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 (1257 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8kwb4zns/python3-bleach_6.3.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Fetched 43.6 kB in 0s (3843 kB/s) dpkg-name: info: moved 'file_1%3a5.46-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp1eyz5yw3/file_5.46-5_amd64.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 (5124 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3s131cyb/python3-psutil_7.1.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsqlite3-0 amd64 3.46.1-8 [968 kB] Fetched 968 kB in 0s (53.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsg7extv0/libsqlite3-0_3.46.1-8_amd64.deb' Downloading dependency 129 of 318: libcom-err2:amd64=1.47.2-3+b4 Downloading dependency 130 of 318: python3-mistune:amd64=3.1.4-1 Downloading dependency 131 of 318: libdebhelper-perl:amd64=13.28 Downloading dependency 132 of 318: gcc-15-base:amd64=15.2.0-10 Downloading dependency 133 of 318: g++-15:amd64=15.2.0-10 Downloading dependency 134 of 318: libcrypt-dev:amd64=1:4.5.1-1 Downloading dependency 135 of 318: 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dependency 227 of 318: libzstd1:amd64=1.5.7+dfsg-2 Downloading dependency 228 of 318: libnetcdf22:amd64=1:4.9.3-1+b1 Downloading dependency 229 of 318: python3-pandas:amd64=2.3.3+dfsg-3 Downloading dependency 230 of 318: libsodium23:amd64=1.0.18-1+b2 Downloading dependency 231 of 318: bsdextrautils:amd64=2.41.2-4 Downloading dependency 232 of 318: pybuild-plugin-pyproject:amd64=6.20251204.1 Downloading dependency 233 of 318: python3-nbclient:amd64=0.8.0-3 Downloading dependency 234 of 318: libgdbm6t64:amd64=1.26-1 Downloading dependency 235 of 318: autoconf:amd64=2.72-3.1 Downloading dependency 236 of 318: po-debconf:amd64=1.0.22 Downloading dependency 237 of 318: libctf-nobfd0:amd64=2.45.50.20251201-1 Downloading dependency 238 of 318: init-system-helpers:amd64=1.69 Downloading dependency 239 of 318: liblzma5:amd64=5.8.1-2 Downloading dependency 240 of 318: python3-roman-numerals:amd64=3.1.0-2 Downloading dependency 241 of 318: automake:amd64=1:1.18.1-3 Downloading dependency 242 of 318: perl-modules-5.40:amd64=5.40.1-7 Downloading dependency 243 of 318: python3-decorator:amd64=5.2.1-2 Downloading dependency 244 of 318: readline-common:amd64=8.3-3 Downloading dependency 245 of 318: python3-imagesize:amd64=1.4.1-1 Downloading dependency 246 of 318: python3-numpy:amd64=1:2.3.5+ds-2+b1 Downloading dependency 247 of 318: tar:amd64=1.35+dfsg-3.1 Downloading dependency 248 of 318: python3-nbsphinx:amd64=0.9.5+ds-1 Downloading dependency 249 of 318: python3-pyproject-hooks:amd64=1.2.0-1 Downloading dependency 250 of 318: gcc:amd64=4:15.2.0-4 Downloading dependency 251 of 318: python3-bleach:amd64=6.3.0-1 Downloading dependency 252 of 318: file:amd64=1:5.46-5 Downloading dependency 253 of 318: python3-psutil:amd64=7.1.0-1 Downloading dependency 254 of 318: libsqlite3-0:amd64=3.46.1-8 Downloading dependency 255 of 318: diffutils:amd64=1:3.12-1Get:1 http://deb.debian.org/debian unstable/main amd64 diffutils amd64 1:3.12-1 [405 kB] Fetched 405 kB in 0s (30.7 MB/s) dpkg-name: info: moved 'diffutils_1%3a3.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp7je17w8w/diffutils_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-2 [325 kB] Fetched 325 kB in 0s (19.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq_z9jsm8/m4_1.4.20-2_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 (2049 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6osyi2oo/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-core all 5.7.2-5 [35.3 kB] Fetched 35.3 kB in 0s (1480 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4iyoygd7/python3-jupyter-core_5.7.2-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libgcc-15-dev amd64 15.2.0-10 [2718 kB] Fetched 2718 kB in 0s (8288 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaxmea94c/libgcc-15-dev_15.2.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python-tables-data all 3.10.2-3 [47.3 kB] Fetched 47.3 kB in 0s (1828 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuuxx5ajn/python-tables-data_3.10.2-3_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 (1708 kB/s) dpkg-name: info: moved 'libaudit1_1%3a4.1.2-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp1v4qfhmu/libaudit1_4.1.2-1+b1_amd64.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 (560 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp12djnkrv/python3-pandocfilters_1.5.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libuuid1 amd64 2.41.2-4 [38.7 kB] Fetched 38.7 kB in 0s (3329 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt68lrky9/libuuid1_2.41.2-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.11-1+b1 [866 kB] Fetched 866 kB in 0s (14.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw0py93ab/libpython3.13-minimal_3.13.11-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libacl1 amd64 2.3.2-2+b1 [32.9 kB] Fetched 32.9 kB in 0s (3156 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaytavphn/libacl1_2.3.2-2+b1_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/tmpa8048tt1/dwz_0.16-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 python3-soupsieve all 2.7-2 [39.0 kB] Fetched 39.0 kB in 0s (2234 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo_2nd2po/python3-soupsieve_2.7-2_all.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 (22.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsf6m0uqz/python3-setuptools_78.1.1-0.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 python3-pluggy all 1.6.0-1 [27.1 kB] Fetched 27.1 kB in 0s (2560 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx8vi8w38/python3-pluggy_1.6.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-2+b1 [139 kB] Fetched 139 kB in 0s (2497 kB/s) dpkg-name: info: moved 'python3-numpy-dev_1%3a2.3.5+ds-2+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpn1odbcoy/python3-numpy-dev_2.3.5+ds-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libhwasan0 amd64 15.2.0-10 [1538 kB] Fetched 1538 kB in 0s (13.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp51vkbdfy/libhwasan0_15.2.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python-tinycss2-common all 1.4.0-2 [44.7 kB] Fetched 44.7 kB in 0s (1488 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpou7lccex/python-tinycss2-common_1.4.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libstdc++6 amd64 15.2.0-10 [736 kB] Fetched 736 kB in 0s (8192 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphs1ecxbx/libstdc++6_15.2.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Fetched 185 kB in 0s (15.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpurl3y98d/libelf1t64_0.194-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 build-essential amd64 12.12 [4624 B] Fetched 4624 B in 0s (439 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd46ig5ha/build-essential_12.12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpfr6 amd64 4.2.2-2 [742 kB] Fetched 742 kB in 0s (47.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvz4w9yrt/libmpfr6_4.2.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.46.1-2 [21.7 kB] Fetched 21.7 kB in 0s (439 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3vwblohb/python3-wheel_0.46.1-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules-bin amd64 1.7.0-5 [49.1 kB] Fetched 49.1 kB in 0s (4695 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5pqs0mg9/libpam-modules-bin_1.7.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.14-minimal amd64 3.14.2-1+b1 [896 kB] Fetched 896 kB in 0s (4359 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjcupj3nf/libpython3.14-minimal_3.14.2-1+b1_amd64.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 (14.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxzio8ya4/cython3_3.1.6+dfsg-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 binutils amd64 2.45.50.20251201-1 [281 kB] Fetched 281 kB in 0s (3049 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxt0c8ag4/binutils_2.45.50.20251201-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcap-ng0 amd64 0.8.5-4+b2 [17.5 kB] Fetched 17.5 kB in 0s (481 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpghj3rd6t/libcap-ng0_0.8.5-4+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1+b1 [162 kB] Fetched 162 kB in 0s (5805 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps9pf_5kq/libpgm-5.3-0t64_5.3.128~dfsg-2.1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Fetched 338 kB in 0s (24.5 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.46-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp4m1mlllf/libmagic-mgc_5.46-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Fetched 57.2 kB in 0s (5321 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyv3ifokq/libpsl5t64_0.21.2-1.1+b1_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 (1301 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiw0s8gp8/python3-inflect_7.5.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Fetched 6096 B in 0s (204 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6ch9sp9k/python3-jupyterlab-pygments_0.2.2-3_all.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 (998 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpryu1w9c1/python3-referencing_0.36.2-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4 [1196 B] Fetched 1196 B in 0s (115 kB/s) dpkg-name: info: moved 'g++-x86-64-linux-gnu_4%3a15.2.0-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpfxeg0g9g/g++-x86-64-linux-gnu_15.2.0-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libcc1-0 amd64 15.2.0-10 [42.7 kB] Fetched 42.7 kB in 0s (711 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2axh__ig/libcc1-0_15.2.0-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 util-linux amd64 2.41.2-4 [1163 kB] Fetched 1163 kB in 0s (69.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr78w3f4s/util-linux_2.41.2-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 docutils-common all 0.22.3+dfsg-1 [128 kB] Fetched 128 kB in 0s (3310 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6kmrahsv/docutils-common_0.22.3+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-traitlets all 5.14.3+really5.14.3-2 [71.1 kB] Fetched 71.1 kB in 0s (1103 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpljhp0u_i/python3-traitlets_5.14.3+really5.14.3-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bash amd64 5.3-1 [1556 kB] Fetched 1556 kB in 0s (56.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf0f0qrn7/bash_5.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.9-2 [27.5 kB] Fetched 27.5 kB in 0s (1104 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5op8i116/python3-minimal_3.13.9-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Fetched 56.6 kB in 0s (1839 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdrntdo8g/python3-packaging_25.0-1_all.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 (63.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprdk8ab1y/man-db_2.13.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmd0 amd64 1.1.0-2+b1 [36.3 kB] Fetched 36.3 kB in 0s (3577 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw5p2x_w1/libmd0_1.1.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Fetched 836 kB in 0s (12.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvfdf19dl/python3-pygments_2.18.0+dfsg-2_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 (1511 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp66l9k_f/python3-zmq_27.1.0-1+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 (7688 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa5ab4h_1/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libzmq5 amd64 4.3.5-1+b3 [283 kB] Fetched 283 kB in 0s (7781 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy9qnd9_s/libzmq5_4.3.5-1+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libc-gconv-modules-extra amd64 2.42-5 [1127 kB] Fetched 1127 kB in 0s (8194 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptxo4d7a_/libc-gconv-modules-extra_2.42-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Fetched 477 kB in 0s (33.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8tfdnpyn/libunistring5_1.3-2_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 (1292 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmxhu2j8s/python3-fastjsonschema_2.21.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sed amd64 4.9-2 [329 kB] Fetched 329 kB in 0s (26.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk1o8tgru/sed_4.9-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Fetched 191 kB in 0s (15.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmur29qxx/libreadline8t64_8.3-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libatomic1 amd64 15.2.0-10 [9496 B] Fetched 9496 B in 0s (464 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyi1_m_kl/libatomic1_15.2.0-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251207T204132Z sid/main amd64 libc6-dev amd64 2.42-5 [2091 kB] Fetched 2091 kB in 0s (9892 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa7muqo2z/libc6-dev_2.42-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251223T083714Z sid/main amd64 libjs-sphinxdoc all 8.2.3-11 [27.8 kB] Fetched 27.8 kB in 0s (378 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6l9rtt93/libjs-sphinxdoc_8.2.3-11_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-cffi-backend amd64 2.0.0-2+b1 [112 kB] Fetched 112 kB in 0s (3331 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpauzeuhwv/python3-cffi-backend_2.0.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Fetched 194 kB in 0s (17.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnxfjhusz/libldap2_2.6.10+dfsg-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Fetched 12.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpreevwite/dh-autoreconf_21_all.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 (509 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfgnwya1c/python3-jaraco.text_4.0.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.5.0-1 [116 kB] Fetched 116 kB in 0s (3901 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_h7sao8d/python3-urllib3_2.5.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Fetched 9456 B in 0s (792 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6wub5ec8/libkeyutils1_1.6.3-6_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 (2588 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptqrisv6t/libngtcp2-crypto-ossl0_1.16.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libisl23 amd64 0.27-1 [659 kB] Fetched 659 kB in 0s (44.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2y2h6xy3/libisl23_0.27-1_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-buildpackage: info: host architecture amd64 dpkg-source --before-build . debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/debootsnap-dummy/ dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'debootsnap-dummy' in '../debootsnap-dummy_1.0_all.deb'. dpkg-genbuildinfo --build=binary -O../debootsnap-dummy_1.0_amd64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) The package has been created. Attention, the package has been created in the /srv/rebuilderd/tmp/tmpxrdbk9os/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.8zzKtyhNy4 as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.8zzKtyhNy4 127.0.0.1 - - [27/Dec/2025 15:37:42] code 404, message File not found 127.0.0.1 - - [27/Dec/2025 15:37:42] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:35125 ./ InRelease 127.0.0.1 - - [27/Dec/2025 15:37:42] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:35125 ./ Release [462 B] 127.0.0.1 - - [27/Dec/2025 15:37:42] code 404, message File not found 127.0.0.1 - - [27/Dec/2025 15:37:42] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:35125 ./ Release.gpg 127.0.0.1 - - [27/Dec/2025 15:37:42] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:35125 ./ Packages [397 kB] Fetched 398 kB in 0s (18.5 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 - 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I: extracting archives... I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.8zzKtyhNy4 127.0.0.1 - - [27/Dec/2025 15:37:44] code 404, message File not found 127.0.0.1 - - [27/Dec/2025 15:37:44] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:35125 ./ InRelease 127.0.0.1 - - [27/Dec/2025 15:37:44] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:35125 ./ Release 127.0.0.1 - - [27/Dec/2025 15:37:44] code 404, message File not found 127.0.0.1 - - [27/Dec/2025 15:37:44] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:35125 ./ 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 - - [27/Dec/2025 15:38:00] "GET /./python3-jupyter-client_8.6.3-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:00] "GET /./python3-fastjsonschema_2.21.1-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:00] "GET /./python3-nbformat_5.9.1-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:00] "GET /./python3-nbclient_0.8.0-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:00] "GET /./python3-pandocfilters_1.5.1-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:00] "GET /./python3-nbconvert_7.16.6-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:00] "GET /./python3-gsd_4.2.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:00] "GET /./dh-python_6.20251204.1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:00] "GET /./python3-installer_0.7.0%2bdfsg1-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:00] "GET /./libjs-mathjax_2.7.9%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:00] "GET /./python3-networkx_3.4.2-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:01] "GET /./python3-pandas_2.3.3%2bdfsg-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:01] "GET /./pybuild-plugin-pyproject_6.20251204.1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:01] "GET /./python3-nbsphinx_0.9.5%2bds-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Dec/2025 15:38:01] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpxrdbk9os/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.8zzKtyhNy4 Reading package lists... Building dependency tree... Reading state information... cpp is already the newest version (4:15.2.0-4). cpp set to manually installed. mawk is already the newest version (1.3.4.20250131-1). python3-webencodings is already the newest version (0.5.1-5). python3-webencodings set to manually installed. libpam-modules is already the newest version (1.7.0-5). libmpc3 is already the newest version (1.3.1-2). libmpc3 set to manually installed. librtmp1 is already the newest version (2.4+20151223.gitfa8646d.1-3). librtmp1 set to manually installed. libexpat1 is already the newest version (2.7.3-1). libexpat1 set to manually installed. libhdf5-310 is already the newest version (1.14.5+repack-4). libhdf5-310 set to manually installed. sysvinit-utils is already the newest version (3.15-6). hostname is already the newest version (3.25). python3-all is already the newest version (3.13.9-2). python3-all set to manually installed. libuchardet0 is already the newest version (0.0.8-2). libuchardet0 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-typeguard is already the newest version (4.4.4-1). python3-typeguard set to manually installed. python3-requests is already the newest version (2.32.5+dfsg-1). python3-requests set to manually installed. python3.14-minimal is already the newest version (3.14.2-1+b1). python3.14-minimal set to manually installed. libsmartcols1 is already the newest version (2.41.2-4). python3-html5lib is already the newest version (1.2-2). python3-html5lib set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). ncurses-bin is already the newest version (6.5+20251123-1). autotools-dev is already the newest version (20240727.1). autotools-dev set to manually installed. libperl5.40 is already the newest version (5.40.1-7). libperl5.40 set to manually installed. libssh2-1t64 is already the newest version (1.11.1-1). libssh2-1t64 set to manually installed. dh-strip-nondeterminism is already the newest version (1.15.0-1). dh-strip-nondeterminism set to manually installed. python3-autocommand is already the newest version (2.2.2-3). python3-autocommand set to manually installed. libmagic1t64 is already the newest version (1:5.46-5). libmagic1t64 set to manually installed. perl-base is already the newest version (5.40.1-7). libffi8 is already the newest version (3.5.2-3). libffi8 set to manually installed. libcap2 is already the newest version (1:2.75-10+b2). libxxhash0 is already the newest version (0.8.3-2). libxxhash0 set to manually installed. python3-more-itertools is already the newest version (10.8.0-1). python3-more-itertools set to manually installed. tzdata is already the newest version (2025b-5). tzdata set to manually installed. libsnappy1v5 is already the newest version (1.2.2-2). libsnappy1v5 set to manually installed. python3-numexpr is already the newest version (2.14.1-1+b1). python3-numexpr set to manually installed. python3-jsonschema is already the newest version (4.25.1-2). python3-jsonschema set to manually installed. libpam0g is already the newest version (1.7.0-5). libseccomp2 is already the newest version (2.6.0-2+b1). libseccomp2 set to manually installed. groff-base is already the newest version (1.23.0-10). groff-base set to manually installed. python3-pyparsing is already the newest version (3.1.3-1). python3-pyparsing set to manually installed. python3-snowballstemmer is already the newest version (3.0.1-1). python3-snowballstemmer set to manually installed. python3-iniconfig is already the newest version (2.1.0-1). python3-iniconfig set to manually installed. liblapack3 is already the newest version (3.12.1-7). liblapack3 set to manually installed. libtsan2 is already the newest version (15.2.0-10). libtsan2 set to manually installed. python3-tinycss2 is already the newest version (1.4.0-2). python3-tinycss2 set to manually installed. make is already the newest version (4.4.1-3). make set to manually installed. libngtcp2-crypto-gnutls8 is already the newest version (1.16.0-1). libngtcp2-crypto-gnutls8 set to manually installed. python3.14-dev is already the newest version (3.14.2-1+b1). python3.14-dev set to manually installed. debianutils is already the newest version (5.23.2). libgmp10 is already the newest version (2:6.3.0+dfsg-5). libbinutils is already the newest version (2.45.50.20251201-1). libbinutils set to manually installed. libsystemd0 is already the newest version (259~rc2-1). libselinux1 is already the newest version (3.9-4+b1). debconf is already the newest version (1.5.91). libitm1 is already the newest version (15.2.0-10). libitm1 set to manually installed. libmount1 is already the newest version (2.41.2-4). python3-certifi is already the newest version (2025.11.12+ds-1). python3-certifi set to manually installed. python3.13 is already the newest version (3.13.11-1+b1). python3.13 set to manually installed. python3-typing-extensions is already the newest version (4.15.0-1). python3-typing-extensions set to manually installed. python3-platformdirs is already the newest version (4.4.0-1). python3-platformdirs set to manually installed. python3-attr is already the newest version (25.4.0-1). python3-attr set to manually installed. libpython3-stdlib is already the newest version (3.13.9-2). libpython3-stdlib set to manually installed. libblkid1 is already the newest version (2.41.2-4). g++-15-x86-64-linux-gnu is already the newest version (15.2.0-10). g++-15-x86-64-linux-gnu set to manually installed. libgcc-s1 is already the newest version (15.2.0-10). binutils-x86-64-linux-gnu is already the newest version (2.45.50.20251201-1). binutils-x86-64-linux-gnu set to manually installed. python3-jaraco.functools is already the newest version (4.1.0-1). python3-jaraco.functools set to manually installed. bzip2 is already the newest version (1.0.8-6). bzip2 set to manually installed. python3-pytz is already the newest version (2025.2-5). python3-pytz set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-10). libsasl2-2 set to manually installed. liblzo2-2 is already the newest version (2.10-3+b1). liblzo2-2 set to manually installed. libdpkg-perl is already the newest version (1.22.21). libdpkg-perl set to manually installed. gzip is already the newest version (1.13-1). python3.13-minimal is already the newest version (3.13.11-1+b1). python3.13-minimal set to manually installed. python3.14 is already the newest version (3.14.2-1+b1). python3.14 set to manually installed. cpp-15-x86-64-linux-gnu is already the newest version (15.2.0-10). cpp-15-x86-64-linux-gnu set to manually installed. libcurl4t64 is already the newest version (8.17.0-3). libcurl4t64 set to manually installed. libpipeline1 is already the newest version (1.5.8-2). libpipeline1 set to manually installed. python3-pytest-rerunfailures is already the newest version (16.1-1). python3-pytest-rerunfailures set to manually installed. ca-certificates is already the newest version (20250419). ca-certificates set to manually installed. libgprofng0 is already the newest version (2.45.50.20251201-1). libgprofng0 set to manually installed. dpkg is already the newest version (1.22.21). libidn2-0 is already the newest version (2.3.8-4). libidn2-0 set to manually installed. libcurl3t64-gnutls is already the newest version (8.17.0-3). libcurl3t64-gnutls set to manually installed. libjson-perl is already the newest version (4.10000-1). libjson-perl set to manually installed. libblosc2-4 is already the newest version (2.17.1+ds-2). libblosc2-4 set to manually installed. openssl is already the newest version (3.5.4-1). openssl set to manually installed. python3-sphinx is already the newest version (8.2.3-11). python3-sphinx set to manually installed. python3-tables is already the newest version (3.10.2-3). python3-tables set to manually installed. linux-libc-dev is already the newest version (6.17.10-1). linux-libc-dev set to manually installed. libaudit-common is already the newest version (1:4.1.2-1). libncursesw6 is already the newest version (6.5+20251123-1). libncursesw6 set to manually installed. libxml2-16 is already the newest version (2.15.1+dfsg-2+b1). libxml2-16 set to manually installed. findutils is already the newest version (4.10.0-3). python3-tables-lib is already the newest version (3.10.2-3+b1). python3-tables-lib set to manually installed. cpp-15 is already the newest version (15.2.0-10). cpp-15 set to manually installed. libjansson4 is already the newest version (2.14-2+b3). libjansson4 set to manually installed. python3-versioneer is already the newest version (0.29-1). python3-versioneer set to manually installed. libexpat1-dev is already the newest version (2.7.3-1). libexpat1-dev set to manually installed. python3-chardet is already the newest version (5.2.0+dfsg-2). python3-chardet set to manually installed. gettext-base is already the newest version (0.23.2-1). gettext-base set to manually installed. libnorm1t64 is already the newest version (1.5.9+dfsg-4). libnorm1t64 set to manually installed. python3-dev is already the newest version (3.13.9-2). python3-dev set to manually installed. libc6 is already the newest version (2.42-5). libsz2 is already the newest version (1.1.4-2). libsz2 set to manually installed. python3-cpuinfo is already the newest version (9.0.0+git20221119-3). python3-cpuinfo set to manually installed. netbase is already the newest version (6.5). netbase set to manually installed. python3-all-dev is already the newest version (3.13.9-2). python3-all-dev set to manually installed. perl is already the newest version (5.40.1-7). perl set to manually installed. python3-jaraco.context is already the newest version (6.0.1-1). python3-jaraco.context set to manually installed. libblosc1 is already the newest version (1.21.5+ds-2). libblosc1 set to manually installed. rpcsvc-proto is already the newest version (1.4.3-1). rpcsvc-proto set to manually installed. binutils-common is already the newest version (2.45.50.20251201-1). binutils-common set to manually installed. media-types is already the newest version (14.0.0). media-types set to manually installed. libgnutls30t64 is already the newest version (3.8.11-3). libgnutls30t64 set to manually installed. fonts-mathjax is already the newest version (2.7.9+dfsg-1). fonts-mathjax set to manually installed. python3-zipp is already the newest version (3.23.0-1). python3-zipp set to manually installed. python3-alabaster is already the newest version (0.7.16-0.1). python3-alabaster set to manually installed. libqhull-r8.0 is already the newest version (2020.2-7). libqhull-r8.0 set to manually installed. python-babel-localedata is already the newest version (2.17.0-2). python-babel-localedata set to manually installed. gcc-15 is already the newest version (15.2.0-10). gcc-15 set to manually installed. libgfortran5 is already the newest version (15.2.0-10). libgfortran5 set to manually installed. python3-netcdf4 is already the newest version (1.7.3-1+b1). python3-netcdf4 set to manually installed. python3-pkg-resources is already the newest version (78.1.1-0.1). python3-pkg-resources set to manually installed. python3 is already the newest version (3.13.9-2). python3 set to manually installed. libpam-runtime is already the newest version (1.7.0-5). libkrb5-3 is already the newest version (1.22.1-2). libkrb5-3 set to manually installed. libstdc++-15-dev is already the newest version (15.2.0-10). libstdc++-15-dev set to manually installed. libpython3-all-dev is already the newest version (3.13.9-2). libpython3-all-dev set to manually installed. libcom-err2 is already the newest version (1.47.2-3+b4). libcom-err2 set to manually installed. python3-mistune is already the newest version (3.1.4-1). python3-mistune set to manually installed. libdebhelper-perl is already the newest version (13.28). libdebhelper-perl set to manually installed. gcc-15-base is already the newest version (15.2.0-10). g++-15 is already the newest version (15.2.0-10). g++-15 set to manually installed. libcrypt-dev is already the newest version (1:4.5.1-1). libcrypt-dev set to manually installed. libquadmath0 is already the newest version (15.2.0-10). libquadmath0 set to manually installed. autopoint is already the newest version (0.23.2-1). autopoint set to manually installed. gettext is already the newest version (0.23.2-1). gettext set to manually installed. libnghttp2-14 is already the newest version (1.64.0-1.1+b1). libnghttp2-14 set to manually installed. libnettle8t64 is already the newest version (3.10.2-1). libnettle8t64 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 (1.2.2-4). python3-build set to manually installed. sphinx-common is already the newest version (8.2.3-11). sphinx-common set to manually installed. libpython3.14-dev is already the newest version (3.14.2-1+b1). libpython3.14-dev set to manually installed. gcc-x86-64-linux-gnu is already the newest version (4:15.2.0-4). gcc-x86-64-linux-gnu set to manually installed. libpython3.14 is already the newest version (3.14.2-1+b1). libpython3.14 set to manually installed. cpp-x86-64-linux-gnu is already the newest version (4:15.2.0-4). cpp-x86-64-linux-gnu set to manually installed. libkrb5support0 is already the newest version (1.22.1-2). libkrb5support0 set to manually installed. libpcre2-8-0 is already the newest version (10.46-1). grep is already the newest version (3.12-1). python3-bs4 is already the newest version (4.14.3-1). python3-bs4 set to manually installed. libngtcp2-16 is already the newest version (1.16.0-1). libngtcp2-16 set to manually installed. openssl-provider-legacy is already the newest version (3.5.4-1). libaec0 is already the newest version (1.1.4-2). libaec0 set to manually installed. python3-tornado is already the newest version (6.5.2-3). python3-tornado set to manually installed. libbsd0 is already the newest version (0.12.2-2). libbsd0 set to manually installed. libpython3-dev is already the newest version (3.13.9-2). libpython3-dev set to manually installed. python3-markupsafe is already the newest version (3.0.3-1+b1). python3-markupsafe set to manually installed. libp11-kit0 is already the newest version (0.25.10-1). libp11-kit0 set to manually installed. libdb5.3t64 is already the newest version (5.3.28+dfsg2-11). libubsan1 is already the newest version (15.2.0-10). libubsan1 set to manually installed. libnghttp3-9 is already the newest version (1.12.0-1). libnghttp3-9 set to manually installed. libsframe2 is already the newest version (2.45.50.20251201-1). libsframe2 set to manually installed. libhogweed6t64 is already the newest version (3.10.2-1). libhogweed6t64 set to manually installed. python3-scipy is already the newest version (1.16.3-2). python3-scipy set to manually installed. gcc-15-x86-64-linux-gnu is already the newest version (15.2.0-10). gcc-15-x86-64-linux-gnu set to manually installed. dpkg-dev is already the newest version (1.22.21). dpkg-dev set to manually installed. dash is already the newest version (0.5.12-12). libgdbm-compat4t64 is already the newest version (1.26-1). libgdbm-compat4t64 set to manually installed. python3-nbconvert is already the newest version (7.16.6-1). python3-nbconvert set to manually installed. python3-gsd is already the newest version (4.2.0-1). python3-gsd set to manually installed. libtinfo6 is already the newest version (6.5+20251123-1). patch is already the newest version (2.8-2). patch set to manually installed. liblsan0 is already the newest version (15.2.0-10). liblsan0 set to manually installed. python3-docutils is already the newest version (0.22.3+dfsg-1). python3-docutils set to manually installed. python3-pytest is already the newest version (8.4.2-1). python3-pytest set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.15.0-1). libfile-stripnondeterminism-perl set to manually installed. libblas3 is already the newest version (3.12.1-7). libblas3 set to manually installed. ncurses-base is already the newest version (6.5+20251123-1). coreutils is already the newest version (9.7-3). libgomp1 is already the newest version (15.2.0-10). libgomp1 set to manually installed. dh-python is already the newest version (6.20251204.1). dh-python set to manually installed. python3-idna is already the newest version (3.10-1). python3-idna set to manually installed. python3-jinja2 is already the newest version (3.1.6-1). python3-jinja2 set to manually installed. python3-installer is already the newest version (0.7.0+dfsg1-3). python3-installer set to manually installed. libpython3.13 is already the newest version (3.13.11-1+b1). libpython3.13 set to manually installed. libjs-mathjax is already the newest version (2.7.9+dfsg-1). libjs-mathjax set to manually installed. python3-nbformat is already the newest version (5.9.1-1). python3-nbformat set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils set to manually installed. xml-core is already the newest version (0.19). xml-core set to manually installed. python3-dateutil is already the newest version (2.9.0-4). python3-dateutil set to manually installed. python3-babel is already the newest version (2.17.0-2). python3-babel set to manually installed. python3-charset-normalizer is already the newest version (3.4.4-2). python3-charset-normalizer set to manually installed. libhdf5-hl-310 is already the newest version (1.14.5+repack-4). libhdf5-hl-310 set to manually installed. libattr1 is already the newest version (1:2.5.2-3). libc-dev-bin is already the newest version (2.42-5). libc-dev-bin set to manually installed. libpython3.14-stdlib is already the newest version (3.14.2-1+b1). libpython3.14-stdlib set to manually installed. libpython3.13-stdlib is already the newest version (3.13.11-1+b1). libpython3.13-stdlib set to manually installed. python3-networkx is already the newest version (3.4.2-4). python3-networkx set to manually installed. python3-jupyter-client is already the newest version (8.6.3-3). python3-jupyter-client set to manually installed. python3-jsonschema-specifications is already the newest version (2023.12.1-4). python3-jsonschema-specifications set to manually installed. libtasn1-6 is already the newest version (4.20.0-2). libtasn1-6 set to manually installed. libpython3.13-dev is already the newest version (3.13.11-1+b1). libpython3.13-dev set to manually installed. debhelper is already the newest version (13.28). debhelper set to manually installed. base-files is already the newest version (14). libc-bin is already the newest version (2.42-5). python3.13-dev is already the newest version (3.13.11-1+b1). python3.13-dev set to manually installed. libctf0 is already the newest version (2.45.50.20251201-1). libctf0 set to manually installed. python3-rpds-py is already the newest version (0.28.0-1). python3-rpds-py set to manually installed. base-passwd is already the newest version (3.6.8). libssl3t64 is already the newest version (3.5.4-1). libbz2-1.0 is already the newest version (1.0.8-6). zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). zlib1g-dev set to manually installed. libdebconfclient0 is already the newest version (0.282). liblz4-1 is already the newest version (1.10.0-6). liblz4-1 set to manually installed. libgssapi-krb5-2 is already the newest version (1.22.1-2). libgssapi-krb5-2 set to manually installed. libsasl2-modules-db is already the newest version (2.1.28+dfsg1-10). libsasl2-modules-db set to manually installed. libasan8 is already the newest version (15.2.0-10). libasan8 set to manually installed. python3-defusedxml is already the newest version (0.7.1-3). python3-defusedxml set to manually installed. g++ is already the newest version (4:15.2.0-4). g++ set to manually installed. libcrypt1 is already the newest version (1:4.5.1-1). libbrotli1 is already the newest version (1.1.0-2+b9). libbrotli1 set to manually installed. sgml-base is already the newest version (1.31+nmu1). sgml-base set to manually installed. libudev1 is already the newest version (259~rc2-1). libtool is already the newest version (2.5.4-9). libtool set to manually installed. xz-utils is already the newest version (5.8.1-2). xz-utils set to manually installed. libk5crypto3 is already the newest version (1.22.1-2). libk5crypto3 set to manually installed. libzstd1 is already the newest version (1.5.7+dfsg-2). libnetcdf22 is already the newest version (1:4.9.3-1+b1). libnetcdf22 set to manually installed. python3-pandas is already the newest version (2.3.3+dfsg-3). python3-pandas set to manually installed. libsodium23 is already the newest version (1.0.18-1+b2). libsodium23 set to manually installed. bsdextrautils is already the newest version (2.41.2-4). bsdextrautils set to manually installed. pybuild-plugin-pyproject is already the newest version (6.20251204.1). pybuild-plugin-pyproject set to manually installed. python3-nbclient is already the newest version (0.8.0-3). python3-nbclient set to manually installed. libgdbm6t64 is already the newest version (1.26-1). libgdbm6t64 set to manually installed. autoconf is already the newest version (2.72-3.1). autoconf set to manually installed. po-debconf is already the newest version (1.0.22). po-debconf set to manually installed. libctf-nobfd0 is already the newest version (2.45.50.20251201-1). libctf-nobfd0 set to manually installed. init-system-helpers is already the newest version (1.69). liblzma5 is already the newest version (5.8.1-2). python3-roman-numerals is already the newest version (3.1.0-2). python3-roman-numerals set to manually installed. automake is already the newest version (1:1.18.1-3). automake 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-decorator is already the newest version (5.2.1-2). python3-decorator set to manually installed. readline-common is already the newest version (8.3-3). readline-common set to manually installed. python3-imagesize is already the newest version (1.4.1-1). python3-imagesize set to manually installed. python3-numpy is already the newest version (1:2.3.5+ds-2+b1). python3-numpy set to manually installed. tar is already the newest version (1.35+dfsg-3.1). python3-nbsphinx is already the newest version (0.9.5+ds-1). python3-nbsphinx set to manually installed. python3-pyproject-hooks is already the newest version (1.2.0-1). python3-pyproject-hooks set to manually installed. gcc is already the newest version (4:15.2.0-4). gcc set to manually installed. python3-bleach is already the newest version (6.3.0-1). python3-bleach set to manually installed. file is already the newest version (1:5.46-5). file set to manually installed. python3-psutil is already the newest version (7.1.0-1). python3-psutil set to manually installed. libsqlite3-0 is already the newest version (3.46.1-8). libsqlite3-0 set to manually installed. diffutils is already the newest version (1:3.12-1). m4 is already the newest version (1.4.20-2). m4 set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. python3-jupyter-core is already the newest version (5.7.2-5). python3-jupyter-core set to manually installed. libgcc-15-dev is already the newest version (15.2.0-10). libgcc-15-dev set to manually installed. python-tables-data is already the newest version (3.10.2-3). python-tables-data set to manually installed. libaudit1 is already the newest version (1:4.1.2-1+b1). python3-pandocfilters is already the newest version (1.5.1-1). python3-pandocfilters set to manually installed. libuuid1 is already the newest version (2.41.2-4). libpython3.13-minimal is already the newest version (3.13.11-1+b1). libpython3.13-minimal set to manually installed. libacl1 is already the newest version (2.3.2-2+b1). dwz is already the newest version (0.16-2). dwz set to manually installed. python3-soupsieve is already the newest version (2.7-2). python3-soupsieve set to manually installed. python3-setuptools is already the newest version (78.1.1-0.1). python3-setuptools set to manually installed. python3-pluggy is already the newest version (1.6.0-1). python3-pluggy set to manually installed. python3-numpy-dev is already the newest version (1:2.3.5+ds-2+b1). python3-numpy-dev set to manually installed. libhwasan0 is already the newest version (15.2.0-10). libhwasan0 set to manually installed. python-tinycss2-common is already the newest version (1.4.0-2). python-tinycss2-common set to manually installed. libstdc++6 is already the newest version (15.2.0-10). libstdc++6 set to manually installed. libelf1t64 is already the newest version (0.194-1). libelf1t64 set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. libmpfr6 is already the newest version (4.2.2-2). libmpfr6 set to manually installed. python3-wheel is already the newest version (0.46.1-2). python3-wheel set to manually installed. libpam-modules-bin is already the newest version (1.7.0-5). libpython3.14-minimal is already the newest version (3.14.2-1+b1). libpython3.14-minimal set to manually installed. cython3 is already the newest version (3.1.6+dfsg-2+b1). cython3 set to manually installed. binutils is already the newest version (2.45.50.20251201-1). binutils set to manually installed. libcap-ng0 is already the newest version (0.8.5-4+b2). libpgm-5.3-0t64 is already the newest version (5.3.128~dfsg-2.1+b1). libpgm-5.3-0t64 set to manually installed. libmagic-mgc is already the newest version (1:5.46-5). libmagic-mgc set to manually installed. libpsl5t64 is already the newest version (0.21.2-1.1+b1). libpsl5t64 set to manually installed. python3-inflect is already the newest version (7.5.0-1). python3-inflect set to manually installed. python3-jupyterlab-pygments is already the newest version (0.2.2-3). python3-jupyterlab-pygments set to manually installed. python3-referencing is already the newest version (0.36.2-2). python3-referencing set to manually installed. g++-x86-64-linux-gnu is already the newest version (4:15.2.0-4). g++-x86-64-linux-gnu set to manually installed. libcc1-0 is already the newest version (15.2.0-10). libcc1-0 set to manually installed. util-linux is already the newest version (2.41.2-4). docutils-common is already the newest version (0.22.3+dfsg-1). docutils-common set to manually installed. python3-traitlets is already the newest version (5.14.3+really5.14.3-2). python3-traitlets set to manually installed. bash is already the newest version (5.3-1). python3-minimal is already the newest version (3.13.9-2). python3-minimal set to manually installed. python3-packaging is already the newest version (25.0-1). python3-packaging set to manually installed. man-db is already the newest version (2.13.1-1). man-db set to manually installed. libmd0 is already the newest version (1.1.0-2+b1). python3-pygments is already the newest version (2.18.0+dfsg-2). python3-pygments set to manually installed. python3-zmq is already the newest version (27.1.0-1+b1). python3-zmq set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libzmq5 is already the newest version (4.3.5-1+b3). libzmq5 set to manually installed. libc-gconv-modules-extra is already the newest version (2.42-5). libunistring5 is already the newest version (1.3-2). libunistring5 set to manually installed. python3-fastjsonschema is already the newest version (2.21.1-1). python3-fastjsonschema set to manually installed. sed is already the newest version (4.9-2). libreadline8t64 is already the newest version (8.3-3). libreadline8t64 set to manually installed. libatomic1 is already the newest version (15.2.0-10). libatomic1 set to manually installed. libc6-dev is already the newest version (2.42-5). libc6-dev set to manually installed. libjs-sphinxdoc is already the newest version (8.2.3-11). libjs-sphinxdoc set to manually installed. python3-cffi-backend is already the newest version (2.0.0-2+b1). python3-cffi-backend set to manually installed. libldap2 is already the newest version (2.6.10+dfsg-1). libldap2 set to manually installed. dh-autoreconf is already the newest version (21). dh-autoreconf set to manually installed. python3-jaraco.text is already the newest version (4.0.0-1). python3-jaraco.text set to manually installed. python3-urllib3 is already the newest version (2.5.0-1). python3-urllib3 set to manually installed. libkeyutils1 is already the newest version (1.6.3-6). libkeyutils1 set to manually installed. libngtcp2-crypto-ossl0 is already the newest version (1.16.0-1). libngtcp2-crypto-ossl0 set to manually installed. libisl23 is already the newest version (0.27-1). libisl23 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.8zzKtyhNy4 (Reading database ... 35533 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.8zzKtyhNy4 I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.8zzKtyhNy4 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.8zzKtyhNy4... I: success in 179.5290 seconds Downloading dependency 256 of 318: m4:amd64=1.4.20-2 Downloading dependency 257 of 318: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 258 of 318: python3-jupyter-core:amd64=5.7.2-5 Downloading dependency 259 of 318: libgcc-15-dev:amd64=15.2.0-10 Downloading dependency 260 of 318: python-tables-data:amd64=3.10.2-3 Downloading dependency 261 of 318: libaudit1:amd64=1:4.1.2-1+b1 Downloading dependency 262 of 318: python3-pandocfilters:amd64=1.5.1-1 Downloading dependency 263 of 318: libuuid1:amd64=2.41.2-4 Downloading dependency 264 of 318: libpython3.13-minimal:amd64=3.13.11-1+b1 Downloading dependency 265 of 318: libacl1:amd64=2.3.2-2+b1 Downloading dependency 266 of 318: dwz:amd64=0.16-2 Downloading dependency 267 of 318: python3-soupsieve:amd64=2.7-2 Downloading dependency 268 of 318: python3-setuptools:amd64=78.1.1-0.1 Downloading dependency 269 of 318: python3-pluggy:amd64=1.6.0-1 Downloading dependency 270 of 318: python3-numpy-dev:amd64=1:2.3.5+ds-2+b1 Downloading dependency 271 of 318: libhwasan0:amd64=15.2.0-10 Downloading dependency 272 of 318: python-tinycss2-common:amd64=1.4.0-2 Downloading dependency 273 of 318: libstdc++6:amd64=15.2.0-10 Downloading dependency 274 of 318: libelf1t64:amd64=0.194-1 Downloading dependency 275 of 318: build-essential:amd64=12.12 Downloading dependency 276 of 318: libmpfr6:amd64=4.2.2-2 Downloading dependency 277 of 318: python3-wheel:amd64=0.46.1-2 Downloading dependency 278 of 318: libpam-modules-bin:amd64=1.7.0-5 Downloading dependency 279 of 318: libpython3.14-minimal:amd64=3.14.2-1+b1 Downloading dependency 280 of 318: cython3:amd64=3.1.6+dfsg-2+b1 Downloading dependency 281 of 318: binutils:amd64=2.45.50.20251201-1 Downloading dependency 282 of 318: libcap-ng0:amd64=0.8.5-4+b2 Downloading dependency 283 of 318: libpgm-5.3-0t64:amd64=5.3.128~dfsg-2.1+b1 Downloading dependency 284 of 318: libmagic-mgc:amd64=1:5.46-5 Downloading dependency 285 of 318: libpsl5t64:amd64=0.21.2-1.1+b1 Downloading dependency 286 of 318: python3-inflect:amd64=7.5.0-1 Downloading dependency 287 of 318: python3-jupyterlab-pygments:amd64=0.2.2-3 Downloading dependency 288 of 318: python3-referencing:amd64=0.36.2-2 Downloading dependency 289 of 318: g++-x86-64-linux-gnu:amd64=4:15.2.0-4 Downloading dependency 290 of 318: libcc1-0:amd64=15.2.0-10 Downloading dependency 291 of 318: util-linux:amd64=2.41.2-4 Downloading dependency 292 of 318: docutils-common:amd64=0.22.3+dfsg-1 Downloading dependency 293 of 318: python3-traitlets:amd64=5.14.3+really5.14.3-2 Downloading dependency 294 of 318: bash:amd64=5.3-1 Downloading dependency 295 of 318: python3-minimal:amd64=3.13.9-2 Downloading dependency 296 of 318: python3-packaging:amd64=25.0-1 Downloading dependency 297 of 318: man-db:amd64=2.13.1-1 Downloading dependency 298 of 318: libmd0:amd64=1.1.0-2+b1 Downloading dependency 299 of 318: python3-pygments:amd64=2.18.0+dfsg-2 Downloading dependency 300 of 318: python3-zmq:amd64=27.1.0-1+b1 Downloading dependency 301 of 318: libarchive-zip-perl:amd64=1.68-1 Downloading dependency 302 of 318: libzmq5:amd64=4.3.5-1+b3 Downloading dependency 303 of 318: libc-gconv-modules-extra:amd64=2.42-5 Downloading dependency 304 of 318: libunistring5:amd64=1.3-2 Downloading dependency 305 of 318: python3-fastjsonschema:amd64=2.21.1-1 Downloading dependency 306 of 318: sed:amd64=4.9-2 Downloading dependency 307 of 318: libreadline8t64:amd64=8.3-3 Downloading dependency 308 of 318: libatomic1:amd64=15.2.0-10 Downloading dependency 309 of 318: libc6-dev:amd64=2.42-5 Downloading dependency 310 of 318: libjs-sphinxdoc:amd64=8.2.3-11 Downloading dependency 311 of 318: python3-cffi-backend:amd64=2.0.0-2+b1 Downloading dependency 312 of 318: libldap2:amd64=2.6.10+dfsg-1 Downloading dependency 313 of 318: dh-autoreconf:amd64=21 Downloading dependency 314 of 318: python3-jaraco.text:amd64=4.0.0-1 Downloading dependency 315 of 318: python3-urllib3:amd64=2.5.0-1 Downloading dependency 316 of 318: libkeyutils1:amd64=1.6.3-6 Downloading dependency 317 of 318: libngtcp2-crypto-ossl0:amd64=1.16.0-1 Downloading dependency 318 of 318: libisl23:amd64=0.27-1 env --chdir=/srv/rebuilderd/tmp/rebuilderdr14PJq/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1765295332 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildDUIyBo/debrebuild.sbuildrc.VM2AJAgcIeHe sbuild --build=amd64 --host=amd64 --no-source --arch-any --no-arch-all --binNMU-changelog= mdtraj (1.11.0-2+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild with Python 3.14 as supported -- amd64 / i386 Build Daemon (x86-ubc-02) Tue, 09 Dec 2025 15:48:52 +0000 --chroot=/srv/rebuilderd/tmp/debrebuildDUIyBo/debrebuild.tar.3X90IOuHLbKz --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-1.11.0 /srv/rebuilderd/tmp/rebuilderdr14PJq/inputs/mdtraj_1.11.0-2.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: warning: descr(l1): found blank line where expected first heading sbuild (Debian sbuild) 0.89.3+deb13u1 (16 August 2025) on osuosl43-amd64.novalocal +==============================================================================+ | mdtraj 1.11.0-2+b1 (amd64) Sat, 27 Dec 2025 15:40:43 +0000 | +==============================================================================+ Package: mdtraj Version: 1.11.0-2+b1 Source Version: 1.11.0-2 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/debrebuildDUIyBo/debrebuild.tar.3X90IOuHLbKz to /srv/rebuilderd/tmp/tmp.sbuild.BdIDDQ_3xx... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Sat, 27 Dec 2025 15:40:52 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdr14PJq/inputs/mdtraj_1.11.0-2.dsc exists in /srv/rebuilderd/tmp/rebuilderdr14PJq/inputs; copying to chroot sbuild: warning: descr(l1): found blank line where expected first heading +------------------------------------------------------------------------------+ | Install package build dependencies Sat, 27 Dec 2025 15:40:53 +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-ul6xwq/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Sat, 27 Dec 2025 15:40:58 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any-amd64 arm64 i386 all) +------------------------------------------------------------------------------+ | Build environment Sat, 27 Dec 2025 15:40:58 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.57+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) amd64 (x86_64) Toolchain package versions: binutils_2.45.50.20251201-1 dpkg-dev_1.22.21 g++-15_15.2.0-10 gcc-15_15.2.0-10 libc6-dev_2.42-5 libstdc++-15-dev_15.2.0-10 libstdc++6_15.2.0-10 linux-libc-dev_6.17.10-1 Package versions: autoconf_2.72-3.1 automake_1:1.18.1-3 autopoint_0.23.2-1 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-1 binutils_2.45.50.20251201-1 binutils-common_2.45.50.20251201-1 binutils-x86-64-linux-gnu_2.45.50.20251201-1 bsdextrautils_2.41.2-4 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20250419 coreutils_9.7-3 cpp_4:15.2.0-4 cpp-15_15.2.0-10 cpp-15-x86-64-linux-gnu_15.2.0-10 cpp-x86-64-linux-gnu_4:15.2.0-4 cython3_3.1.6+dfsg-2+b1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.28 debianutils_5.23.2 dh-autoreconf_21 dh-python_6.20251204.1 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 docutils-common_0.22.3+dfsg-1 dpkg_1.22.21 dpkg-dev_1.22.21 dwz_0.16-2 file_1:5.46-5 findutils_4.10.0-3 fonts-mathjax_2.7.9+dfsg-1 g++_4:15.2.0-4 g++-15_15.2.0-10 g++-15-x86-64-linux-gnu_15.2.0-10 g++-x86-64-linux-gnu_4:15.2.0-4 gcc_4:15.2.0-4 gcc-15_15.2.0-10 gcc-15-base_15.2.0-10 gcc-15-x86-64-linux-gnu_15.2.0-10 gcc-x86-64-linux-gnu_4:15.2.0-4 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_2.3.2-2+b1 libaec0_1.1.4-2 libarchive-zip-perl_1.68-1 libasan8_15.2.0-10 libatomic1_15.2.0-10 libattr1_1:2.5.2-3 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.45.50.20251201-1 libblas3_3.12.1-7 libblkid1_2.41.2-4 libblosc1_1.21.5+ds-2 libblosc2-4_2.17.1+ds-2 libbrotli1_1.1.0-2+b9 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.42-5 libc-dev-bin_2.42-5 libc-gconv-modules-extra_2.42-5 libc6_2.42-5 libc6-dev_2.42-5 libcap-ng0_0.8.5-4+b2 libcap2_1:2.75-10+b2 libcc1-0_15.2.0-10 libcom-err2_1.47.2-3+b4 libcrypt-dev_1:4.5.1-1 libcrypt1_1:4.5.1-1 libctf-nobfd0_2.45.50.20251201-1 libctf0_2.45.50.20251201-1 libcurl3t64-gnutls_8.17.0-3 libcurl4t64_8.17.0-3 libdb5.3t64_5.3.28+dfsg2-11 libdebconfclient0_0.282 libdebhelper-perl_13.28 libdpkg-perl_1.22.21 libelf1t64_0.194-1 libexpat1_2.7.3-1 libexpat1-dev_2.7.3-1 libffi8_3.5.2-3 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-15-dev_15.2.0-10 libgcc-s1_15.2.0-10 libgdbm-compat4t64_1.26-1 libgdbm6t64_1.26-1 libgfortran5_15.2.0-10 libgmp10_2:6.3.0+dfsg-5 libgnutls30t64_3.8.11-3 libgomp1_15.2.0-10 libgprofng0_2.45.50.20251201-1 libgssapi-krb5-2_1.22.1-2 libhdf5-310_1.14.5+repack-4 libhdf5-hl-310_1.14.5+repack-4 libhogweed6t64_3.10.2-1 libhwasan0_15.2.0-10 libidn2-0_2.3.8-4 libisl23_0.27-1 libitm1_15.2.0-10 libjansson4_2.14-2+b3 libjs-mathjax_2.7.9+dfsg-1 libjs-sphinxdoc_8.2.3-11 libjson-perl_4.10000-1 libk5crypto3_1.22.1-2 libkeyutils1_1.6.3-6 libkrb5-3_1.22.1-2 libkrb5support0_1.22.1-2 liblapack3_3.12.1-7 libldap2_2.6.10+dfsg-1 liblsan0_15.2.0-10 liblz4-1_1.10.0-6 liblzma5_5.8.1-2 liblzo2-2_2.10-3+b1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41.2-4 libmpc3_1.3.1-2 libmpfr6_4.2.2-2 libncursesw6_6.5+20251123-1 libnetcdf22_1:4.9.3-1+b1 libnettle8t64_3.10.2-1 libnghttp2-14_1.64.0-1.1+b1 libnghttp3-9_1.12.0-1 libngtcp2-16_1.16.0-1 libngtcp2-crypto-gnutls8_1.16.0-1 libngtcp2-crypto-ossl0_1.16.0-1 libnorm1t64_1.5.9+dfsg-4 libp11-kit0_0.25.10-1 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.46-1 libperl5.40_5.40.1-7 libpgm-5.3-0t64_5.3.128~dfsg-2.1+b1 libpipeline1_1.5.8-2 libpsl5t64_0.21.2-1.1+b1 libpython3-all-dev_3.13.9-2 libpython3-dev_3.13.9-2 libpython3-stdlib_3.13.9-2 libpython3.13_3.13.11-1+b1 libpython3.13-dev_3.13.11-1+b1 libpython3.13-minimal_3.13.11-1+b1 libpython3.13-stdlib_3.13.11-1+b1 libpython3.14_3.14.2-1+b1 libpython3.14-dev_3.14.2-1+b1 libpython3.14-minimal_3.14.2-1+b1 libpython3.14-stdlib_3.14.2-1+b1 libqhull-r8.0_2020.2-7 libquadmath0_15.2.0-10 libreadline8t64_8.3-3 librtmp1_2.4+20151223.gitfa8646d.1-3 libsasl2-2_2.1.28+dfsg1-10 libsasl2-modules-db_2.1.28+dfsg1-10 libseccomp2_2.6.0-2+b1 libselinux1_3.9-4+b1 libsframe2_2.45.50.20251201-1 libsmartcols1_2.41.2-4 libsnappy1v5_1.2.2-2 libsodium23_1.0.18-1+b2 libsqlite3-0_3.46.1-8 libssh2-1t64_1.11.1-1 libssl3t64_3.5.4-1 libstdc++-15-dev_15.2.0-10 libstdc++6_15.2.0-10 libsystemd0_259~rc2-1 libsz2_1.1.4-2 libtasn1-6_4.20.0-2 libtinfo6_6.5+20251123-1 libtool_2.5.4-9 libtsan2_15.2.0-10 libubsan1_15.2.0-10 libuchardet0_0.0.8-2 libudev1_259~rc2-1 libunistring5_1.3-2 libuuid1_2.41.2-4 libxml2-16_2.15.1+dfsg-2+b1 libxxhash0_0.8.3-2 libzmq5_4.3.5-1+b3 libzstd1_1.5.7+dfsg-2 linux-libc-dev_6.17.10-1 m4_1.4.20-2 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20250131-1 media-types_14.0.0 ncurses-base_6.5+20251123-1 ncurses-bin_6.5+20251123-1 netbase_6.5 openssl_3.5.4-1 openssl-provider-legacy_3.5.4-1 patch_2.8-2 perl_5.40.1-7 perl-base_5.40.1-7 perl-modules-5.40_5.40.1-7 po-debconf_1.0.22 pybuild-plugin-pyproject_6.20251204.1 python-babel-localedata_2.17.0-2 python-tables-data_3.10.2-3 python-tinycss2-common_1.4.0-2 python3_3.13.9-2 python3-alabaster_0.7.16-0.1 python3-all_3.13.9-2 python3-all-dev_3.13.9-2 python3-attr_25.4.0-1 python3-autocommand_2.2.2-3 python3-babel_2.17.0-2 python3-bleach_6.3.0-1 python3-bs4_4.14.3-1 python3-build_1.2.2-4 python3-certifi_2025.11.12+ds-1 python3-cffi-backend_2.0.0-2+b1 python3-cftime_1.6.5-1+b1 python3-chardet_5.2.0+dfsg-2 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_3.13.9-2 python3-docutils_0.22.3+dfsg-1 python3-fastjsonschema_2.21.1-1 python3-gsd_4.2.0-1 python3-html5lib_1.2-2 python3-idna_3.10-1 python3-imagesize_1.4.1-1 python3-inflect_7.5.0-1 python3-iniconfig_2.1.0-1 python3-installer_0.7.0+dfsg1-3 python3-jaraco.context_6.0.1-1 python3-jaraco.functools_4.1.0-1 python3-jaraco.text_4.0.0-1 python3-jinja2_3.1.6-1 python3-jsonschema_4.25.1-2 python3-jsonschema-specifications_2023.12.1-4 python3-jupyter-client_8.6.3-3 python3-jupyter-core_5.7.2-5 python3-jupyterlab-pygments_0.2.2-3 python3-markupsafe_3.0.3-1+b1 python3-minimal_3.13.9-2 python3-mistune_3.1.4-1 python3-more-itertools_10.8.0-1 python3-nbclient_0.8.0-3 python3-nbconvert_7.16.6-1 python3-nbformat_5.9.1-1 python3-nbsphinx_0.9.5+ds-1 python3-netcdf4_1.7.3-1+b1 python3-networkx_3.4.2-4 python3-numexpr_2.14.1-1+b1 python3-numpy_1:2.3.5+ds-2+b1 python3-numpy-dev_1:2.3.5+ds-2+b1 python3-packaging_25.0-1 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_4.4.0-1 python3-pluggy_1.6.0-1 python3-psutil_7.1.0-1 python3-pygments_2.18.0+dfsg-2 python3-pyparsing_3.1.3-1 python3-pyproject-hooks_1.2.0-1 python3-pytest_8.4.2-1 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_3.1.0-2 python3-rpds-py_0.28.0-1 python3-scipy_1.16.3-2 python3-setuptools_78.1.1-0.1 python3-snowballstemmer_3.0.1-1 python3-soupsieve_2.7-2 python3-sphinx_8.2.3-11 python3-tables_3.10.2-3 python3-tables-lib_3.10.2-3+b1 python3-tinycss2_1.4.0-2 python3-tornado_6.5.2-3 python3-traitlets_5.14.3+really5.14.3-2 python3-typeguard_4.4.4-1 python3-typing-extensions_4.15.0-1 python3-urllib3_2.5.0-1 python3-versioneer_0.29-1 python3-webencodings_0.5.1-5 python3-wheel_0.46.1-2 python3-zipp_3.23.0-1 python3-zmq_27.1.0-1+b1 python3.13_3.13.11-1+b1 python3.13-dev_3.13.11-1+b1 python3.13-minimal_3.13.11-1+b1 python3.14_3.14.2-1+b1 python3.14-dev_3.14.2-1+b1 python3.14-minimal_3.14.2-1+b1 readline-common_8.3-3 rpcsvc-proto_1.4.3-1 sed_4.9-2 sensible-utils_0.0.26 sgml-base_1.31+nmu1 sphinx-common_8.2.3-11 sysvinit-utils_3.15-6 tar_1.35+dfsg-3.1 tzdata_2025b-5 util-linux_2.41.2-4 xml-core_0.19 xz-utils_5.8.1-2 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Sat, 27 Dec 2025 15:40:58 +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: 1.11.0-2 Maintainer: Debichem Team Uploaders: Drew Parsons Homepage: https://mdtraj.org/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/debichem-team/mdtraj Vcs-Git: https://salsa.debian.org/debichem-team/mdtraj.git Testsuite: autopkgtest Testsuite-Triggers: 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: 21e669632e858df798f129cfeb9a9a3d31ccb394 22723159 mdtraj_1.11.0.orig.tar.gz 1e7c8a8c72f088799169256b68f1b3a852e48867 300368 mdtraj_1.11.0-2.debian.tar.xz Checksums-Sha256: fefca787f882d0716a7aeb01b4d8e30caddbd2be0b2893acfa7201c31d13c786 22723159 mdtraj_1.11.0.orig.tar.gz 8553fdf5130d41f5881b2c8cc7d509e3b3b2a9c05699998bafdb905550db2a15 300368 mdtraj_1.11.0-2.debian.tar.xz Files: 7ad9ab16d7cbca7b7aee5e88ff440586 22723159 mdtraj_1.11.0.orig.tar.gz 9b7162ed8040c2b3cdc7f3cca4780460 300368 mdtraj_1.11.0-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmj/YuIACgkQVz7x5L1a AfoqFw//UY2dliAF2dJx9lqE2dFYfskQzXrdT9JUe3WMrwXh5qfnE+kujrwR9LFK 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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 Check disk space ---------------- Sufficient free space for build Hack binNMU version ------------------- Created changelog entry for binNMU version 1.11.0-2+b1 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=1765295332 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package mdtraj dpkg-buildpackage: info: source version 1.11.0-2+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-ubc-02) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from mdtraj-1.11.0/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-1.11.0' 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-1.11.0' 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:131: Building wheel for python3.14 with "build" module I: pybuild base:317: python3.14 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdtraj-1.11.0/.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 15.2.0-10' --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 15.2.0-10) 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. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:0: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:0: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:0: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. 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/__init__.py -> build/lib.linux-x86_64-cpython-314/mdtraj copying mdtraj/io.py -> build/lib.linux-x86_64-cpython-314/mdtraj creating build/lib.linux-x86_64-cpython-314/mdtraj/testing copying mdtraj/testing/__init__.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/docscrape.py -> build/lib.linux-x86_64-cpython-314/mdtraj/testing copying mdtraj/testing/testing.py -> build/lib.linux-x86_64-cpython-314/mdtraj/testing creating build/lib.linux-x86_64-cpython-314/mdtraj/scripts copying mdtraj/scripts/__init__.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/mdinspect.py -> build/lib.linux-x86_64-cpython-314/mdtraj/scripts creating 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/lammpstrj.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/arc.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/gro.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/hoomdxml.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/xyzfile.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/mdcrd.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/registry.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/netcdf.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats copying mdtraj/formats/mol2.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats creating 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/__init__.py -> 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/zipped.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/contextmanagers.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils copying mdtraj/utils/singleton.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils creating 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/order.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/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/dssp.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/__init__.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/internal.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/dihedral.py -> 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/rdf.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/distance.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry copying mdtraj/geometry/angle.py -> build/lib.linux-x86_64-cpython-314/mdtraj/geometry 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/__init__.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 creating 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/__init__.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/netcdfreporter.py -> build/lib.linux-x86_64-cpython-314/mdtraj/reporters creating build/lib.linux-x86_64-cpython-314/mdtraj/core copying mdtraj/core/selection.py -> 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/__init__.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/residue_names.py -> build/lib.linux-x86_64-cpython-314/mdtraj/core copying mdtraj/core/topology.py -> build/lib.linux-x86_64-cpython-314/mdtraj/core creating 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 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/PdbxContainers.py -> build/lib.linux-x86_64-cpython-314/mdtraj/formats/pdbx 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/__init__.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 creating 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 copying mdtraj/utils/unit/__init__.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/basedimension.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/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/doctests.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/quantity.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/unit_definitions.py -> build/lib.linux-x86_64-cpython-314/mdtraj/utils/unit 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 '1.11.0' running build_ext building 'mdtraj.formats.xtc' extension creating build/temp.linux-x86_64-cpython-314/mdtraj/formats/xtc/src x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 -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-1.11.0=. -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.formats.trr' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-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-1.11.0=. -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.formats.dcd' extension creating build/temp.linux-x86_64-cpython-314/mdtraj/formats/dcd 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-1.11.0=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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 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-1.11.0=. -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.formats.dtr' extension creating build/temp.linux-x86_64-cpython-314/mdtraj/formats/dtr 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-1.11.0=. -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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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 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} 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-1.11.0=. -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-1.11.0=. -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 building 'mdtraj._rmsd' extension creating build/temp.linux-x86_64-cpython-314/mdtraj/rmsd 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-1.11.0=. -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-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 building 'mdtraj._lprmsd' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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 building 'mdtraj.core.lib.libtheobald' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 building 'mdtraj.geometry.drid' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 building 'mdtraj.geometry.neighbors' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 building 'mdtraj.geometry.neighborlist' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 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/testing copying build/lib.linux-x86_64-cpython-314/mdtraj/testing/__init__.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/docscrape.py -> 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/_version.py -> 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/__init__.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/mdinspect.py -> build/bdist.linux-x86_64/wheel/./mdtraj/scripts copying build/lib.linux-x86_64-cpython-314/mdtraj/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj creating build/bdist.linux-x86_64/wheel/mdtraj/formats 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/lammpstrj.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats 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/arc.py -> 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 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/openmmxml.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/hdf5.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/prmtop.py -> 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/lh5.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 creating 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/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/PdbxContainers.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdbx 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/amberrst.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/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/__init__.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/pdbstructure.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdb 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/mol2.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/_lprmsd.cpython-314-x86_64-linux-gnu.so -> 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/unitcell.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 creating 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/unit/__init__.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/basedimension.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/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/doctests.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/quantity.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/unit_definitions.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit 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 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/delay_import.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 copying build/lib.linux-x86_64-cpython-314/mdtraj/utils/singleton.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils creating 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/order.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/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/dssp.py -> 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/__init__.py -> 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/shape.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/_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/rg.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/sasa.py -> 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/hbond.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/angle.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/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/__init__.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 creating 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/__init__.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/netcdfreporter.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters creating 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/core/trajectory.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/element.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 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/center.h -> 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/topology.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 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-1.11.0.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/mdtraj-1.11.0.dist-info/WHEEL creating '/build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.14_mdtraj/.tmp-dkuqiqa0/mdtraj-1.11.0-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-1.11.0.dist-info/licenses/LICENSE' adding 'mdtraj-1.11.0.dist-info/METADATA' adding 'mdtraj-1.11.0.dist-info/WHEEL' adding 'mdtraj-1.11.0.dist-info/entry_points.txt' adding 'mdtraj-1.11.0.dist-info/top_level.txt' adding 'mdtraj-1.11.0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built mdtraj-1.11.0-cp314-cp314-linux_x86_64.whl I: pybuild plugin_pyproject:155: Unpacking wheel built for python3.14 with "installer" module I: pybuild plugin_pyproject:131: Building wheel for python3.13 with "build" module I: pybuild base:317: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdtraj-1.11.0/.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 15.2.0-10' --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 15.2.0-10) 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. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:0: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:0: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:0: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. 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/__init__.py -> build/lib.linux-x86_64-cpython-313/mdtraj copying mdtraj/io.py -> build/lib.linux-x86_64-cpython-313/mdtraj creating build/lib.linux-x86_64-cpython-313/mdtraj/testing copying mdtraj/testing/__init__.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/docscrape.py -> build/lib.linux-x86_64-cpython-313/mdtraj/testing copying mdtraj/testing/testing.py -> build/lib.linux-x86_64-cpython-313/mdtraj/testing creating build/lib.linux-x86_64-cpython-313/mdtraj/scripts copying mdtraj/scripts/__init__.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/mdinspect.py -> build/lib.linux-x86_64-cpython-313/mdtraj/scripts creating 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/lammpstrj.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/arc.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/gro.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/hoomdxml.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/xyzfile.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/mdcrd.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/registry.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/netcdf.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats copying mdtraj/formats/mol2.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats creating 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/__init__.py -> 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/zipped.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/contextmanagers.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils copying mdtraj/utils/singleton.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils creating 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/order.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/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/dssp.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/__init__.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/internal.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/dihedral.py -> 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/rdf.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/distance.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry copying mdtraj/geometry/angle.py -> build/lib.linux-x86_64-cpython-313/mdtraj/geometry 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/__init__.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 creating 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/__init__.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/netcdfreporter.py -> build/lib.linux-x86_64-cpython-313/mdtraj/reporters creating build/lib.linux-x86_64-cpython-313/mdtraj/core copying mdtraj/core/selection.py -> 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/__init__.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/residue_names.py -> build/lib.linux-x86_64-cpython-313/mdtraj/core copying mdtraj/core/topology.py -> build/lib.linux-x86_64-cpython-313/mdtraj/core creating 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 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/PdbxContainers.py -> build/lib.linux-x86_64-cpython-313/mdtraj/formats/pdbx 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/__init__.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 creating 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 copying mdtraj/utils/unit/__init__.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/basedimension.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/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/doctests.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/quantity.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/unit_definitions.py -> build/lib.linux-x86_64-cpython-313/mdtraj/utils/unit 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 '1.11.0' running build_ext building 'mdtraj.formats.xtc' extension creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 -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-1.11.0=. -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.formats.trr' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-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-1.11.0=. -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 building 'mdtraj.formats.dcd' extension creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/src x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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 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-1.11.0=. -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.formats.dtr' extension creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr 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-1.11.0=. -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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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 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} 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-1.11.0=. -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-1.11.0=. -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 building 'mdtraj._rmsd' extension 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-1.11.0=. -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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 building 'mdtraj._lprmsd' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 building 'mdtraj.core.lib.libtheobald' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 building 'mdtraj.geometry.drid' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 building 'mdtraj.geometry.neighbors' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 building 'mdtraj.geometry.neighborlist' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -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-1.11.0=. -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-1.11.0=. -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 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/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/testing/docstrings.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/testing.py -> build/bdist.linux-x86_64/wheel/./mdtraj/testing 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/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/scripts/mdconvert.py -> 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/__init__.py -> build/bdist.linux-x86_64/wheel/./mdtraj creating build/bdist.linux-x86_64/wheel/mdtraj/formats 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/lammpstrj.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/psf.py -> 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/__init__.py -> 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/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/openmmxml.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/hdf5.py -> 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 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/prmtop.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/lh5.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/registry.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/__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/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/PdbxContainers.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdbx 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/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-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/__init__.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/pdbstructure.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats/pdb copying build/lib.linux-x86_64-cpython-313/mdtraj/formats/mol2.py -> build/bdist.linux-x86_64/wheel/./mdtraj/formats creating 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/__init__.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/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/unit/__init__.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/basedimension.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/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/doctests.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/quantity.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/unit_definitions.py -> build/bdist.linux-x86_64/wheel/./mdtraj/utils/unit 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 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/delay_import.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 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/_lprmsd.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj creating 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/order.py -> 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/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/dssp.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 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/shape.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/rg.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/sasa.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/rdf.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/distance.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/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/neighborlist.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj/geometry 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/__init__.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 creating 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/__init__.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/netcdfreporter.py -> build/bdist.linux-x86_64/wheel/./mdtraj/reporters copying build/lib.linux-x86_64-cpython-313/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mdtraj creating 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/core/trajectory.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/element.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 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/center.h -> 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/topology.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 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-1.11.0.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/mdtraj-1.11.0.dist-info/WHEEL creating '/build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/.tmp-irts9cql/mdtraj-1.11.0-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-1.11.0.dist-info/licenses/LICENSE' adding 'mdtraj-1.11.0.dist-info/METADATA' adding 'mdtraj-1.11.0.dist-info/WHEEL' adding 'mdtraj-1.11.0.dist-info/entry_points.txt' adding 'mdtraj-1.11.0.dist-info/top_level.txt' adding 'mdtraj-1.11.0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built mdtraj-1.11.0-cp313-cp313-linux_x86_64.whl I: pybuild plugin_pyproject:155: 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:317: cd /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.14_mdtraj/build; python3.14 -m pytest -k 'not (mdconvert or pi_stacking.ipynb or nmr.ipynb or test_image_molecules) and not (test_3 or test_pdb_from_url or test_1vii_url_and_gz)' ============================= test session starts ============================== platform linux -- Python 3.14.2, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3.14 cachedir: .pytest_cache rootdir: /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.14_mdtraj/build configfile: pyproject.toml testpaths: tests, examples plugins: rerunfailures-16.1, typeguard-4.4.4 collecting ... collected 1161 items / 22 deselected / 1139 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 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(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...) [ 4%] 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 [ 5%] 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 [ 6%] 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 [ 7%] 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 [ 8%] 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 [ 9%] 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 [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.order] PASSED [ 10%] 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 [ 11%] 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 [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.basedimension] PASSED [ 12%] 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 [ 13%] 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 [ 14%] tests/test_dssp.py::test_7 PASSED [ 14%] 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 [ 15%] tests/test_dtr.py::test_write_1 PASSED [ 15%] 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 [ 16%] tests/test_geometry.py::test_center_of_mass PASSED [ 16%] 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 [ 17%] tests/test_geometry.py::test_dihedral_performance SKIPPED (Not doing...) [ 17%] tests/test_geometry.py::test_angle_performance SKIPPED (Not doing pe...) [ 17%] tests/test_geometry.py::test_angle_nan PASSED [ 17%] tests/test_geometry.py::test_angle_pbc PASSED [ 17%] tests/test_geometry.py::test_dihedral_pbc PASSED [ 17%] tests/test_geometry.py::test_dihedral_pbc_fails1 PASSED [ 17%] tests/test_geometry.py::test_dihedral_pbc_fails2 PASSED [ 17%] tests/test_geometry.py::test_angle_pbc_fails1 PASSED [ 17%] tests/test_geometry.py::test_no_indices PASSED [ 17%] tests/test_gro.py::test_read_write PASSED [ 17%] tests/test_gro.py::test_read_write_precision PASSED [ 17%] tests/test_gro.py::test_no_whitespace_gro PASSED [ 18%] tests/test_gro.py::test_load PASSED [ 18%] tests/test_gro.py::test_load_with_given_top PASSED [ 18%] tests/test_gro.py::test_against_gmx PASSED [ 18%] tests/test_gsd.py::test_read PASSED [ 18%] tests/test_gsd.py::test_read_start PASSED [ 18%] tests/test_gsd.py::test_read_frame PASSED [ 18%] tests/test_gsd.py::test_read_stride PASSED [ 18%] tests/test_gsd.py::test_read_variable_top_error PASSED [ 18%] tests/test_gsd.py::test_write PASSED [ 18%] tests/test_gsd.py::test_write_frame PASSED [ 18%] tests/test_hbonds.py::test_hbonds PASSED [ 19%] tests/test_hbonds.py::test_hbonds_against_dssp PASSED [ 19%] tests/test_hbonds.py::test_baker_hubbard_0 PASSED [ 19%] tests/test_hbonds.py::test_baker_hubbard_1 PASSED [ 19%] tests/test_hbonds.py::test_baker_hubbard_2 PASSED [ 19%] tests/test_hbonds.py::test_baker_hubbard_3 PASSED [ 19%] tests/test_hbonds.py::test_wernet_nilsson_0 PASSED [ 19%] tests/test_hbonds.py::test_wernet_nilsson_1 PASSED [ 19%] tests/test_hdf5.py::test_write_coordinates PASSED [ 19%] tests/test_hdf5.py::test_write_coordinates_reshape PASSED [ 19%] tests/test_hdf5.py::test_write_multiple PASSED [ 19%] tests/test_hdf5.py::test_write_inconsistent PASSED [ 20%] tests/test_hdf5.py::test_write_inconsistent_2 PASSED [ 20%] tests/test_hdf5.py::test_write_units SKIPPED (requires openmm.units) [ 20%] tests/test_hdf5.py::test_write_units2 PASSED [ 20%] tests/test_hdf5.py::test_write_units_mismatch SKIPPED (requires open...) [ 20%] tests/test_hdf5.py::test_topology PASSED [ 20%] tests/test_hdf5.py::test_constraints PASSED [ 20%] tests/test_hdf5.py::test_constraints2 PASSED [ 20%] tests/test_hdf5.py::test_read_0 PASSED [ 20%] tests/test_hdf5.py::test_read_1 SKIPPED (requires openmm.units) [ 20%] tests/test_hdf5.py::test_read_slice_0 PASSED [ 20%] tests/test_hdf5.py::test_read_slice_1 PASSED [ 20%] tests/test_hdf5.py::test_read_slice_2 PASSED [ 21%] tests/test_hdf5.py::test_read_slice_3 PASSED [ 21%] tests/test_hdf5.py::test_do_overwrite PASSED [ 21%] tests/test_hdf5.py::test_vsite_elements PASSED [ 21%] tests/test_hdf5.py::test_dont_overwrite PASSED [ 21%] tests/test_hdf5.py::test_attributes PASSED [ 21%] tests/test_hdf5.py::test_append PASSED [ 21%] tests/test_hdf5.py::test_topology_None PASSED [ 21%] tests/test_hoomdxml.py::test_load PASSED [ 21%] tests/test_hoomdxml.py::test_load_no_chains PASSED [ 21%] tests/test_hoomdxml.py::test_load_no_ions PASSED [ 21%] tests/test_hoomdxml.py::test_correct_ordering PASSED [ 22%] tests/test_io.py::test_overwrite_1 PASSED [ 22%] tests/test_io.py::test_overwrite_2 PASSED [ 22%] tests/test_io.py::test_io::test_load_1 PASSED [ 22%] tests/test_io.py::test_io::test_load_2 PASSED [ 22%] tests/test_io.py::test_io::test_load_3 PASSED [ 22%] tests/test_io.py::test_io::test_save PASSED [ 22%] tests/test_io.py::test_io_int::test_load_1 PASSED [ 22%] tests/test_io.py::test_io_int::test_load_2 PASSED [ 22%] tests/test_io.py::test_io_int::test_load_3 PASSED [ 22%] tests/test_io.py::test_io_int::test_save PASSED [ 22%] tests/test_io.py::test_groups PASSED [ 23%] tests/test_lammpstrj.py::test_read_0 PASSED [ 23%] tests/test_lammpstrj.py::test_read_1 PASSED [ 23%] tests/test_lammpstrj.py::test_read_write_0 PASSED [ 23%] tests/test_lammpstrj.py::test_mdwrite PASSED [ 23%] 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%] tests/test_lprmsd.py::test_lprmsd_0 PASSED [ 25%] tests/test_lprmsd.py::test_lprmsd_1 PASSED [ 25%] tests/test_lprmsd.py::test_lprmsd_2 PASSED [ 25%] tests/test_lprmsd.py::test_lprmsd_3 PASSED [ 25%] tests/test_lprmsd.py::test_lprmsd_4 PASSED [ 25%] tests/test_lprmsd.py::test_lprmsd_5 PASSED [ 25%] tests/test_mdcrd.py::test_read_0 PASSED [ 25%] tests/test_mdcrd.py::test_read_1 PASSED [ 25%] tests/test_mdcrd.py::test_read_write_0 PASSED [ 25%] tests/test_mdcrd.py::test_read_write_1 PASSED [ 25%] tests/test_mdcrd.py::test_read_write_2 PASSED [ 25%] tests/test_mdcrd.py::test_multiread PASSED [ 25%] tests/test_mdcrd.py::test_seek PASSED [ 26%] tests/test_mdcrd.py::test_atom_indices_0 PASSED [ 26%] tests/test_mdcrd.py::test_atom_indices_1 PASSED [ 26%] tests/test_mol2.py::test_load_mol2 PASSED [ 26%] tests/test_mol2.py::test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb SKIPPED [ 26%] tests/test_mol2.py::test_mol2_dataframe PASSED [ 26%] tests/test_mol2.py::test_mol2_dataframe_status PASSED [ 26%] tests/test_mol2.py::test_mol2_warnings PASSED [ 26%] tests/test_mol2.py::test_mol2_status_bits PASSED [ 26%] tests/test_mol2.py::test_mol2_without_bonds PASSED [ 26%] tests/test_mol2.py::test_mol2_element_name PASSED [ 26%] tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 27%] tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 27%] tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 27%] tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 27%] tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 27%] tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 27%] tests/test_mol2.py::test_mol2_n_residues PASSED [ 27%] tests/test_neighborlist.py::test_nonperiodic PASSED [ 27%] tests/test_neighborlist.py::test_periodic PASSED [ 27%] tests/test_neighborlist.py::test_triclinic PASSED [ 27%] tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 27%] 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 [ 28%] 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) [ 30%] 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_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 [ 34%] tests/test_pdbx.py::test_residue_selection_from_cif PASSED [ 34%] tests/test_pi_stacking.py::test_pi_stacking PASSED [ 34%] tests/test_pi_stacking.py::test_t_stacking_more_relaxed_radius PASSED [ 34%] tests/test_pi_stacking.py::test_t_stacking_default_settings PASSED [ 34%] tests/test_prmtop.py::test_load_prmtop PASSED [ 34%] 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...) [ 35%] tests/test_quaternion.py::test_quaternion_0 PASSED [ 35%] tests/test_quaternion.py::test_quaternion_1 PASSED [ 35%] tests/test_quaternion.py::test_quaternion_2 PASSED [ 35%] tests/test_rdf.py::test_rdf_norm PASSED [ 35%] tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 35%] tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 35%] 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 [ 36%] tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 36%] tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 36%] tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 36%] tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 36%] tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 36%] tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 36%] 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 [ 37%] tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 37%] tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 37%] tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 37%] tests/test_restart.py::test_read_after_close PASSED [ 37%] tests/test_restart.py::test_shape PASSED [ 37%] 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 [ 38%] tests/test_rmsd.py::test_trajectory_rmsd[superpose-serial] PASSED [ 38%] tests/test_rmsd.py::test_trajectory_rmsd[qcp-parallel] PASSED [ 38%] tests/test_rmsd.py::test_trajectory_rmsd[qcp-serial] PASSED [ 38%] tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 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 [ 39%] tests/test_rmsd.py::test_average_structure PASSED [ 39%] tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 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 [ 40%] tests/test_sasa.py::test_sasa_5 PASSED [ 40%] tests/test_sasa.py::test_sasa_6 PASSED [ 40%] tests/test_sasa.py::test_sasa_7 PASSED [ 40%] tests/test_selection.py::test_range PASSED [ 40%] tests/test_selection.py::test_unary_2 PASSED [ 40%] 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 [ 41%] tests/test_selection.py::test_raises PASSED [ 41%] tests/test_selection.py::test_raises2 PASSED [ 41%] tests/test_selection.py::test_bool PASSED [ 41%] tests/test_selection.py::test_nested_bool PASSED [ 41%] tests/test_selection.py::test_values PASSED [ 41%] 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 [ 42%] tests/test_selection.py::test_top_2 PASSED [ 42%] tests/test_selection.py::test_backbone PASSED [ 42%] tests/test_selection.py::test_sidechain PASSED [ 42%] tests/test_selection.py::test_literal PASSED [ 42%] tests/test_selection.py::test_in PASSED [ 42%] 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 [ 43%] tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] tests/test_topology.py::test_topology_openmm_preserve_chain_id_when_specified SKIPPED [ 43%] 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 [ 44%] tests/test_topology.py::test_topology_pandas PASSED [ 44%] tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] tests/test_topology.py::test_topology_numbers PASSED [ 44%] tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] tests/test_topology.py::test_chain PASSED [ 44%] 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 [ 45%] tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 45%] tests/test_topology.py::test_n_bonds PASSED [ 45%] tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] tests/test_topology.py::test_unique_pairs PASSED [ 45%] tests/test_topology.py::test_select_pairs PASSED [ 45%] 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 [ 46%] tests/test_topology.py::test_copy[1ply_charge.pdb] PASSED [ 46%] tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 46%] tests/test_topology.py::test_topology_join PASSED [ 46%] tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] tests/test_topology.py::test_topology_join_formal_charge PASSED [ 46%] tests/test_topology.py::test_delete_atom_by_index PASSED [ 46%] 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 [ 47%] tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 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...) [ 48%] tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 48%] tests/test_trajectory.py::test_slice PASSED [ 48%] tests/test_trajectory.py::test_slice2 PASSED [ 48%] tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 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 [ 49%] tests/test_trajectory.py::test_read_path[xyz] PASSED [ 49%] tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 49%] tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 49%] tests/test_trajectory.py::test_read_path[lh5] PASSED [ 49%] tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 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 [ 50%] tests/test_trajectory.py::test_write_path[trr] PASSED [ 50%] tests/test_trajectory.py::test_write_path[dcd] PASSED [ 50%] tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 50%] tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 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 ...) [ 51%] tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 51%] tests/test_trajectory.py::test_write_path[gro] PASSED [ 51%] tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 51%] tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 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 [ 52%] tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 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 [ 53%] tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 53%] tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 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 [ 54%] tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 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 [ 55%] tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 55%] tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 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 [ 56%] tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 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 [ 57%] tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 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...) [ 58%] tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 58%] tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 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 (...) [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 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 ...) [ 60%] tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 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 [ 61%] tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 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 [ 62%] tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 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 [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 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 [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 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...) [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 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 [ 66%] tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 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 ...) [ 67%] tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 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 [ 68%] tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 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 [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 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...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 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...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 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...) [ 72%] tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 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 [ 73%] tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 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 [ 74%] tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 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 [ 75%] tests/test_trajectory.py::test_center_aind PASSED [ 75%] tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 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 [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 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 [ 77%] tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 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 ...) [ 78%] tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 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 [ 79%] tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 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...) [ 80%] tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 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 [ 81%] tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 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 [ 82%] tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 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 [ 83%] tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 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...) [ 84%] tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 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 [ 85%] tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 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 [ 86%] 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 [ 87%] tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 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 [ 88%] 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 [ 89%] tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 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...) [ 90%] 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 [ 91%] 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 [ 92%] 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 [ 93%] 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 [ 94%] 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 [ 95%] 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 [ 97%] 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:59: 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:49: needs OpenMM SKIPPED [1] tests/test_topology.py:66: needs OpenMM SKIPPED [1] tests/test_topology.py:76: needs OpenMM SKIPPED [1] tests/test_topology.py:85: needs OpenMM SKIPPED [1] tests/test_topology.py:95: needs OpenMM SKIPPED [1] tests/test_topology.py:102: requires openmm >= 8.2 SKIPPED [1] tests/test_topology.py:284: 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 = 975 passed, 103 skipped, 22 deselected, 61 xfailed, 1 warning in 242.06s (0:04:02) = 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) 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:317: cd /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build; python3.13 -m pytest -k 'not (mdconvert or pi_stacking.ipynb or nmr.ipynb or test_image_molecules) and not (test_3 or test_pdb_from_url or test_1vii_url_and_gz)' ============================= test session starts ============================== platform linux -- Python 3.13.11, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3.13 cachedir: .pytest_cache rootdir: /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build configfile: pyproject.toml testpaths: tests, examples plugins: rerunfailures-16.1, typeguard-4.4.4 collecting ... collected 1161 items / 22 deselected / 1139 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 [ 2%] 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...) [ 4%] 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 [ 5%] 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 [ 6%] 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 [ 7%] 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 [ 8%] 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 [ 9%] 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 [ 10%] tests/test_docstrings.py::test_docstrings[mdtraj.geometry.order] PASSED [ 10%] 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 [ 11%] 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 [ 12%] tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.basedimension] PASSED [ 12%] 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 [ 13%] 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 [ 14%] tests/test_dssp.py::test_7 PASSED [ 14%] 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 [ 15%] tests/test_dtr.py::test_write_1 PASSED [ 15%] 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 [ 16%] tests/test_geometry.py::test_center_of_mass PASSED [ 16%] 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 [ 17%] tests/test_geometry.py::test_dihedral_performance SKIPPED (Not doing...) [ 17%] tests/test_geometry.py::test_angle_performance SKIPPED (Not doing pe...) [ 17%] tests/test_geometry.py::test_angle_nan PASSED [ 17%] tests/test_geometry.py::test_angle_pbc PASSED [ 17%] tests/test_geometry.py::test_dihedral_pbc PASSED [ 17%] tests/test_geometry.py::test_dihedral_pbc_fails1 PASSED [ 17%] tests/test_geometry.py::test_dihedral_pbc_fails2 PASSED [ 17%] tests/test_geometry.py::test_angle_pbc_fails1 PASSED [ 17%] tests/test_geometry.py::test_no_indices PASSED [ 17%] tests/test_gro.py::test_read_write PASSED [ 17%] tests/test_gro.py::test_read_write_precision PASSED [ 17%] tests/test_gro.py::test_no_whitespace_gro PASSED [ 18%] tests/test_gro.py::test_load PASSED [ 18%] tests/test_gro.py::test_load_with_given_top PASSED [ 18%] tests/test_gro.py::test_against_gmx PASSED [ 18%] tests/test_gsd.py::test_read PASSED [ 18%] tests/test_gsd.py::test_read_start PASSED [ 18%] tests/test_gsd.py::test_read_frame PASSED [ 18%] tests/test_gsd.py::test_read_stride PASSED [ 18%] tests/test_gsd.py::test_read_variable_top_error PASSED [ 18%] tests/test_gsd.py::test_write PASSED [ 18%] tests/test_gsd.py::test_write_frame PASSED [ 18%] tests/test_hbonds.py::test_hbonds PASSED [ 19%] tests/test_hbonds.py::test_hbonds_against_dssp PASSED [ 19%] tests/test_hbonds.py::test_baker_hubbard_0 PASSED [ 19%] tests/test_hbonds.py::test_baker_hubbard_1 PASSED [ 19%] tests/test_hbonds.py::test_baker_hubbard_2 PASSED [ 19%] tests/test_hbonds.py::test_baker_hubbard_3 PASSED [ 19%] tests/test_hbonds.py::test_wernet_nilsson_0 PASSED [ 19%] tests/test_hbonds.py::test_wernet_nilsson_1 PASSED [ 19%] tests/test_hdf5.py::test_write_coordinates PASSED [ 19%] tests/test_hdf5.py::test_write_coordinates_reshape PASSED [ 19%] tests/test_hdf5.py::test_write_multiple PASSED [ 19%] tests/test_hdf5.py::test_write_inconsistent PASSED [ 20%] tests/test_hdf5.py::test_write_inconsistent_2 PASSED [ 20%] tests/test_hdf5.py::test_write_units SKIPPED (requires openmm.units) [ 20%] tests/test_hdf5.py::test_write_units2 PASSED [ 20%] tests/test_hdf5.py::test_write_units_mismatch SKIPPED (requires open...) [ 20%] tests/test_hdf5.py::test_topology PASSED [ 20%] tests/test_hdf5.py::test_constraints PASSED [ 20%] tests/test_hdf5.py::test_constraints2 PASSED [ 20%] tests/test_hdf5.py::test_read_0 PASSED [ 20%] tests/test_hdf5.py::test_read_1 SKIPPED (requires openmm.units) [ 20%] tests/test_hdf5.py::test_read_slice_0 PASSED [ 20%] tests/test_hdf5.py::test_read_slice_1 PASSED [ 20%] tests/test_hdf5.py::test_read_slice_2 PASSED [ 21%] tests/test_hdf5.py::test_read_slice_3 PASSED [ 21%] tests/test_hdf5.py::test_do_overwrite PASSED [ 21%] tests/test_hdf5.py::test_vsite_elements PASSED [ 21%] tests/test_hdf5.py::test_dont_overwrite PASSED [ 21%] tests/test_hdf5.py::test_attributes PASSED [ 21%] tests/test_hdf5.py::test_append PASSED [ 21%] tests/test_hdf5.py::test_topology_None PASSED [ 21%] tests/test_hoomdxml.py::test_load PASSED [ 21%] tests/test_hoomdxml.py::test_load_no_chains PASSED [ 21%] tests/test_hoomdxml.py::test_load_no_ions PASSED [ 21%] tests/test_hoomdxml.py::test_correct_ordering PASSED [ 22%] tests/test_io.py::test_overwrite_1 PASSED [ 22%] tests/test_io.py::test_overwrite_2 PASSED [ 22%] tests/test_io.py::test_io::test_load_1 PASSED [ 22%] tests/test_io.py::test_io::test_load_2 PASSED [ 22%] tests/test_io.py::test_io::test_load_3 PASSED [ 22%] tests/test_io.py::test_io::test_save PASSED [ 22%] tests/test_io.py::test_io_int::test_load_1 PASSED [ 22%] tests/test_io.py::test_io_int::test_load_2 PASSED [ 22%] tests/test_io.py::test_io_int::test_load_3 PASSED [ 22%] tests/test_io.py::test_io_int::test_save PASSED [ 22%] tests/test_io.py::test_groups PASSED [ 23%] tests/test_lammpstrj.py::test_read_0 PASSED [ 23%] tests/test_lammpstrj.py::test_read_1 PASSED [ 23%] tests/test_lammpstrj.py::test_read_write_0 PASSED [ 23%] tests/test_lammpstrj.py::test_mdwrite PASSED [ 23%] 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%] tests/test_lprmsd.py::test_lprmsd_0 PASSED [ 25%] tests/test_lprmsd.py::test_lprmsd_1 PASSED [ 25%] tests/test_lprmsd.py::test_lprmsd_2 PASSED [ 25%] tests/test_lprmsd.py::test_lprmsd_3 PASSED [ 25%] tests/test_lprmsd.py::test_lprmsd_4 PASSED [ 25%] tests/test_lprmsd.py::test_lprmsd_5 PASSED [ 25%] tests/test_mdcrd.py::test_read_0 PASSED [ 25%] tests/test_mdcrd.py::test_read_1 PASSED [ 25%] tests/test_mdcrd.py::test_read_write_0 PASSED [ 25%] tests/test_mdcrd.py::test_read_write_1 PASSED [ 25%] tests/test_mdcrd.py::test_read_write_2 PASSED [ 25%] tests/test_mdcrd.py::test_multiread PASSED [ 25%] tests/test_mdcrd.py::test_seek PASSED [ 26%] tests/test_mdcrd.py::test_atom_indices_0 PASSED [ 26%] tests/test_mdcrd.py::test_atom_indices_1 PASSED [ 26%] tests/test_mol2.py::test_load_mol2 PASSED [ 26%] tests/test_mol2.py::test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb SKIPPED [ 26%] tests/test_mol2.py::test_mol2_dataframe PASSED [ 26%] tests/test_mol2.py::test_mol2_dataframe_status PASSED [ 26%] tests/test_mol2.py::test_mol2_warnings PASSED [ 26%] tests/test_mol2.py::test_mol2_status_bits PASSED [ 26%] tests/test_mol2.py::test_mol2_without_bonds PASSED [ 26%] tests/test_mol2.py::test_mol2_element_name PASSED [ 26%] tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 27%] tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 27%] tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 27%] tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 27%] tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 27%] tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 27%] tests/test_mol2.py::test_mol2_n_residues PASSED [ 27%] tests/test_neighborlist.py::test_nonperiodic PASSED [ 27%] tests/test_neighborlist.py::test_periodic PASSED [ 27%] tests/test_neighborlist.py::test_triclinic PASSED [ 27%] tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 27%] 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 [ 28%] 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) [ 30%] 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_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 [ 34%] tests/test_pdbx.py::test_residue_selection_from_cif PASSED [ 34%] tests/test_pi_stacking.py::test_pi_stacking PASSED [ 34%] tests/test_pi_stacking.py::test_t_stacking_more_relaxed_radius PASSED [ 34%] tests/test_pi_stacking.py::test_t_stacking_default_settings PASSED [ 34%] tests/test_prmtop.py::test_load_prmtop PASSED [ 34%] 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...) [ 35%] tests/test_quaternion.py::test_quaternion_0 PASSED [ 35%] tests/test_quaternion.py::test_quaternion_1 PASSED [ 35%] tests/test_quaternion.py::test_quaternion_2 PASSED [ 35%] tests/test_rdf.py::test_rdf_norm PASSED [ 35%] tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 35%] tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 35%] 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 [ 36%] tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 36%] tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 36%] tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 36%] tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 36%] tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 36%] tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 36%] 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 [ 37%] tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 37%] tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 37%] tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 37%] tests/test_restart.py::test_read_after_close PASSED [ 37%] tests/test_restart.py::test_shape PASSED [ 37%] 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 [ 38%] tests/test_rmsd.py::test_trajectory_rmsd[superpose-serial] PASSED [ 38%] tests/test_rmsd.py::test_trajectory_rmsd[qcp-parallel] PASSED [ 38%] tests/test_rmsd.py::test_trajectory_rmsd[qcp-serial] PASSED [ 38%] tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 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 [ 39%] tests/test_rmsd.py::test_average_structure PASSED [ 39%] tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 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 [ 40%] tests/test_sasa.py::test_sasa_5 PASSED [ 40%] tests/test_sasa.py::test_sasa_6 PASSED [ 40%] tests/test_sasa.py::test_sasa_7 PASSED [ 40%] tests/test_selection.py::test_range PASSED [ 40%] tests/test_selection.py::test_unary_2 PASSED [ 40%] 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 [ 41%] tests/test_selection.py::test_raises PASSED [ 41%] tests/test_selection.py::test_raises2 PASSED [ 41%] tests/test_selection.py::test_bool PASSED [ 41%] tests/test_selection.py::test_nested_bool PASSED [ 41%] tests/test_selection.py::test_values PASSED [ 41%] 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 [ 42%] tests/test_selection.py::test_top_2 PASSED [ 42%] tests/test_selection.py::test_backbone PASSED [ 42%] tests/test_selection.py::test_sidechain PASSED [ 42%] tests/test_selection.py::test_literal PASSED [ 42%] tests/test_selection.py::test_in PASSED [ 42%] 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 [ 43%] tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] tests/test_topology.py::test_topology_openmm_preserve_chain_id_when_specified SKIPPED [ 43%] 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 [ 44%] tests/test_topology.py::test_topology_pandas PASSED [ 44%] tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] tests/test_topology.py::test_topology_numbers PASSED [ 44%] tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] tests/test_topology.py::test_chain PASSED [ 44%] 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 [ 45%] tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 45%] tests/test_topology.py::test_n_bonds PASSED [ 45%] tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] tests/test_topology.py::test_unique_pairs PASSED [ 45%] tests/test_topology.py::test_select_pairs PASSED [ 45%] 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 [ 46%] tests/test_topology.py::test_copy[1ply_charge.pdb] PASSED [ 46%] tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 46%] tests/test_topology.py::test_topology_join PASSED [ 46%] tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] tests/test_topology.py::test_topology_join_formal_charge PASSED [ 46%] tests/test_topology.py::test_delete_atom_by_index PASSED [ 46%] 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 [ 47%] tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 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...) [ 48%] tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 48%] tests/test_trajectory.py::test_slice PASSED [ 48%] tests/test_trajectory.py::test_slice2 PASSED [ 48%] tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 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 [ 49%] tests/test_trajectory.py::test_read_path[xyz] PASSED [ 49%] tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 49%] tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 49%] tests/test_trajectory.py::test_read_path[lh5] PASSED [ 49%] tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 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 [ 50%] tests/test_trajectory.py::test_write_path[trr] PASSED [ 50%] tests/test_trajectory.py::test_write_path[dcd] PASSED [ 50%] tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 50%] tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 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 ...) [ 51%] tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 51%] tests/test_trajectory.py::test_write_path[gro] PASSED [ 51%] tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 51%] tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 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 [ 52%] tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 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 [ 53%] tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 53%] tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 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 [ 54%] tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 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 [ 55%] tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 55%] tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 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 [ 56%] tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 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 [ 57%] tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 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...) [ 58%] tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 58%] tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 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 (...) [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 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 ...) [ 60%] tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 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 [ 61%] tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 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 [ 62%] tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 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 [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 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 [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 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...) [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 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 [ 66%] tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 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 ...) [ 67%] tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 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 [ 68%] tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 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 [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 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...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 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...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 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...) [ 72%] tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 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 [ 73%] tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 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 [ 74%] tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 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 [ 75%] tests/test_trajectory.py::test_center_aind PASSED [ 75%] tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 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 [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 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 [ 77%] tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 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 ...) [ 78%] tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 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 [ 79%] tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 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...) [ 80%] tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 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 [ 81%] tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 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 [ 82%] tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 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 [ 83%] tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 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...) [ 84%] tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 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 [ 85%] tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 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 [ 86%] 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 [ 87%] tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 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 [ 88%] 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 [ 89%] tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 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...) [ 90%] 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 [ 91%] 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 [ 92%] 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 [ 93%] 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 [ 94%] 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 [ 95%] 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 [ 97%] 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:59: 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:49: needs OpenMM SKIPPED [1] tests/test_topology.py:66: needs OpenMM SKIPPED [1] tests/test_topology.py:76: needs OpenMM SKIPPED [1] tests/test_topology.py:85: needs OpenMM SKIPPED [1] tests/test_topology.py:95: needs OpenMM SKIPPED [1] tests/test_topology.py:102: requires openmm >= 8.2 SKIPPED [1] tests/test_topology.py:284: 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 = 975 passed, 103 skipped, 22 deselected, 61 xfailed, 1 warning in 255.34s (0:04:15) = 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) 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-acFr5tbV 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-1.11.0/debian/tmp pybuild --install -i python{version} -p "3.14 3.13" --dest-dir=/build/reproducible-path/mdtraj-1.11.0/debian/tmp I: pybuild plugin_pyproject:186: Copying package built for python3.14 to destdir I: pybuild plugin_pyproject:186: 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 install -p -m0644 debian/.debhelper/generated/python3-mdtraj/dh_installchangelogs.dch.binnmu debian/python3-mdtraj/usr/share/doc/python3-mdtraj/changelog.Debian.amd64 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_python3:184: version: 6.20251204.1 D: dh_python3 dh_python3:185: argv: ['/usr/bin/dh_python3', '-a', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:186: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=True, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild']) D: dh_python3 dh_python3:187: supported Python versions: 3.13,3.14 (default=3.13) D: dh_python3 debhelper:174: source=mdtraj, binary packages=['python3-mdtraj'] D: dh_python3 dh_python3:209: processing package python3-mdtraj... D: dh_python3 fs:51: 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:51: moving files from debian/python3-mdtraj/usr/lib/python3.14/dist-packages to debian/python3-mdtraj/usr/lib/python3/dist-packages/ D: dh_python3 fs:249: removing dist-packages/.pytest_cache D: dh_python3 fs:178: Writing INSTALLER in debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.11.0.dist-info D: dh_python3 fs:189: Deleting RECORD in debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.11.0.dist-info I: dh_python3 tools:114: replacing shebang in debian/python3-mdtraj/usr/bin/mdinspect I: dh_python3 tools:114: replacing shebang in debian/python3-mdtraj/usr/bin/mdconvert-mdtraj D: dh_python3 fs:349: package python3-mdtraj details = {'requires.txt': set(), 'egg-info': set(), 'dist-info': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.11.0.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:103: generating dependencies for package python3-mdtraj D: dh_python3 pydist:175: trying to find dependency for numpy<3,>=1.25.0 (python=None) D: dh_python3 pydist:209: dependency: module numpy is known to pydist: [{'name': 'numpy', 'vrange': '', 'dependency': 'python3-numpy', 'standard': None, 'rules': [], 'versions': {Version('3.14'), Version('3.13')}}] D: dh_python3 pydist:277: dependency: included in build-deps with limits D: dh_python3 pydist:175: trying to find dependency for scipy (python=None) D: dh_python3 pydist:209: dependency: module scipy is known to pydist: [{'name': 'scipy', 'vrange': '', 'dependency': 'python3-scipy', 'standard': None, 'rules': [], 'versions': {Version('3.14'), Version('3.13')}}] D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 pydist:175: trying to find dependency for pyparsing (python=None) D: dh_python3 pydist:209: dependency: module pyparsing is known to pydist: [{'name': 'pyparsing', 'vrange': '', 'dependency': 'python3-pyparsing', 'standard': None, 'rules': [], 'versions': {Version('3.14'), Version('3.13')}}] D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 pydist:175: trying to find dependency for packaging (python=None) D: dh_python3 pydist:209: dependency: module packaging is known to pydist: [{'name': 'packaging', 'vrange': '', 'dependency': 'python3-packaging', 'standard': None, 'rules': [], 'versions': {Version('3.14'), Version('3.13')}}] D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 depends:252: D={'python3:any', 'python3 (>= 3.13~)', 'python3-scipy', 'python3 (<< 3.15)', 'python3-packaging', 'python3-pyparsing', 'python3-numpy (>= 2.0.0~)'}; R=[]; S=[]; E=[], B=[]; RT=[] debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/mdtraj-1.11.0' # 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-1.11.0' 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/doc/python3-mdtraj/changelog.Debian.amd64 usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1 gzip -9nf usr/share/doc/python3-mdtraj/changelog.Debian usr/share/doc/python3-mdtraj/changelog.Debian.amd64 usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1 cd '/build/reproducible-path/mdtraj-1.11.0' 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/e8 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/e8/fb0a70efedef37b33d4d68c19f809d494d052b.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e8/fb0a70efedef37b33d4d68c19f809d494d052b.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/e8/fb0a70efedef37b33d4d68c19f809d494d052b.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/f5 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/f5/634046e6cf2b6d23552068dda7ba0707eab760.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f5/634046e6cf2b6d23552068dda7ba0707eab760.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/f5/634046e6cf2b6d23552068dda7ba0707eab760.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/6d 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/6d/3a20554a86b232f6a93b5541c8364e0a4eb3dd.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6d/3a20554a86b232f6a93b5541c8364e0a4eb3dd.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/6d/3a20554a86b232f6a93b5541c8364e0a4eb3dd.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/97 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/97/d1b42b3c14519d441bd1769f40e86cb25153d5.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/97/d1b42b3c14519d441bd1769f40e86cb25153d5.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/97/d1b42b3c14519d441bd1769f40e86cb25153d5.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/cc 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/cc/d0e910aa248a6a833c2d3918034db719714d19.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/cc/d0e910aa248a6a833c2d3918034db719714d19.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/cc/d0e910aa248a6a833c2d3918034db719714d19.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/ac 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/ac/67f8ad8efc8d3a6ec34e650501211552a623a4.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ac/67f8ad8efc8d3a6ec34e650501211552a623a4.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/ac/67f8ad8efc8d3a6ec34e650501211552a623a4.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/01 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/01/6386227fe20e07bd7d68a53f4b653a821bae74.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/01/6386227fe20e07bd7d68a53f4b653a821bae74.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/01/6386227fe20e07bd7d68a53f4b653a821bae74.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/7b 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/7b/56ec09ee9fa30885995dc88559fe725e7eabf8.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/7b/56ec09ee9fa30885995dc88559fe725e7eabf8.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/7b/56ec09ee9fa30885995dc88559fe725e7eabf8.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/f6 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/f6/c742605f79c9f5064d0490503bc78220ef59f4.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f6/c742605f79c9f5064d0490503bc78220ef59f4.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/f6/c742605f79c9f5064d0490503bc78220ef59f4.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/9d 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/9d/1347daffebb3a93d4a82b78dd20a214ecea547.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/9d/1347daffebb3a93d4a82b78dd20a214ecea547.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/9d/1347daffebb3a93d4a82b78dd20a214ecea547.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/43 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/43/b3cb117b9b878edf472b599019ebb4eb737944.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/43/b3cb117b9b878edf472b599019ebb4eb737944.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/43/b3cb117b9b878edf472b599019ebb4eb737944.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/35 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/35/78d45438000ecf3fcfa5cbfb63f0757afe2e02.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/35/78d45438000ecf3fcfa5cbfb63f0757afe2e02.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/35/78d45438000ecf3fcfa5cbfb63f0757afe2e02.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/53 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/53/18c4394dd9489ae6365d4fcce177d9dc0885e3.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/53/18c4394dd9489ae6365d4fcce177d9dc0885e3.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/53/18c4394dd9489ae6365d4fcce177d9dc0885e3.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/fb 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/fb/6ae5999e1a728e15637814b106dc776c457ae1.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fb/6ae5999e1a728e15637814b106dc776c457ae1.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/fb/6ae5999e1a728e15637814b106dc776c457ae1.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/07 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/07/a37e466c089cbeb8abf777f5981e3120cef8de.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/07/a37e466c089cbeb8abf777f5981e3120cef8de.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/07/a37e466c089cbeb8abf777f5981e3120cef8de.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/8a 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/8a/9a3b5947621f82f40ad7de99c9822d2889f5ff.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/8a/9a3b5947621f82f40ad7de99c9822d2889f5ff.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/8a/9a3b5947621f82f40ad7de99c9822d2889f5ff.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/47 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/47/b066dffc576eb741dfb254f73ac090569fe6cd.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/47/b066dffc576eb741dfb254f73ac090569fe6cd.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/47/b066dffc576eb741dfb254f73ac090569fe6cd.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-314-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d7 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/d7/0c710082abfb51a3cf7bd2b7fcb29317b33d05.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d7/0c710082abfb51a3cf7bd2b7fcb29317b33d05.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/d7/0c710082abfb51a3cf7bd2b7fcb29317b33d05.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/a7 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/a7/7082e3d6494da62787977e47052ce1cee9a2ad.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a7/7082e3d6494da62787977e47052ce1cee9a2ad.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/a7/7082e3d6494da62787977e47052ce1cee9a2ad.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/6a 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/6a/cda67c112c4e5fb6e97a6d4d09d0252a887103.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6a/cda67c112c4e5fb6e97a6d4d09d0252a887103.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/6a/cda67c112c4e5fb6e97a6d4d09d0252a887103.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-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/_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/_rmsd.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/formats/xtc.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/trr.cpython-313-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/trr.cpython-314-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/xtc.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/geometry/neighborlist.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/neighbors.cpython-314-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/_geometry.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/drid.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-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="016386227fe20e07bd7d68a53f4b653a821bae74 07a37e466c089cbeb8abf777f5981e3120cef8de 3578d45438000ecf3fcfa5cbfb63f0757afe2e02 43b3cb117b9b878edf472b599019ebb4eb737944 47b066dffc576eb741dfb254f73ac090569fe6cd 5318c4394dd9489ae6365d4fcce177d9dc0885e3 6acda67c112c4e5fb6e97a6d4d09d0252a887103 6d3a20554a86b232f6a93b5541c8364e0a4eb3dd 7b56ec09ee9fa30885995dc88559fe725e7eabf8 8a9a3b5947621f82f40ad7de99c9822d2889f5ff 97d1b42b3c14519d441bd1769f40e86cb25153d5 9d1347daffebb3a93d4a82b78dd20a214ecea547 a77082e3d6494da62787977e47052ce1cee9a2ad ac67f8ad8efc8d3a6ec34e650501211552a623a4 ccd0e910aa248a6a833c2d3918034db719714d19 d70c710082abfb51a3cf7bd2b7fcb29317b33d05 e8fb0a70efedef37b33d4d68c19f809d494d052b f5634046e6cf2b6d23552068dda7ba0707eab760 f6c742605f79c9f5064d0490503bc78220ef59f4 fb6ae5999e1a728e15637814b106dc776c457ae1" -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-dbgsym' in '../python3-mdtraj-dbgsym_1.11.0-2+b1_amd64.deb'. dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.11.0-2+b1_amd64.deb'. dpkg-genbuildinfo --build=any -O../mdtraj_1.11.0-2+b1_amd64.buildinfo dpkg-genchanges --build=any -O../mdtraj_1.11.0-2+b1_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-1.11.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2025-12-27T15:55:01Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sat, 27 Dec 2025 15:55:02 +0000 | +------------------------------------------------------------------------------+ mdtraj_1.11.0-2+b1_amd64.changes: --------------------------------- Format: 1.8 Date: Tue, 09 Dec 2025 15:48:52 +0000 Source: mdtraj (1.11.0-2) Binary: python3-mdtraj python3-mdtraj-dbgsym Binary-Only: yes Architecture: amd64 Version: 1.11.0-2+b1 Distribution: unstable Urgency: low Maintainer: Debichem Team Changed-By: amd64 / i386 Build Daemon (x86-ubc-02) Description: python3-mdtraj - Read, write and analyze MD trajectories in Python Changes: mdtraj (1.11.0-2+b1) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild with Python 3.14 as supported Checksums-Sha1: 71147d1664502289b2f09ba15b064ede8fc93e11 10920 mdtraj_1.11.0-2+b1_amd64.buildinfo dc835a41a93f1f70962651584649e95593795547 11752124 python3-mdtraj-dbgsym_1.11.0-2+b1_amd64.deb 0931c8afdcff391dd922476ac9486ce7b7d6cb70 1426044 python3-mdtraj_1.11.0-2+b1_amd64.deb Checksums-Sha256: 0cd59252000296bd5bdb62980f410ff45872864e321e2ad81f85fa094911644f 10920 mdtraj_1.11.0-2+b1_amd64.buildinfo 2a383003fb0f14466541c8c21b558ef73376f558f17e630a09b955013934db5a 11752124 python3-mdtraj-dbgsym_1.11.0-2+b1_amd64.deb 2a874dee9a02f3dc4d57973580efe3ee07d46431533fb85ca1776e12dc91172b 1426044 python3-mdtraj_1.11.0-2+b1_amd64.deb Files: b4aedde4a233b67668585a9695885761 10920 python optional mdtraj_1.11.0-2+b1_amd64.buildinfo 7e7d3696a70d6087d06bee2e4556b924 11752124 debug optional python3-mdtraj-dbgsym_1.11.0-2+b1_amd64.deb b37ef66e781d870468bbb65cfea007ad 1426044 python optional python3-mdtraj_1.11.0-2+b1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sat, 27 Dec 2025 15:55:03 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: mdtraj (1.11.0-2) Binary: python3-mdtraj python3-mdtraj-dbgsym Architecture: amd64 Version: 1.11.0-2+b1 Binary-Only-Changes: mdtraj (1.11.0-2+b1) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild with Python 3.14 as supported . -- amd64 / i386 Build Daemon (x86-ubc-02) Tue, 09 Dec 2025 15:48:52 +0000 Checksums-Md5: 7e7d3696a70d6087d06bee2e4556b924 11752124 python3-mdtraj-dbgsym_1.11.0-2+b1_amd64.deb b37ef66e781d870468bbb65cfea007ad 1426044 python3-mdtraj_1.11.0-2+b1_amd64.deb Checksums-Sha1: dc835a41a93f1f70962651584649e95593795547 11752124 python3-mdtraj-dbgsym_1.11.0-2+b1_amd64.deb 0931c8afdcff391dd922476ac9486ce7b7d6cb70 1426044 python3-mdtraj_1.11.0-2+b1_amd64.deb Checksums-Sha256: 2a383003fb0f14466541c8c21b558ef73376f558f17e630a09b955013934db5a 11752124 python3-mdtraj-dbgsym_1.11.0-2+b1_amd64.deb 2a874dee9a02f3dc4d57973580efe3ee07d46431533fb85ca1776e12dc91172b 1426044 python3-mdtraj_1.11.0-2+b1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 27 Dec 2025 15:55:01 +0000 Build-Path: /build/reproducible-path/mdtraj-1.11.0 Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.18.1-3), autopoint (= 0.23.2-1), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.8), bash (= 5.3-1), binutils (= 2.45.50.20251201-1), binutils-common (= 2.45.50.20251201-1), binutils-x86-64-linux-gnu (= 2.45.50.20251201-1), bsdextrautils (= 2.41.2-4), build-essential (= 12.12), bzip2 (= 1.0.8-6), ca-certificates (= 20250419), coreutils (= 9.7-3), cpp (= 4:15.2.0-4), cpp-15 (= 15.2.0-10), cpp-15-x86-64-linux-gnu (= 15.2.0-10), cpp-x86-64-linux-gnu (= 4:15.2.0-4), cython3 (= 3.1.6+dfsg-2+b1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.28), debianutils (= 5.23.2), dh-autoreconf (= 21), dh-python (= 6.20251204.1), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), docutils-common (= 0.22.3+dfsg-1), dpkg (= 1.22.21), dpkg-dev (= 1.22.21), dwz (= 0.16-2), file (= 1:5.46-5), findutils (= 4.10.0-3), fonts-mathjax (= 2.7.9+dfsg-1), g++ (= 4:15.2.0-4), g++-15 (= 15.2.0-10), g++-15-x86-64-linux-gnu (= 15.2.0-10), g++-x86-64-linux-gnu (= 4:15.2.0-4), gcc (= 4:15.2.0-4), gcc-15 (= 15.2.0-10), gcc-15-base (= 15.2.0-10), gcc-15-x86-64-linux-gnu (= 15.2.0-10), gcc-x86-64-linux-gnu (= 4:15.2.0-4), 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 (= 2.3.2-2+b1), libaec0 (= 1.1.4-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-10), libatomic1 (= 15.2.0-10), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.45.50.20251201-1), libblas3 (= 3.12.1-7), libblkid1 (= 2.41.2-4), libblosc1 (= 1.21.5+ds-2), libblosc2-4 (= 2.17.1+ds-2), libbrotli1 (= 1.1.0-2+b9), libbsd0 (= 0.12.2-2), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.42-5), libc-dev-bin (= 2.42-5), libc-gconv-modules-extra (= 2.42-5), libc6 (= 2.42-5), libc6-dev (= 2.42-5), libcap-ng0 (= 0.8.5-4+b2), libcap2 (= 1:2.75-10+b2), libcc1-0 (= 15.2.0-10), libcom-err2 (= 1.47.2-3+b4), libcrypt-dev (= 1:4.5.1-1), libcrypt1 (= 1:4.5.1-1), libctf-nobfd0 (= 2.45.50.20251201-1), libctf0 (= 2.45.50.20251201-1), libcurl3t64-gnutls (= 8.17.0-3), libcurl4t64 (= 8.17.0-3), libdb5.3t64 (= 5.3.28+dfsg2-11), libdebconfclient0 (= 0.282), libdebhelper-perl (= 13.28), libdpkg-perl (= 1.22.21), libelf1t64 (= 0.194-1), libexpat1 (= 2.7.3-1), libexpat1-dev (= 2.7.3-1), libffi8 (= 3.5.2-3), libfile-stripnondeterminism-perl (= 1.15.0-1), libgcc-15-dev (= 15.2.0-10), libgcc-s1 (= 15.2.0-10), libgdbm-compat4t64 (= 1.26-1), libgdbm6t64 (= 1.26-1), libgfortran5 (= 15.2.0-10), libgmp10 (= 2:6.3.0+dfsg-5), libgnutls30t64 (= 3.8.11-3), libgomp1 (= 15.2.0-10), libgprofng0 (= 2.45.50.20251201-1), libgssapi-krb5-2 (= 1.22.1-2), libhdf5-310 (= 1.14.5+repack-4), libhdf5-hl-310 (= 1.14.5+repack-4), libhogweed6t64 (= 3.10.2-1), libhwasan0 (= 15.2.0-10), libidn2-0 (= 2.3.8-4), libisl23 (= 0.27-1), libitm1 (= 15.2.0-10), libjansson4 (= 2.14-2+b3), libjs-mathjax (= 2.7.9+dfsg-1), libjs-sphinxdoc (= 8.2.3-11), libjson-perl (= 4.10000-1), libk5crypto3 (= 1.22.1-2), libkeyutils1 (= 1.6.3-6), libkrb5-3 (= 1.22.1-2), libkrb5support0 (= 1.22.1-2), liblapack3 (= 3.12.1-7), libldap2 (= 2.6.10+dfsg-1), liblsan0 (= 15.2.0-10), liblz4-1 (= 1.10.0-6), liblzma5 (= 5.8.1-2), liblzo2-2 (= 2.10-3+b1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.2-4), libmpc3 (= 1.3.1-2), libmpfr6 (= 4.2.2-2), libncursesw6 (= 6.5+20251123-1), libnetcdf22 (= 1:4.9.3-1+b1), libnettle8t64 (= 3.10.2-1), libnghttp2-14 (= 1.64.0-1.1+b1), libnghttp3-9 (= 1.12.0-1), libngtcp2-16 (= 1.16.0-1), libngtcp2-crypto-gnutls8 (= 1.16.0-1), libngtcp2-crypto-ossl0 (= 1.16.0-1), libnorm1t64 (= 1.5.9+dfsg-4), libp11-kit0 (= 0.25.10-1), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.46-1), libperl5.40 (= 5.40.1-7), libpgm-5.3-0t64 (= 5.3.128~dfsg-2.1+b1), libpipeline1 (= 1.5.8-2), libpsl5t64 (= 0.21.2-1.1+b1), libpython3-all-dev (= 3.13.9-2), libpython3-dev (= 3.13.9-2), libpython3-stdlib (= 3.13.9-2), libpython3.13 (= 3.13.11-1+b1), libpython3.13-dev (= 3.13.11-1+b1), libpython3.13-minimal (= 3.13.11-1+b1), libpython3.13-stdlib (= 3.13.11-1+b1), libpython3.14 (= 3.14.2-1+b1), libpython3.14-dev (= 3.14.2-1+b1), libpython3.14-minimal (= 3.14.2-1+b1), libpython3.14-stdlib (= 3.14.2-1+b1), libqhull-r8.0 (= 2020.2-7), libquadmath0 (= 15.2.0-10), libreadline8t64 (= 8.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-3), libsasl2-2 (= 2.1.28+dfsg1-10), libsasl2-modules-db (= 2.1.28+dfsg1-10), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.9-4+b1), libsframe2 (= 2.45.50.20251201-1), libsmartcols1 (= 2.41.2-4), libsnappy1v5 (= 1.2.2-2), libsodium23 (= 1.0.18-1+b2), libsqlite3-0 (= 3.46.1-8), libssh2-1t64 (= 1.11.1-1), libssl3t64 (= 3.5.4-1), libstdc++-15-dev (= 15.2.0-10), libstdc++6 (= 15.2.0-10), libsystemd0 (= 259~rc2-1), libsz2 (= 1.1.4-2), libtasn1-6 (= 4.20.0-2), libtinfo6 (= 6.5+20251123-1), libtool (= 2.5.4-9), libtsan2 (= 15.2.0-10), libubsan1 (= 15.2.0-10), libuchardet0 (= 0.0.8-2), libudev1 (= 259~rc2-1), libunistring5 (= 1.3-2), libuuid1 (= 2.41.2-4), libxml2-16 (= 2.15.1+dfsg-2+b1), libxxhash0 (= 0.8.3-2), libzmq5 (= 4.3.5-1+b3), libzstd1 (= 1.5.7+dfsg-2), linux-libc-dev (= 6.17.10-1), m4 (= 1.4.20-2), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), media-types (= 14.0.0), ncurses-base (= 6.5+20251123-1), ncurses-bin (= 6.5+20251123-1), netbase (= 6.5), openssl (= 3.5.4-1), openssl-provider-legacy (= 3.5.4-1), patch (= 2.8-2), perl (= 5.40.1-7), perl-base (= 5.40.1-7), perl-modules-5.40 (= 5.40.1-7), po-debconf (= 1.0.22), pybuild-plugin-pyproject (= 6.20251204.1), python-babel-localedata (= 2.17.0-2), python-tables-data (= 3.10.2-3), python-tinycss2-common (= 1.4.0-2), python3 (= 3.13.9-2), python3-alabaster (= 0.7.16-0.1), python3-all (= 3.13.9-2), python3-all-dev (= 3.13.9-2), python3-attr (= 25.4.0-1), python3-autocommand (= 2.2.2-3), python3-babel (= 2.17.0-2), python3-bleach (= 6.3.0-1), python3-bs4 (= 4.14.3-1), python3-build (= 1.2.2-4), python3-certifi (= 2025.11.12+ds-1), python3-cffi-backend (= 2.0.0-2+b1), python3-cftime (= 1.6.5-1+b1), python3-chardet (= 5.2.0+dfsg-2), 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 (= 3.13.9-2), python3-docutils (= 0.22.3+dfsg-1), python3-fastjsonschema (= 2.21.1-1), python3-gsd (= 4.2.0-1), python3-html5lib (= 1.2-2), python3-idna (= 3.10-1), python3-imagesize (= 1.4.1-1), python3-inflect (= 7.5.0-1), python3-iniconfig (= 2.1.0-1), python3-installer (= 0.7.0+dfsg1-3), python3-jaraco.context (= 6.0.1-1), python3-jaraco.functools (= 4.1.0-1), python3-jaraco.text (= 4.0.0-1), python3-jinja2 (= 3.1.6-1), python3-jsonschema (= 4.25.1-2), python3-jsonschema-specifications (= 2023.12.1-4), python3-jupyter-client (= 8.6.3-3), python3-jupyter-core (= 5.7.2-5), python3-jupyterlab-pygments (= 0.2.2-3), python3-markupsafe (= 3.0.3-1+b1), python3-minimal (= 3.13.9-2), python3-mistune (= 3.1.4-1), python3-more-itertools (= 10.8.0-1), python3-nbclient (= 0.8.0-3), python3-nbconvert (= 7.16.6-1), python3-nbformat (= 5.9.1-1), python3-nbsphinx (= 0.9.5+ds-1), python3-netcdf4 (= 1.7.3-1+b1), python3-networkx (= 3.4.2-4), python3-numexpr (= 2.14.1-1+b1), python3-numpy (= 1:2.3.5+ds-2+b1), python3-numpy-dev (= 1:2.3.5+ds-2+b1), python3-packaging (= 25.0-1), 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 (= 4.4.0-1), python3-pluggy (= 1.6.0-1), python3-psutil (= 7.1.0-1), python3-pygments (= 2.18.0+dfsg-2), python3-pyparsing (= 3.1.3-1), python3-pyproject-hooks (= 1.2.0-1), python3-pytest (= 8.4.2-1), 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 (= 3.1.0-2), python3-rpds-py (= 0.28.0-1), python3-scipy (= 1.16.3-2), python3-setuptools (= 78.1.1-0.1), python3-snowballstemmer (= 3.0.1-1), python3-soupsieve (= 2.7-2), python3-sphinx (= 8.2.3-11), python3-tables (= 3.10.2-3), python3-tables-lib (= 3.10.2-3+b1), python3-tinycss2 (= 1.4.0-2), python3-tornado (= 6.5.2-3), python3-traitlets (= 5.14.3+really5.14.3-2), python3-typeguard (= 4.4.4-1), python3-typing-extensions (= 4.15.0-1), python3-urllib3 (= 2.5.0-1), python3-versioneer (= 0.29-1), python3-webencodings (= 0.5.1-5), python3-wheel (= 0.46.1-2), python3-zipp (= 3.23.0-1), python3-zmq (= 27.1.0-1+b1), python3.13 (= 3.13.11-1+b1), python3.13-dev (= 3.13.11-1+b1), python3.13-minimal (= 3.13.11-1+b1), python3.14 (= 3.14.2-1+b1), python3.14-dev (= 3.14.2-1+b1), python3.14-minimal (= 3.14.2-1+b1), readline-common (= 8.3-3), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.26), sgml-base (= 1.31+nmu1), sphinx-common (= 8.2.3-11), sysvinit-utils (= 3.15-6), tar (= 1.35+dfsg-3.1), tzdata (= 2025b-5), util-linux (= 2.41.2-4), xml-core (= 0.19), xz-utils (= 5.8.1-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 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2025-12-09 15:48 ./usr/lib/debug/.dwz/x86_64-linux-gnu/python3-mdtraj.debug drwxr-xr-x root/root 0 2025-12-09 15:48 ./usr/share/ drwxr-xr-x root/root 0 2025-12-09 15:48 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-12-09 15:48 ./usr/share/doc/python3-mdtraj-dbgsym -> python3-mdtraj python3-mdtraj_1.11.0-2+b1_amd64.deb ------------------------------------ new Debian package, version 2.0. size 1426044 bytes: control archive=4656 bytes. 1490 bytes, 32 lines control 11792 bytes, 124 lines md5sums 275 bytes, 12 lines * postinst #!/bin/sh 421 bytes, 12 lines * prerm #!/bin/sh Package: python3-mdtraj Source: mdtraj (1.11.0-2) Version: 1.11.0-2+b1 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 7658 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 2025-12-09 15:48 ./ drwxr-xr-x root/root 0 2025-12-09 15:48 ./usr/ drwxr-xr-x root/root 0 2025-12-09 15:48 ./usr/bin/ -rwxr-xr-x root/root 238 2025-12-09 15:48 ./usr/bin/mdconvert-mdtraj -rwxr-xr-x root/root 238 2025-12-09 15:48 ./usr/bin/mdinspect drwxr-xr-x root/root 0 2025-12-09 15:48 ./usr/lib/ drwxr-xr-x root/root 0 2025-12-09 15:48 ./usr/lib/python3/ drwxr-xr-x root/root 0 2025-12-09 15:48 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2025-12-09 15:48 ./usr/lib/python3/dist-packages/mdtraj-1.11.0.dist-info/ -rw-r--r-- root/root 7 2025-12-09 15:48 ./usr/lib/python3/dist-packages/mdtraj-1.11.0.dist-info/INSTALLER -rw-r--r-- root/root 2567 2025-12-09 15:48 ./usr/lib/python3/dist-packages/mdtraj-1.11.0.dist-info/METADATA -rw-r--r-- root/root 104 2025-12-09 15:48 ./usr/lib/python3/dist-packages/mdtraj-1.11.0.dist-info/WHEEL 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+------------------------------------------------------------------------------+ | Summary Sat, 27 Dec 2025 15:55:08 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 304004 Build-Time: 840 Distribution: unstable Host Architecture: amd64 Install-Time: 5 Job: /srv/rebuilderd/tmp/rebuilderdr14PJq/inputs/mdtraj_1.11.0-2.dsc Machine Architecture: amd64 Package: mdtraj Package-Time: 858 Source-Version: 1.11.0-2 Space: 304004 Status: successful Version: 1.11.0-2+b1 -------------------------------------------------------------------------------- Finished at 2025-12-27T15:55:01Z Build needed 00:14:18, 304004k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderdr14PJq/out checking python3-mdtraj-dbgsym_1.11.0-2+b1_amd64.deb: size differs for python3-mdtraj-dbgsym_1.11.0-2+b1_amd64.deb