=============================================================================== 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/rebuilderdekgDYI/inputs/mdtraj_1.11.0-2+b1_arm64.buildinfo Source: mdtraj Version: 1.11.0-2 rebuilderd-worker node: codethink02-arm64 +------------------------------------------------------------------------------+ | Downloading sources Fri, 26 Dec 2025 06:54:23 +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 [6548 B] Get:11 https://deb.debian.org/debian-security trixie-security/main Sources [116 kB] Get:12 https://deb.debian.org/debian-security trixie-security/non-free-firmware Sources [696 B] Get:13 https://deb.debian.org/debian trixie-updates/main Sources [2788 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 [147 kB] Get:16 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [2468 B] Get:17 https://deb.debian.org/debian trixie-backports/main Sources [112 kB] Get:18 https://deb.debian.org/debian forky/non-free-firmware Sources [7696 B] Get:19 https://deb.debian.org/debian forky/main Sources [10.6 MB] Get:20 https://deb.debian.org/debian sid/main Sources [11.2 MB] Get:21 https://deb.debian.org/debian sid/non-free-firmware Sources [9692 B] Get:22 https://deb.debian.org/debian experimental/non-free-firmware Sources [3180 B] Get:23 https://deb.debian.org/debian experimental/main Sources [357 kB] Fetched 33.9 MB in 32s (1060 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 Fri, 26 Dec 2025 06:54:56 +0000 | +------------------------------------------------------------------------------+ Rebuilding mdtraj=1.11.0-2 in /srv/rebuilderd/tmp/rebuilderdekgDYI/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdekgDYI/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdekgDYI/inputs/mdtraj_1.11.0-2+b1_arm64.buildinfo /srv/rebuilderd/tmp/rebuilderdekgDYI/inputs/mdtraj_1.11.0-2+b1_arm64.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/20251208T143746Z sid InRelease [176 kB] Get:3 http://deb.debian.org/debian unstable/main arm64 Packages [10.1 MB] Get:4 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 Packages [10.2 MB] Fetched 20.7 MB in 4s (5571 kB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20251208T143746Z/dists/sid/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://deb.debian.org/debian unstable/main arm64 perl-modules-5.40 all 5.40.1-7 [3012 kB] Fetched 3012 kB in 0s (46.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyk0qmdvp/perl-modules-5.40_5.40.1-7_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 base-files arm64 14 [72.9 kB] Fetched 72.9 kB in 0s (3231 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp39h8465f/base-files_14_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-platformdirs all 4.4.0-1 [16.7 kB] Fetched 16.7 kB in 0s (707 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpphksd7st/python3-platformdirs_4.4.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.2-1 [1613 kB] Fetched 1613 kB in 0s (45.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6q0csha1/gettext_0.23.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgdbm6t64 arm64 1.26-1 [77.5 kB] Fetched 77.5 kB in 0s (3681 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf5njdpn5/libgdbm6t64_1.26-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-3+b1 [49.6 kB] Fetched 49.6 kB in 0s (2615 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp937e0qlo/liblzo2-2_2.10-3+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4 [1196 B] Fetched 1196 B in 0s (0 B/s) dpkg-name: info: moved 'g++-aarch64-linux-gnu_4%3a15.2.0-4_arm64.deb' to '/srv/rebuilderd/tmp/tmp_nlov8q6/g++-aarch64-linux-gnu_15.2.0-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31+nmu1 [10.9 kB] Fetched 10.9 kB in 0s (601 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6mu692d4/sgml-base_1.31+nmu1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 python3-docutils all 0.22.3+dfsg-1 [432 kB] Fetched 432 kB in 0s (17.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8dmp3z2f/python3-docutils_0.22.3+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libcurl4t64 arm64 8.17.0-3 [369 kB] Fetched 369 kB in 0s (9363 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpux0y551g/libcurl4t64_8.17.0-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-7 [1846 kB] Fetched 1846 kB in 0s (99.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp78mokddv/liblapack3_3.12.1-7_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 rpcsvc-proto arm64 1.4.3-1+b1 [60.5 kB] Fetched 60.5 kB in 0s (2469 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyqrxgptm/rpcsvc-proto_1.4.3-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnorm1t64 arm64 1.5.9+dfsg-4 [205 kB] Fetched 205 kB in 0s (7122 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp10i6vpd1/libnorm1t64_1.5.9+dfsg-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 debconf all 1.5.91 [121 kB] Fetched 121 kB in 0s (5668 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp58y_txp/debconf_1.5.91_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libaec0 arm64 1.1.4-2 [22.6 kB] Fetched 22.6 kB in 0s (1223 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsh6nmcq4/libaec0_1.1.4-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 tar arm64 1.35+dfsg-3.1 [802 kB] Fetched 802 kB in 0s (23.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppqpyt3n3/tar_1.35+dfsg-3.1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 liblsan0 arm64 15.2.0-10 [1194 kB] Fetched 1194 kB in 0s (49.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi9w0iqwd/liblsan0_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Fetched 27.0 kB in 0s (1047 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphv_cu3yg/sensible-utils_0.0.26_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libjs-sphinxdoc all 8.2.3-11 [27.8 kB] Fetched 27.8 kB in 0s (1442 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprjj4cgmo/libjs-sphinxdoc_8.2.3-11_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libudev1 arm64 259~rc2-1 [147 kB] Fetched 147 kB in 0s (8863 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxu8exkw1/libudev1_259~rc2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.11-1+b1 [1903 kB] Fetched 1903 kB in 0s (107 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprn3p4moa/libpython3.13-stdlib_3.13.11-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB] Fetched 43.4 kB in 0s (3261 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdh291y7k/python3-defusedxml_0.7.1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libbz2-1.0 arm64 1.0.8-6 [37.8 kB] Fetched 37.8 kB in 0s (1839 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpddcyzfj7/libbz2-1.0_1.0.8-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 bash arm64 5.3-1 [1507 kB] Fetched 1507 kB in 0s (37.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwwbpwpbn/bash_5.3-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.5.0-1 [116 kB] Fetched 116 kB in 0s (8984 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpudhol8zv/python3-urllib3_2.5.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.7.3-1 [150 kB] Fetched 150 kB in 0s (8860 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv4urx1_r/libexpat1-dev_2.7.3-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libaudit-common all 1:4.1.2-1 [14.3 kB] Fetched 14.3 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit-common_1%3a4.1.2-1_all.deb' to '/srv/rebuilderd/tmp/tmpsjqrx6rr/libaudit-common_4.1.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.17.0-2 [6052 kB] Fetched 6052 kB in 0s (150 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn6ryg3e9/python-babel-localedata_2.17.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-cffi-backend arm64 2.0.0-2+b1 [110 kB] Fetched 110 kB in 0s (8556 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphv7c3jwr/python3-cffi-backend_2.0.0-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libdebconfclient0 arm64 0.282 [11.0 kB] Fetched 11.0 kB in 0s (607 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz0xvddvr/libdebconfclient0_0.282_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-pandocfilters all 1.5.1-1 [23.7 kB] Fetched 23.7 kB in 0s (1506 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1x083nlb/python3-pandocfilters_1.5.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Fetched 2210 kB in 0s (109 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8iy9jm4r/fonts-mathjax_2.7.9+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libcom-err2 arm64 1.47.2-3+b4 [24.9 kB] Fetched 24.9 kB in 0s (2195 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplitll1nv/libcom-err2_1.47.2-3+b4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libperl5.40 arm64 5.40.1-7 [4134 kB] Fetched 4134 kB in 0s (79.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp4de21p0/libperl5.40_5.40.1-7_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsnappy1v5 arm64 1.2.2-2 [28.4 kB] Fetched 28.4 kB in 0s (1655 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxvc_7pzc/libsnappy1v5_1.2.2-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-tornado arm64 6.5.2-3 [357 kB] Fetched 357 kB in 0s (18.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0t8xsl_3/python3-tornado_6.5.2-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Fetched 69.0 kB in 0s (4082 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9a4as_mm/libuchardet0_0.0.8-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpam0g arm64 1.7.0-5 [68.8 kB] Fetched 68.8 kB in 0s (3114 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeg2adi21/libpam0g_1.7.0-5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.4-1 [37.1 kB] Fetched 37.1 kB in 0s (1981 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmposugr8fp/python3-typeguard_4.4.4-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 liblz4-1 arm64 1.10.0-6 [66.7 kB] Fetched 66.7 kB in 0s (3941 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb6yete9g/liblz4-1_1.10.0-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.5.0-1 [33.0 kB] Fetched 33.0 kB in 0s (3150 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmnzecgd7/python3-inflect_7.5.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Fetched 8812 B in 0s (519 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppqb47ifk/dh-strip-nondeterminism_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.22 [216 kB] Fetched 216 kB in 0s (9592 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppnp4_067/po-debconf_1.0.22_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Fetched 100 kB in 0s (5509 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph7j5mozj/dwz_0.16-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libc6-dev arm64 2.42-5 [1697 kB] Fetched 1697 kB in 0s (66.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi64byc0_/libc6-dev_2.42-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libtsan2 arm64 15.2.0-10 [2400 kB] Fetched 2400 kB in 0s (58.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3fxmx0v2/libtsan2_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Fetched 6096 B in 0s (312 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp72zg1kk/python3-jupyterlab-pygments_0.2.2-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 openssl-provider-legacy arm64 3.5.4-1 [306 kB] Fetched 306 kB in 0s (11.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpak7yg1tn/openssl-provider-legacy_3.5.4-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 2.1.0-1 [7432 B] Fetched 7432 B in 0s (339 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppgu96zev/python3-iniconfig_2.1.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 init-system-helpers all 1.69 [39.3 kB] Fetched 39.3 kB in 0s (2120 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0ghcc46i/init-system-helpers_1.69_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libblosc2-4 arm64 2.17.1+ds-2 [164 kB] Fetched 164 kB in 0s (8236 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfx5cjztc/libblosc2-4_2.17.1+ds-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-nbformat all 5.9.1-1 [45.1 kB] Fetched 45.1 kB in 0s (1911 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp23l47uwk/python3-nbformat_5.9.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.2-1 [242 kB] Fetched 242 kB in 0s (10.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzhmvii78/gettext-base_0.23.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpam-modules-bin arm64 1.7.0-5 [48.3 kB] Fetched 48.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplo9m4n_v/libpam-modules-bin_1.7.0-5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmpc3 arm64 1.3.1-2 [50.2 kB] Fetched 50.2 kB in 0s (2057 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm8bu0b07/libmpc3_1.3.1-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 3.0.1-1 [63.5 kB] Fetched 63.5 kB in 0s (6325 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpecf_4__9/python3-snowballstemmer_3.0.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libisl23 arm64 0.27-1 [601 kB] Fetched 601 kB in 0s (25.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpocpk0bjk/libisl23_0.27-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Fetched 179 kB in 0s (5881 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphr12es2f/libldap2_2.6.10+dfsg-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpcre2-8-0 arm64 10.46-1 [262 kB] Fetched 262 kB in 0s (12.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpri98ebn7/libpcre2-8-0_10.46-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 ncurses-bin arm64 6.5+20251123-1 [438 kB] Fetched 438 kB in 0s (20.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx2qqwz8v/ncurses-bin_6.5+20251123-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.17.0-2 [117 kB] Fetched 117 kB in 0s (6021 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0ydnn40g/python3-babel_2.17.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-9 [540 kB] Fetched 540 kB in 0s (22.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfbtb61hk/libtool_2.5.4-9_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-jsonschema all 4.25.1-2 [75.7 kB] Fetched 75.7 kB in 0s (3483 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd5h7fr14/python3-jsonschema_4.25.1-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Fetched 103 kB in 0s (3760 kB/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.46-5_arm64.deb' to '/srv/rebuilderd/tmp/tmp1ie05xp8/libmagic1t64_5.46-5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-10 [1130 kB] Fetched 1130 kB in 0s (20.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0wh7ehpy/groff-base_1.23.0-10_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 util-linux arm64 2.41.2-4 [1121 kB] Fetched 1121 kB in 0s (34.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp53y9xttx/util-linux_2.41.2-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-decorator all 5.2.1-2 [33.0 kB] Fetched 33.0 kB in 0s (726 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprka4p8xi/python3-decorator_5.2.1-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libcap-ng0 arm64 0.8.5-4+b2 [17.0 kB] Fetched 17.0 kB in 0s (933 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8g8gh3i5/libcap-ng0_0.8.5-4+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-traitlets all 5.14.3+really5.14.3-2 [71.1 kB] Fetched 71.1 kB in 0s (3498 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk7ol9si9/python3-traitlets_5.14.3+really5.14.3-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-cftime arm64 1.6.5-1+b1 [445 kB] Fetched 445 kB in 0s (19.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcha5qmhj/python3-cftime_1.6.5-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libctf-nobfd0 arm64 2.45.50.20251201-1 [154 kB] Fetched 154 kB in 0s (15.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnwnp55k7/libctf-nobfd0_2.45.50.20251201-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Fetched 836 kB in 0s (46.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaetevi11/python3-pygments_2.18.0+dfsg-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.13.9-2 [1072 B] Fetched 1072 B in 0s (61.0 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcgap3pfn/libpython3-all-dev_3.13.9-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 tzdata all 2025b-5 [260 kB] Fetched 260 kB in 0s (13.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprwjuabfw/tzdata_2025b-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.11-1+b1 [859 kB] Fetched 859 kB in 0s (36.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpden4qdyf/libpython3.13-minimal_3.13.11-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-referencing all 0.36.2-2 [23.8 kB] Fetched 23.8 kB in 0s (1373 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3n48wy41/python3-referencing_0.36.2-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 findutils arm64 4.10.0-3 [696 kB] Fetched 696 kB in 0s (30.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa77kkw7v/findutils_4.10.0-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-4 [79.4 kB] Fetched 79.4 kB in 0s (4459 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyzhvuxj0/python3-dateutil_2.9.0-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.5.4-1 [1457 kB] Fetched 1457 kB in 0s (52.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjopr699s/openssl_3.5.4-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxxhash0 arm64 0.8.3-2 [22.3 kB] Fetched 22.3 kB in 0s (1296 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_qt1pkv5/libxxhash0_0.8.3-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-2 [40.3 kB] Fetched 40.3 kB in 0s (2361 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprnlrd7l2/libpipeline1_1.5.8-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Fetched 917 kB in 0s (35.1 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmpx_pfq_r7/zlib1g-dev_1.3.dfsg+really1.3.1-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 make arm64 4.4.1-3 [453 kB] Fetched 453 kB in 0s (21.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz_296j1k/make_4.4.1-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-rpds-py arm64 0.28.0-1 [295 kB] Fetched 295 kB in 0s (14.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprgnio12k/python3-rpds-py_0.28.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-jsonschema-specifications all 2023.12.1-4 [9092 B] Fetched 9092 B in 0s (534 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpusbiv6iw/python3-jsonschema-specifications_2023.12.1-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.22.1-2 [77.1 kB] Fetched 77.1 kB in 0s (4221 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsemenprg/libk5crypto3_1.22.1-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libc-dev-bin arm64 2.42-5 [59.3 kB] Fetched 59.3 kB in 0s (3479 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwqty4am8/libc-dev-bin_2.42-5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Fetched 453 kB in 0s (22.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphztjor64/libunistring5_1.3-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-netcdf4 arm64 1.7.3-1+b1 [744 kB] Fetched 744 kB in 0s (32.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp55dw41q3/python3-netcdf4_1.7.3-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 coreutils arm64 9.7-3 [2949 kB] Fetched 2949 kB in 0s (70.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyv8cd6st/coreutils_9.7-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libc6 arm64 2.42-5 [1466 kB] Fetched 1466 kB in 0s (49.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb8fu0bsj/libc6_2.42-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-10 [10.1 MB] Fetched 10.1 MB in 0s (191 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm0u8xpjo/cpp-15-aarch64-linux-gnu_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libqhull-r8.0 arm64 2020.2-7 [229 kB] Fetched 229 kB in 0s (9743 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp71ijir6l/libqhull-r8.0_2020.2-7_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-11 [626 kB] Fetched 626 kB in 0s (24.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4ze76iuw/libdb5.3t64_5.3.28+dfsg2-11_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python-tinycss2-common all 1.4.0-2 [44.7 kB] Fetched 44.7 kB in 0s (3991 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr5kh6ze0/python-tinycss2-common_1.4.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 sphinx-common all 8.2.3-11 [619 kB] Fetched 619 kB in 0s (42.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpva_ydecp/sphinx-common_8.2.3-11_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-tables all 3.10.2-3 [354 kB] Fetched 354 kB in 0s (29.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp60uu9l58/python3-tables_3.10.2-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Fetched 57.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuzs1tgx1/libpsl5t64_0.21.2-1.1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Fetched 11.7 kB in 0s (1033 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm6xqcmxm/python3-pyproject-hooks_1.2.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gzip arm64 1.13-1 [135 kB] Fetched 135 kB in 0s (12.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpingc4i8j/gzip_1.13-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.13.9-2 [1052 B] Fetched 1052 B in 0s (87.2 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp30c7792k/python3-all_3.13.9-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt4ujka8z/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmd0 arm64 1.1.0-2+b1 [33.7 kB] Fetched 33.7 kB in 0s (1812 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnp81p92k/libmd0_1.1.0-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libhwasan0 arm64 15.2.0-10 [1480 kB] Fetched 1480 kB in 0s (28.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb1hqen52/libhwasan0_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Fetched 9716 B in 0s (579 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5_h5j4dr/libkeyutils1_1.6.3-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-scipy arm64 1.16.3-2 [16.4 MB] Fetched 16.4 MB in 0s (131 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvx5geheu/python3-scipy_1.16.3-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-bleach all 6.3.0-1 [51.4 kB] Fetched 51.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplx8qcqo_/python3-bleach_6.3.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libacl1 arm64 2.3.2-2+b1 [32.2 kB] Fetched 32.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphbeag1gy/libacl1_2.3.2-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.11-1+b1 [504 kB] Fetched 504 kB in 0s (43.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4oqjhs1m/python3.13-dev_3.13.11-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Fetched 87.5 kB in 0s (7838 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3usj9uhe/libjson-perl_4.10000-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libblosc1 arm64 1.21.5+ds-2 [39.0 kB] Fetched 39.0 kB in 0s (2176 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu11f4yta/libblosc1_1.21.5+ds-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libctf0 arm64 2.45.50.20251201-1 [85.6 kB] Fetched 85.6 kB in 0s (3600 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkwkistaf/libctf0_2.45.50.20251201-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libubsan1 arm64 15.2.0-10 [1064 kB] Fetched 1064 kB in 0s (50.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk85ep7n0/libubsan1_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 25.0-1 [56.6 kB] Fetched 56.6 kB in 0s (3639 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3fj2ojz2/python3-packaging_25.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libuuid1 arm64 2.41.2-4 [37.8 kB] Fetched 37.8 kB in 0s (3757 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuf51xuih/libuuid1_2.41.2-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3.14 arm64 3.14.2-1+b1 [829 kB] Fetched 829 kB in 0s (31.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbd7ftac4/python3.14_3.14.2-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-nbsphinx all 0.9.5+ds-1 [39.9 kB] Fetched 39.9 kB in 0s (512 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpds356rg9/python3-nbsphinx_0.9.5+ds-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Fetched 11.0 kB in 0s (659 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl2isqzre/python3-zipp_3.23.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.22.1-2 [32.2 kB] Fetched 32.2 kB in 0s (1501 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp66f5j93v/libkrb5support0_1.22.1-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 xz-utils arm64 5.8.1-2 [657 kB] Fetched 657 kB in 0s (27.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpht3f9sq5/xz-utils_5.8.1-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpgm-5.3-0t64 arm64 5.3.128~dfsg-2.1+b1 [152 kB] Fetched 152 kB in 0s (9448 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn820n8gl/libpgm-5.3-0t64_5.3.128~dfsg-2.1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libhogweed6t64 arm64 3.10.2-1 [332 kB] Fetched 332 kB in 0s (19.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpterhxe5f/libhogweed6t64_3.10.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.13.9-2 [1072 B] Fetched 1072 B in 0s (61.5 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpibdzdvl6/python3-all-dev_3.13.9-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libstdc++-15-dev arm64 15.2.0-10 [2348 kB] Fetched 2348 kB in 0s (63.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk18c00sz/libstdc++-15-dev_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-psutil arm64 7.1.0-1 [224 kB] Fetched 224 kB in 0s (12.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpix9h4nx0/python3-psutil_7.1.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-versioneer all 0.29-1 [43.0 kB] Fetched 43.0 kB in 0s (2424 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmnm8fscs/python3-versioneer_0.29-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-7 [135 kB] Fetched 135 kB in 0s (6733 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxry0vtjo/libblas3_3.12.1-7_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libc-bin arm64 2.42-5 [575 kB] Fetched 575 kB in 0s (24.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4qpojk2w/libc-bin_2.42-5_arm64.deb' Downloading dependency 1 of 317: perl-modules-5.40:arm64=5.40.1-7 Downloading dependency 2 of 317: base-files:arm64=14 Downloading dependency 3 of 317: python3-platformdirs:arm64=4.4.0-1 Downloading dependency 4 of 317: gettext:arm64=0.23.2-1 Downloading dependency 5 of 317: libgdbm6t64:arm64=1.26-1 Downloading dependency 6 of 317: liblzo2-2:arm64=2.10-3+b1 Downloading dependency 7 of 317: g++-aarch64-linux-gnu:arm64=4:15.2.0-4 Downloading dependency 8 of 317: sgml-base:arm64=1.31+nmu1 Downloading dependency 9 of 317: python3-docutils:arm64=0.22.3+dfsg-1 Downloading dependency 10 of 317: libcurl4t64:arm64=8.17.0-3 Downloading dependency 11 of 317: liblapack3:arm64=3.12.1-7 Downloading dependency 12 of 317: rpcsvc-proto:arm64=1.4.3-1+b1 Downloading dependency 13 of 317: libnorm1t64:arm64=1.5.9+dfsg-4 Downloading dependency 14 of 317: debconf:arm64=1.5.91 Downloading dependency 15 of 317: libaec0:arm64=1.1.4-2 Downloading dependency 16 of 317: tar:arm64=1.35+dfsg-3.1 Downloading dependency 17 of 317: liblsan0:arm64=15.2.0-10 Downloading dependency 18 of 317: sensible-utils:arm64=0.0.26 Downloading dependency 19 of 317: libjs-sphinxdoc:arm64=8.2.3-11 Downloading dependency 20 of 317: 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dependency 113 of 317: libubsan1:arm64=15.2.0-10 Downloading dependency 114 of 317: python3-packaging:arm64=25.0-1 Downloading dependency 115 of 317: libuuid1:arm64=2.41.2-4 Downloading dependency 116 of 317: python3.14:arm64=3.14.2-1+b1 Downloading dependency 117 of 317: python3-nbsphinx:arm64=0.9.5+ds-1 Downloading dependency 118 of 317: python3-zipp:arm64=3.23.0-1 Downloading dependency 119 of 317: libkrb5support0:arm64=1.22.1-2 Downloading dependency 120 of 317: xz-utils:arm64=5.8.1-2 Downloading dependency 121 of 317: libpgm-5.3-0t64:arm64=5.3.128~dfsg-2.1+b1 Downloading dependency 122 of 317: libhogweed6t64:arm64=3.10.2-1 Downloading dependency 123 of 317: python3-all-dev:arm64=3.13.9-2 Downloading dependency 124 of 317: libstdc++-15-dev:arm64=15.2.0-10 Downloading dependency 125 of 317: python3-psutil:arm64=7.1.0-1 Downloading dependency 126 of 317: python3-versioneer:arm64=0.29-1 Downloading dependency 127 of 317: libblas3:arm64=3.12.1-7 Downloading dependency 128 of 317: libc-bin:arm64=2.42-5 Downloading dependency 129 of 317: libitm1:arm64=15.2.0-10Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libitm1 arm64 15.2.0-10 [24.1 kB] Fetched 24.1 kB in 0s (1364 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprte92aj8/libitm1_15.2.0-10_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 python3-pluggy all 1.6.0-1 [27.1 kB] Fetched 27.1 kB in 0s (1564 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpunvvvh2j/python3-pluggy_1.6.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.4-2 [155 kB] Fetched 155 kB in 0s (8544 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfrljws43/python3-charset-normalizer_3.4.4-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libselinux1 arm64 3.9-4+b1 [80.8 kB] Fetched 80.8 kB in 0s (4587 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf197qptz/libselinux1_3.9-4+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Fetched 19.9 kB in 0s (1189 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9eu_5ybw/libfile-stripnondeterminism-perl_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3.14-dev arm64 3.14.2-1+b1 [5209 kB] Fetched 5209 kB in 0s (88.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwx23zaed/libpython3.14-dev_3.14.2-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Fetched 71.7 kB in 0s (3888 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5i8zpr39/libnghttp2-14_1.64.0-1.1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Fetched 92.4 kB in 0s (5234 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnqpjuj83/python3-typing-extensions_4.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Fetched 108 kB in 0s (6327 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmponesxl3y/libidn2-0_2.3.8-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.11-1+b1 [2059 kB] Fetched 2059 kB in 0s (61.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptbngys3_/libpython3.13_3.13.11-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libzmq5 arm64 4.3.5-1+b3 [253 kB] Fetched 253 kB in 0s (13.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps796xt7v/libzmq5_4.3.5-1+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libcrypt-dev arm64 1:4.5.1-1 [126 kB] Fetched 126 kB in 0s (7111 kB/s) dpkg-name: info: moved 'libcrypt-dev_1%3a4.5.1-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpy9avgux1/libcrypt-dev_4.5.1-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Fetched 494 kB in 0s (21.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzqb7087t/autoconf_2.72-3.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-3 [878 kB] Fetched 878 kB in 0s (37.0 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-3_all.deb' to '/srv/rebuilderd/tmp/tmpxc67cilp/automake_1.18.1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:2.3.5+ds-2+b1 [4183 kB] Fetched 4183 kB in 0s (84.0 MB/s) dpkg-name: info: moved 'python3-numpy_1%3a2.3.5+ds-2+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmpt5z3mx2r/python3-numpy_2.3.5+ds-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 gcc-15-base arm64 15.2.0-10 [53.8 kB] Fetched 53.8 kB in 0s (3095 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzf9s4dip/gcc-15-base_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnetcdf22 arm64 1:4.9.3-1+b1 [480 kB] Fetched 480 kB in 0s (22.0 MB/s) dpkg-name: info: moved 'libnetcdf22_1%3a4.9.3-1+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmpbmsazp2z/libnetcdf22_4.9.3-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 gcc-15 arm64 15.2.0-10 [518 kB] Fetched 518 kB in 0s (30.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp154ekar_/gcc-15_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Fetched 18.6 kB in 0s (1087 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps0gbnuph/python3-installer_0.7.0+dfsg1-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libsmartcols1 arm64 2.41.2-4 [139 kB] Fetched 139 kB in 0s (7174 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmr60zwcv/libsmartcols1_2.41.2-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-fastjsonschema all 2.21.1-1 [22.4 kB] Fetched 22.4 kB in 0s (1164 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmzavj0a7/python3-fastjsonschema_2.21.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 python3-html5lib all 1.2-2 [92.1 kB] Fetched 92.1 kB in 0s (5060 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqp9frfoi/python3-html5lib_1.2-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-cpuinfo all 9.0.0+git20221119-3 [23.5 kB] Fetched 23.5 kB in 0s (1404 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo1upfanx/python3-cpuinfo_9.0.0+git20221119-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libhdf5-310 arm64 1.14.5+repack-4 [1177 kB] Fetched 1177 kB in 0s (40.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd2awt628/libhdf5-310_1.14.5+repack-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgmp10 arm64 2:6.3.0+dfsg-5 [535 kB] Fetched 535 kB in 0s (24.9 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5_arm64.deb' to '/srv/rebuilderd/tmp/tmpkk1m1_pa/libgmp10_6.3.0+dfsg-5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-wheel all 0.46.1-2 [21.7 kB] Fetched 21.7 kB in 0s (1208 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp97kil39q/python3-wheel_0.46.1-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 perl arm64 5.40.1-7 [267 kB] Fetched 267 kB in 0s (14.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuxabi28n/perl_5.40.1-7_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmpfr6 arm64 4.2.2-2 [685 kB] Fetched 685 kB in 0s (30.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4wfs8lmw/libmpfr6_4.2.2-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libbsd0 arm64 0.12.2-2 [129 kB] Fetched 129 kB in 0s (7138 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp67_cmtdj/libbsd0_0.12.2-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Fetched 123 kB in 0s (7064 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa9icpumi/libngtcp2-16_1.16.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libsystemd0 arm64 259~rc2-1 [429 kB] Fetched 429 kB in 0s (20.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg2wbvye1/libsystemd0_259~rc2-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libc-gconv-modules-extra arm64 2.42-5 [1158 kB] Fetched 1158 kB in 0s (69.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_q6jj_vg/libc-gconv-modules-extra_2.42-5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libattr1 arm64 1:2.5.2-3 [22.7 kB] Fetched 22.7 kB in 0s (1354 kB/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-3_arm64.deb' to '/srv/rebuilderd/tmp/tmpp4lnabri/libattr1_2.5.2-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 cython3 arm64 3.1.6+dfsg-2+b1 [2917 kB] Fetched 2917 kB in 0s (70.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxk_n8_cq/cython3_3.1.6+dfsg-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Fetched 184 kB in 0s (10.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgdmyatzc/libelf1t64_0.194-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 dpkg arm64 1.22.21 [1521 kB] Fetched 1521 kB in 0s (49.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphep_c043/dpkg_1.22.21_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 binutils arm64 2.45.50.20251201-1 [278 kB] Fetched 278 kB in 0s (12.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz0h4f5wz/binutils_2.45.50.20251201-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-pytz all 2025.2-5 [31.8 kB] Fetched 31.8 kB in 0s (1811 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2j_qer8p/python3-pytz_2025.2-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Fetched 92.4 kB in 0s (8784 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmrgmm1h3/libdebhelper-perl_13.28_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Fetched 235 kB in 0s (14.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsxyx_5m_/libssh2-1t64_1.11.1-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsodium23 arm64 1.0.18-1+b2 [121 kB] Fetched 121 kB in 0s (6660 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpem1258nh/libsodium23_1.0.18-1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libcap2 arm64 1:2.75-10+b2 [28.1 kB] Fetched 28.1 kB in 0s (1649 kB/s) dpkg-name: info: moved 'libcap2_1%3a2.75-10+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmpd4376sxp/libcap2_2.75-10+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 perl-base arm64 5.40.1-7 [1528 kB] Fetched 1528 kB in 0s (50.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1g05ycq6/perl-base_5.40.1-7_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-2+b1 [136 kB] Fetched 136 kB in 0s (7343 kB/s) dpkg-name: info: moved 'python3-numpy-dev_1%3a2.3.5+ds-2+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmpznhb5dmj/python3-numpy-dev_2.3.5+ds-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 3.0.3-1+b1 [14.3 kB] Fetched 14.3 kB in 0s (845 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp42let33k/python3-markupsafe_3.0.3-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libatomic1 arm64 15.2.0-10 [9840 B] Fetched 9840 B in 0s (595 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg8xxj_hx/libatomic1_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.9-2 [10.5 kB] Fetched 10.5 kB in 0s (631 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj1gjpsh4/libpython3-stdlib_3.13.9-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 python3-pandas all 2.3.3+dfsg-2 [2935 kB] Fetched 2935 kB in 0s (56.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbmngwet0/python3-pandas_2.3.3+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 binutils-common arm64 2.45.50.20251201-1 [2543 kB] Fetched 2543 kB in 0s (61.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_u49qa0v/binutils-common_2.45.50.20251201-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.6-1 [107 kB] Fetched 107 kB in 0s (6002 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdxj1tf98/python3-jinja2_3.1.6-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-numexpr arm64 2.14.1-1+b1 [137 kB] Fetched 137 kB in 0s (7597 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0j0np_z6/python3-numexpr_2.14.1-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 python3-pytest all 8.4.2-1 [266 kB] Fetched 266 kB in 0s (13.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4u_29ogl/python3-pytest_8.4.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 patch arm64 2.8-2 [128 kB] Fetched 128 kB in 0s (7157 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaaamrkga/patch_2.8-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 python3-soupsieve all 2.7-2 [39.0 kB] Fetched 39.0 kB in 0s (2217 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdj4rf3v7/python3-soupsieve_2.7-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-tinycss2 all 1.4.0-2 [25.0 kB] Fetched 25.0 kB in 0s (1506 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9vbzn7ut/python3-tinycss2_1.4.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.11-1+b1 [770 kB] Fetched 770 kB in 0s (33.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_l2xqsqb/python3.13_3.13.11-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Fetched 47.3 kB in 0s (2822 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpons3s_7p/libtasn1-6_4.20.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-build all 1.2.2-4 [36.2 kB] Fetched 36.2 kB in 0s (2084 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw6ommjjc/python3-build_1.2.2-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-jupyter-client all 8.6.3-3 [92.4 kB] Fetched 92.4 kB in 0s (5396 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpycre2t9t/python3-jupyter-client_8.6.3-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-4 [68.4 kB] Fetched 68.4 kB in 0s (4022 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbbo9u4pg/libhdf5-hl-310_1.14.5+repack-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Fetched 12.2 kB in 0s (719 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9pzrn8l7/dh-autoreconf_21_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Fetched 43.7 kB in 0s (2486 kB/s) dpkg-name: info: moved 'file_1%3a5.46-5_arm64.deb' to '/srv/rebuilderd/tmp/tmpjk5rl3o5/file_5.46-5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Fetched 63.6 kB in 0s (3445 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4txz3get/libnghttp3-9_1.12.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Fetched 224 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkmpgekmn/python3-pkg-resources_78.1.1-0.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.2-1 [772 kB] Fetched 772 kB in 0s (29.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgzqe4kmt/autopoint_0.23.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libcc1-0 arm64 15.2.0-10 [41.4 kB] Fetched 41.4 kB in 0s (2380 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmwnhr9un/libcc1-0_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-gsd arm64 4.2.0-1 [198 kB] Fetched 198 kB in 0s (10.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwbh5dn86/python3-gsd_4.2.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.8.0-1 [71.7 kB] Fetched 71.7 kB in 0s (3891 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9y2uza3s/python3-more-itertools_10.8.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libseccomp2 arm64 2.6.0-2+b1 [50.9 kB] Fetched 50.9 kB in 0s (2832 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0aii1908/libseccomp2_2.6.0-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Fetched 56.3 kB in 0s (3249 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoo7eh6xh/librtmp1_2.4+20151223.gitfa8646d.1-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.16.0-1 [23.8 kB] Fetched 23.8 kB in 0s (1345 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9ou7zllp/libngtcp2-crypto-gnutls8_1.16.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 g++ arm64 4:15.2.0-4 [1332 B] Fetched 1332 B in 0s (87.6 kB/s) dpkg-name: info: moved 'g++_4%3a15.2.0-4_arm64.deb' to '/srv/rebuilderd/tmp/tmp9m54vyv9/g++_15.2.0-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 base-passwd arm64 3.6.8 [54.0 kB] Fetched 54.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpakl8ez7n/base-passwd_3.6.8_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Fetched 5667 kB in 0s (39.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4oiw6_20/libjs-mathjax_2.7.9+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 cpp arm64 4:15.2.0-4 [1568 B] Fetched 1568 B in 0s (104 kB/s) dpkg-name: info: moved 'cpp_4%3a15.2.0-4_arm64.deb' to '/srv/rebuilderd/tmp/tmp4w_3gswm/cpp_15.2.0-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gcc arm64 4:15.2.0-4 [5156 B] Fetched 5156 B in 0s (310 kB/s) dpkg-name: info: moved 'gcc_4%3a15.2.0-4_arm64.deb' to '/srv/rebuilderd/tmp/tmpo81dr_qz/gcc_15.2.0-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 mawk arm64 1.3.4.20250131-1 [134 kB] Fetched 134 kB in 0s (7566 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkpxdjxa_/mawk_1.3.4.20250131-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Fetched 338 kB in 0s (24.3 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.46-5_arm64.deb' to '/srv/rebuilderd/tmp/tmpmw8d4fjs/libmagic-mgc_5.46-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 python3-roman-numerals all 3.1.0-2 [8740 B] Fetched 8740 B in 0s (525 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_0ctgnq0/python3-roman-numerals_3.1.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Fetched 12.4 kB in 0s (752 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi3trnzux/netbase_6.5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libgprofng0 arm64 2.45.50.20251201-1 [679 kB] Fetched 679 kB in 0s (29.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj1wy96qw/libgprofng0_2.45.50.20251201-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.9-2 [27.5 kB] Fetched 27.5 kB in 0s (1579 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgqiu7n3a/python3-minimal_3.13.9-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3.14-minimal arm64 3.14.2-1+b1 [2233 kB] Fetched 2233 kB in 0s (64.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx2i1pzqu/python3.14-minimal_3.14.2-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libasan8 arm64 15.2.0-10 [2600 kB] Fetched 2600 kB in 0s (65.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp96nice7i/libasan8_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 sysvinit-utils arm64 3.15-6 [34.9 kB] Fetched 34.9 kB in 0s (1988 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0vhau6ma/sysvinit-utils_3.15-6_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 debhelper all 13.28 [941 kB] Fetched 941 kB in 0s (37.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpws2vzy3l/debhelper_13.28_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 diffutils arm64 1:3.12-1 [397 kB] Fetched 397 kB in 0s (19.1 MB/s) dpkg-name: info: moved 'diffutils_1%3a3.12-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpn2aaefqv/diffutils_3.12-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libssl3t64 arm64 3.5.4-1 [2725 kB] Fetched 2725 kB in 0s (62.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpptzmr0k_/libssl3t64_3.5.4-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.5.2-3 [23.0 kB] Fetched 23.0 kB in 0s (1358 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1zdvdct2/libffi8_3.5.2-3_arm64.deb' dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz1y98osr/sed_4.9-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 sed arm64 4.9-2+b1 [326 kB] Fetched 326 kB in 0s (16.8 MB/s) Get:1 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Fetched 12.0 kB in 0s (712 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb9d7_88t/python3-jaraco.functools_4.1.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libbinutils arm64 2.45.50.20251201-1 [670 kB] Fetched 670 kB in 0s (30.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfh393yau/libbinutils_2.45.50.20251201-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b9 [295 kB] Fetched 295 kB in 0s (15.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxnko02ks/libbrotli1_1.1.0-2+b9_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libstdc++6 arm64 15.2.0-10 [647 kB] Fetched 647 kB in 0s (19.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc03eg2ph/libstdc++6_15.2.0-10_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 g++-15 arm64 15.2.0-10 [24.8 kB] Fetched 24.8 kB in 0s (1420 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi4hcxndy/g++-15_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.11-3 [1400 kB] Fetched 1400 kB in 0s (47.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgs_45q5z/libgnutls30t64_3.8.11-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libcurl3t64-gnutls arm64 8.17.0-3 [362 kB] Fetched 362 kB in 0s (18.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6mh30jvu/libcurl3t64-gnutls_8.17.0-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 docutils-common all 0.22.3+dfsg-1 [128 kB] Fetched 128 kB in 0s (7093 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdwc4llrk/docutils-common_0.22.3+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 dpkg-dev all 1.22.21 [1338 kB] Fetched 1338 kB in 0s (47.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw7d_66hw/dpkg-dev_1.22.21_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpam-runtime all 1.7.0-5 [249 kB] Fetched 249 kB in 0s (12.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxsroa9ra/libpam-runtime_1.7.0-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-2+b1 [591 kB] Fetched 591 kB in 0s (27.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7snr5p_m/libxml2-16_2.15.1+dfsg-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsqlite3-0 arm64 3.46.1-8 [884 kB] Fetched 884 kB in 0s (34.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp86xjoq6r/libsqlite3-0_3.46.1-8_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Fetched 8276 B in 0s (414 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphyoy0d5l/python3-jaraco.context_6.0.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgdbm-compat4t64 arm64 1.26-1 [52.8 kB] Fetched 52.8 kB in 0s (2934 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9c7r2xpm/libgdbm-compat4t64_1.26-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 media-types all 14.0.0 [30.8 kB] Fetched 30.8 kB in 0s (1786 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxxq8iswb/media-types_14.0.0_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3.14-minimal arm64 3.14.2-1+b1 [890 kB] Fetched 890 kB in 0s (36.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm7pv2rd5/libpython3.14-minimal_3.14.2-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnettle8t64 arm64 3.10.2-1 [305 kB] Fetched 305 kB in 0s (15.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfuh4piu9/libnettle8t64_3.10.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-mistune all 3.1.4-1 [35.7 kB] Fetched 35.7 kB in 0s (2062 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps9gic880/python3-mistune_3.1.4-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 cpp-15 arm64 15.2.0-10 [1280 B] Fetched 1280 B in 0s (76.8 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaip8t6r1/cpp-15_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.10-1 [42.0 kB] Fetched 42.0 kB in 0s (2451 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaj0fqtnz/python3-idna_3.10-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.9-2 [10.7 kB] Fetched 10.7 kB in 0s (578 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1x88p1lf/libpython3-dev_3.13.9-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpam-modules arm64 1.7.0-5 [172 kB] Fetched 172 kB in 0s (3143 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp08lop0tj/libpam-modules_1.7.0-5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Fetched 169 kB in 0s (8580 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa9zp1ob7/libreadline8t64_8.3-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20250419 [162 kB] Fetched 162 kB in 0s (8079 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgndqyzk2/ca-certificates_20250419_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libblkid1 arm64 2.41.2-4 [167 kB] Fetched 167 kB in 0s (8834 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp__d4o0x4/libblkid1_2.41.2-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-attr all 25.4.0-1 [73.1 kB] Fetched 73.1 kB in 0s (4008 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb8by9a59/python3-attr_25.4.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 build-essential arm64 12.12 [4624 B] Fetched 4624 B in 0s (260 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprztp1no3/build-essential_12.12_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-10 [19.6 MB] Fetched 19.6 MB in 0s (108 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0lcou7cu/gcc-15-aarch64-linux-gnu_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2025.11.12+ds-1 [10.0 kB] Fetched 10.0 kB in 0s (572 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxs070n8s/python3-certifi_2025.11.12+ds-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-jupyter-core all 5.7.2-5 [35.3 kB] Fetched 35.3 kB in 0s (2136 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo5t0dmeo/python3-jupyter-core_5.7.2-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.4.2-4 [24.1 MB] Fetched 24.1 MB in 0s (142 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaxxlvizc/python3-networkx_3.4.2-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 hostname arm64 3.25 [10.8 kB] Fetched 10.8 kB in 0s (158 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq20ibxha/hostname_3.25_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 python3-tables-lib arm64 3.10.2-3+b1 [603 kB] Fetched 603 kB in 0s (28.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxrmjq_vb/python3-tables-lib_3.10.2-3+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 grep arm64 3.12-1 [440 kB] Fetched 440 kB in 0s (21.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt_aguf2f/grep_3.12-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-pytest-rerunfailures all 16.1-1 [18.2 kB] Fetched 18.2 kB in 0s (1073 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa4f6wlg3/python3-pytest-rerunfailures_16.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtinfo6 arm64 6.5+20251123-1 [345 kB] Fetched 345 kB in 0s (17.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjbahcw04/libtinfo6_6.5+20251123-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Fetched 6688 B in 0s (388 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp91xyxyz2/python3-imagesize_1.4.1-1_all.deb' Downloading dependency 130 of 317: python3-pluggy:arm64=1.6.0-1 Downloading dependency 131 of 317: python3-charset-normalizer:arm64=3.4.4-2 Downloading dependency 132 of 317: libselinux1:arm64=3.9-4+b1 Downloading dependency 133 of 317: libfile-stripnondeterminism-perl:arm64=1.15.0-1 Downloading dependency 134 of 317: libpython3.14-dev:arm64=3.14.2-1+b1 Downloading dependency 135 of 317: libnghttp2-14:arm64=1.64.0-1.1+b1 Downloading dependency 136 of 317: python3-typing-extensions:arm64=4.15.0-1 Downloading dependency 137 of 317: libidn2-0:arm64=2.3.8-4 Downloading dependency 138 of 317: libpython3.13:arm64=3.13.11-1+b1 Downloading dependency 139 of 317: libzmq5:arm64=4.3.5-1+b3 Downloading dependency 140 of 317: libcrypt-dev:arm64=1:4.5.1-1 Downloading dependency 141 of 317: autoconf:arm64=2.72-3.1 Downloading 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libpython3.14-minimal:arm64=3.14.2-1+b1 Downloading dependency 235 of 317: libnettle8t64:arm64=3.10.2-1 Downloading dependency 236 of 317: python3-mistune:arm64=3.1.4-1 Downloading dependency 237 of 317: cpp-15:arm64=15.2.0-10 Downloading dependency 238 of 317: python3-idna:arm64=3.10-1 Downloading dependency 239 of 317: libpython3-dev:arm64=3.13.9-2 Downloading dependency 240 of 317: libpam-modules:arm64=1.7.0-5 Downloading dependency 241 of 317: libreadline8t64:arm64=8.3-3 Downloading dependency 242 of 317: ca-certificates:arm64=20250419 Downloading dependency 243 of 317: libblkid1:arm64=2.41.2-4 Downloading dependency 244 of 317: python3-attr:arm64=25.4.0-1 Downloading dependency 245 of 317: build-essential:arm64=12.12 Downloading dependency 246 of 317: gcc-15-aarch64-linux-gnu:arm64=15.2.0-10 Downloading dependency 247 of 317: python3-certifi:arm64=2025.11.12+ds-1 Downloading dependency 248 of 317: python3-jupyter-core:arm64=5.7.2-5 Downloading dependency 249 of 317: python3-networkx:arm64=3.4.2-4 Downloading dependency 250 of 317: hostname:arm64=3.25 Downloading dependency 251 of 317: python3-tables-lib:arm64=3.10.2-3+b1 Downloading dependency 252 of 317: grep:arm64=3.12-1 Downloading dependency 253 of 317: python3-pytest-rerunfailures:arm64=16.1-1 Downloading dependency 254 of 317: libtinfo6:arm64=6.5+20251123-1 Downloading dependency 255 of 317: python3-imagesize:arm64=1.4.1-1 Downloading dependency 256 of 317: gcc-aarch64-linux-gnu:arm64=4:15.2.0-4Get:1 http://deb.debian.org/debian unstable/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4 [1432 B] Fetched 1432 B in 0s (96.5 kB/s) dpkg-name: info: moved 'gcc-aarch64-linux-gnu_4%3a15.2.0-4_arm64.deb' to '/srv/rebuilderd/tmp/tmppesjuwas/gcc-aarch64-linux-gnu_15.2.0-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Fetched 96.5 kB in 0s (5457 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxzhqqdb6/libexpat1_2.7.3-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3.14-stdlib arm64 3.14.2-1+b1 [2172 kB] Fetched 2172 kB in 0s (63.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8y58rism/libpython3.14-stdlib_3.14.2-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.9-2 [26.0 kB] Fetched 26.0 kB in 0s (1425 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfybjxwx3/python3-dev_3.13.9-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 debianutils arm64 5.23.2 [92.4 kB] Fetched 92.4 kB in 0s (5407 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnl2vl2ln/debianutils_5.23.2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Fetched 13.6 kB in 0s (274 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpock2f8rq/python3-autocommand_2.2.2-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 dh-python all 6.20251204.1 [114 kB] Fetched 114 kB in 0s (6285 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpprjqx62c/dh-python_6.20251204.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 dash arm64 0.5.12-12 [95.6 kB] Fetched 95.6 kB in 0s (5221 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr02gdn62/dash_0.5.12-12_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-zmq arm64 27.1.0-1+b1 [207 kB] Fetched 207 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2nmjn_pz/python3-zmq_27.1.0-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libaudit1 arm64 1:4.1.2-1+b1 [59.7 kB] Fetched 59.7 kB in 0s (3415 kB/s) dpkg-name: info: moved 'libaudit1_1%3a4.1.2-1+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmp8l0hqtmm/libaudit1_4.1.2-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libjansson4 arm64 2.14-2+b3 [39.2 kB] Fetched 39.2 kB in 0s (2376 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps8suhj2c/libjansson4_2.14-2+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-nbconvert all 7.16.6-1 [160 kB] Fetched 160 kB in 0s (8704 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplnkyu1_6/python3-nbconvert_7.16.6-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 python3-sphinx all 8.2.3-11 [478 kB] Fetched 478 kB in 0s (20.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxme4fnnw/python3-sphinx_8.2.3-11_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libgcc-s1 arm64 15.2.0-10 [53.4 kB] Fetched 53.4 kB in 0s (3074 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphjw_1x91/libgcc-s1_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (1309 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqja4orpu/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Fetched 315 kB in 0s (15.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbvocj03r/m4_1.4.20-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libdpkg-perl all 1.22.21 [650 kB] Fetched 650 kB in 0s (16.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu26erwre/libdpkg-perl_1.22.21_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 python3-bs4 all 4.14.3-1 [118 kB] Fetched 118 kB in 0s (2290 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp60qud0gd/python3-bs4_4.14.3-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 binutils-aarch64-linux-gnu arm64 2.45.50.20251201-1 [857 kB] Fetched 857 kB in 0s (64.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq4wysgsc/binutils-aarch64-linux-gnu_2.45.50.20251201-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.3-3 [74.8 kB] Fetched 74.8 kB in 0s (3852 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphla_3sp7/readline-common_8.3-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 zlib1g arm64 1:1.3.dfsg+really1.3.1-1+b1 [85.1 kB] Fetched 85.1 kB in 0s (2614 kB/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmp2lw4nfdn/zlib1g_1.3.dfsg+really1.3.1-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Fetched 55.0 kB in 0s (3280 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprid9sndu/libsasl2-2_2.1.28+dfsg1-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 bzip2 arm64 1.0.8-6 [39.5 kB] Fetched 39.5 kB in 0s (2292 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp92my6an7/bzip2_1.0.8-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libzstd1 arm64 1.5.7+dfsg-2 [260 kB] Fetched 260 kB in 0s (11.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4q_dz8vm/libzstd1_1.5.7+dfsg-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Fetched 60.2 kB in 0s (3545 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9ky1xpmb/autotools-dev_20240727.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-10 [11.1 MB] Fetched 11.1 MB in 0s (85.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpop_7iylu/g++-15-aarch64-linux-gnu_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4 [5288 B] Fetched 5288 B in 0s (412 kB/s) dpkg-name: info: moved 'cpp-aarch64-linux-gnu_4%3a15.2.0-4_arm64.deb' to '/srv/rebuilderd/tmp/tmpjlthnmeb/cpp-aarch64-linux-gnu_15.2.0-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.22.1-2 [315 kB] Fetched 315 kB in 0s (15.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdy11k8x_/libkrb5-3_1.22.1-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libgomp1 arm64 15.2.0-10 [126 kB] Fetched 126 kB in 0s (2733 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2x4_jre2/libgomp1_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsz2 arm64 1.1.4-2 [8072 B] Fetched 8072 B in 0s (481 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp62lbweh/libsz2_1.1.4-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.3.3+dfsg-3 [5472 kB] Fetched 5472 kB in 0s (35.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpayj365af/python3-pandas-lib_2.3.3+dfsg-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.5+dfsg-1 [72.4 kB] Fetched 72.4 kB in 0s (4083 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppmgt32n6/python3-requests_2.32.5+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Fetched 738 kB in 0s (32.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy865ift1/python3-setuptools_78.1.1-0.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libsframe2 arm64 2.45.50.20251201-1 [79.6 kB] Fetched 79.6 kB in 0s (1366 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjv60vn0w/libsframe2_2.45.50.20251201-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 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/tmp9z8u3mny/ncurses-base_6.5+20251123-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Fetched 108 kB in 0s (6179 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk8hr0tn9/python3-chardet_5.2.0+dfsg-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-pyparsing all 3.1.3-1 [148 kB] Fetched 148 kB in 0s (7651 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc1rowowa/python3-pyparsing_3.1.3-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Fetched 97.3 kB in 0s (5189 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpygnt2mdj/bsdextrautils_2.41.2-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Fetched 11.4 kB in 0s (653 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx5hmukf2/python3-jaraco.text_4.0.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.11-1+b1 [2060 kB] Fetched 2060 kB in 0s (62.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmhr8dff7/python3.13-minimal_3.13.11-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Fetched 27.9 kB in 0s (1639 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcjxoxjis/python3-alabaster_0.7.16-0.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Fetched 20.1 kB in 0s (1843 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiqvyr5fd/xml-core_0.19_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-ossl0 arm64 1.16.0-1 [25.7 kB] Fetched 25.7 kB in 0s (1455 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj8d90ggn/libngtcp2-crypto-ossl0_1.16.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3.14-dev arm64 3.14.2-1+b1 [507 kB] Fetched 507 kB in 0s (23.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl3n6kppe/python3.14-dev_3.14.2-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libcrypt1 arm64 1:4.5.1-1 [93.9 kB] Fetched 93.9 kB in 0s (5289 kB/s) dpkg-name: info: moved 'libcrypt1_1%3a4.5.1-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpgp757zpp/libcrypt1_4.5.1-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3.14 arm64 3.14.2-1+b1 [2240 kB] Fetched 2240 kB in 0s (62.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbos77wv2/libpython3.14_3.14.2-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.22.1-2 [127 kB] Fetched 127 kB in 0s (6743 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgmforh1_/libgssapi-krb5-2_1.22.1-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Fetched 1453 kB in 0s (28.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9qpg3lvd/man-db_2.13.1-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libmount1 arm64 2.41.2-4 [199 kB] Fetched 199 kB in 0s (2497 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz2g97279/libmount1_2.41.2-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 pybuild-plugin-pyproject all 6.20251204.1 [12.3 kB] Fetched 12.3 kB in 0s (577 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppkgvf7e6/pybuild-plugin-pyproject_6.20251204.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 linux-libc-dev all 6.17.10-1 [2560 kB] Fetched 2560 kB in 0s (20.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd7qjrcbq/linux-libc-dev_6.17.10-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libncursesw6 arm64 6.5+20251123-1 [125 kB] Fetched 125 kB in 0s (2621 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptkrzedeq/libncursesw6_6.5+20251123-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.11-1+b1 [5047 kB] Fetched 5047 kB in 0s (12.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqzban5df/libpython3.13-dev_3.13.11-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libgcc-15-dev arm64 15.2.0-10 [2371 kB] Fetched 2371 kB in 0s (61.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfjekvign/libgcc-15-dev_15.2.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Fetched 19.8 kB in 0s (1171 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp105s4_4z/libsasl2-modules-db_2.1.28+dfsg1-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-nbclient all 0.8.0-3 [62.3 kB] Fetched 62.3 kB in 0s (3689 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8zjzb18j/python3-nbclient_0.8.0-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python-tables-data all 3.10.2-3 [47.3 kB] Fetched 47.3 kB in 0s (2768 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkzxydtr2/python-tables-data_3.10.2-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-webencodings all 0.5.1-5 [11.1 kB] Fetched 11.1 kB in 0s (669 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu27af4nd/python3-webencodings_0.5.1-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 liblzma5 arm64 5.8.1-2 [302 kB] Fetched 302 kB in 0s (14.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp545gra9i/liblzma5_5.8.1-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.9-2 [27.5 kB] Fetched 27.5 kB in 0s (1503 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp8ilcbqw/python3_3.13.9-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.10-1 [420 kB] Fetched 420 kB in 0s (7311 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkvu2v9ac/libp11-kit0_0.25.10-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20251208T143746Z sid/main arm64 libgfortran5 arm64 15.2.0-10 [371 kB] Fetched 371 kB in 0s (9131 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptjzs7cgk/libgfortran5_15.2.0-10_arm64.deb' dpkg-buildpackage: info: source package debootsnap-dummy dpkg-buildpackage: info: source version 1.0 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Equivs Dummy Package Generator dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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_arm64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_arm64.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/tmp4xo3q7kt/cache directory, not in ".." as indicated by the message above! I: automatically chosen mode: unshare I: chroot architecture arm64 is equal to the host's architecture I: using /srv/rebuilderd/tmp/mmdebstrap.aQNLsBTZ4a as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.aQNLsBTZ4a 127.0.0.1 - - [26/Dec/2025 06:58:08] code 404, message File not found 127.0.0.1 - - [26/Dec/2025 06:58:08] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:41795 ./ InRelease 127.0.0.1 - - [26/Dec/2025 06:58:08] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:41795 ./ Release [462 B] 127.0.0.1 - - [26/Dec/2025 06:58:08] code 404, message File not found 127.0.0.1 - - [26/Dec/2025 06:58:08] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:41795 ./ Release.gpg 127.0.0.1 - - [26/Dec/2025 06:58:08] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:41795 ./ Packages [396 kB] Fetched 397 kB in 0s (10.4 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 - - [26/Dec/2025 06:58:09] "GET /./gcc-15-base_15.2.0-10_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./libc-gconv-modules-extra_2.42-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./libc6_2.42-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./libgcc-s1_15.2.0-10_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./mawk_1.3.4.20250131-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./base-files_14_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./libtinfo6_6.5%2b20251123-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./debianutils_5.23.2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./bash_5.3-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./libacl1_2.3.2-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./libattr1_2.5.2-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./libcap2_2.75-10%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./libgmp10_6.3.0%2bdfsg-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./libpcre2-8-0_10.46-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./libselinux1_3.9-4%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./libzstd1_1.5.7%2bdfsg-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./zlib1g_1.3.dfsg%2breally1.3.1-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./libssl3t64_3.5.4-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./openssl-provider-legacy_3.5.4-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./libsystemd0_259%7erc2-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./coreutils_9.7-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./dash_0.5.12-12_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:09] "GET /./diffutils_3.12-1_arm64.deb HTTP/1.1" 200 - 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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.aQNLsBTZ4a 127.0.0.1 - - [26/Dec/2025 06:58:12] code 404, message File not found 127.0.0.1 - - [26/Dec/2025 06:58:12] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:41795 ./ InRelease 127.0.0.1 - - [26/Dec/2025 06:58:12] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:41795 ./ Release 127.0.0.1 - - [26/Dec/2025 06:58:12] code 404, message File not found 127.0.0.1 - - [26/Dec/2025 06:58:12] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:41795 ./ Release.gpg Reading package lists... usr-is-merged found but not real -- not running merged-usr extract hook I: installing essential packages... I: running --essential-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/essential00.sh /srv/rebuilderd/tmp/mmdebstrap.aQNLsBTZ4a usr-is-merged was not installed in a previous hook -- not running merged-usr essential hook I: installing remaining packages inside the chroot... 127.0.0.1 - - [26/Dec/2025 06:58:21] "GET /./libexpat1_2.7.3-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:21] "GET /./libpython3.13-minimal_3.13.11-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:21] "GET /./python3.13-minimal_3.13.11-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:21] "GET /./python3-minimal_3.13.9-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:21] "GET /./media-types_14.0.0_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:21] "GET /./netbase_6.5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:21] "GET /./tzdata_2025b-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:21] "GET /./libffi8_3.5.2-3_arm64.deb HTTP/1.1" 200 - 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127.0.0.1 - - [26/Dec/2025 06:58:22] "GET /./pybuild-plugin-pyproject_6.20251204.1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Dec/2025 06:58:22] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmp4xo3q7kt/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.aQNLsBTZ4a Reading package lists... Building dependency tree... Reading state information... perl-modules-5.40 is already the newest version (5.40.1-7). perl-modules-5.40 set to manually installed. base-files is already the newest version (14). python3-platformdirs is already the newest version (4.4.0-1). python3-platformdirs set to manually installed. gettext is already the newest version (0.23.2-1). gettext set to manually installed. libgdbm6t64 is already the newest version (1.26-1). libgdbm6t64 set to manually installed. liblzo2-2 is already the newest version (2.10-3+b1). liblzo2-2 set to manually installed. g++-aarch64-linux-gnu is already the newest version (4:15.2.0-4). g++-aarch64-linux-gnu set to manually installed. sgml-base is already the newest version (1.31+nmu1). sgml-base set to manually installed. python3-docutils is already the newest version (0.22.3+dfsg-1). python3-docutils set to manually installed. libcurl4t64 is already the newest version (8.17.0-3). libcurl4t64 set to manually installed. liblapack3 is already the newest version (3.12.1-7). liblapack3 set to manually installed. rpcsvc-proto is already the newest version (1.4.3-1+b1). rpcsvc-proto set to manually installed. libnorm1t64 is already the newest version (1.5.9+dfsg-4). libnorm1t64 set to manually installed. debconf is already the newest version (1.5.91). libaec0 is already the newest version (1.1.4-2). libaec0 set to manually installed. tar is already the newest version (1.35+dfsg-3.1). liblsan0 is already the newest version (15.2.0-10). liblsan0 set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils set to manually installed. libjs-sphinxdoc is already the newest version (8.2.3-11). libjs-sphinxdoc set to manually installed. libudev1 is already the newest version (259~rc2-1). libpython3.13-stdlib is already the newest version (3.13.11-1+b1). libpython3.13-stdlib set to manually installed. python3-defusedxml is already the newest version (0.7.1-3). python3-defusedxml set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6). bash is already the newest version (5.3-1). python3-urllib3 is already the newest version (2.5.0-1). python3-urllib3 set to manually installed. libexpat1-dev is already the newest version (2.7.3-1). libexpat1-dev set to manually installed. libaudit-common is already the newest version (1:4.1.2-1). python-babel-localedata is already the newest version (2.17.0-2). python-babel-localedata set to manually installed. python3-cffi-backend is already the newest version (2.0.0-2+b1). python3-cffi-backend set to manually installed. libdebconfclient0 is already the newest version (0.282). python3-pandocfilters is already the newest version (1.5.1-1). python3-pandocfilters set to manually installed. fonts-mathjax is already the newest version (2.7.9+dfsg-1). fonts-mathjax set to manually installed. libcom-err2 is already the newest version (1.47.2-3+b4). libcom-err2 set to manually installed. libperl5.40 is already the newest version (5.40.1-7). libperl5.40 set to manually installed. libsnappy1v5 is already the newest version (1.2.2-2). libsnappy1v5 set to manually installed. python3-tornado is already the newest version (6.5.2-3). python3-tornado set to manually installed. libuchardet0 is already the newest version (0.0.8-2). libuchardet0 set to manually installed. libpam0g is already the newest version (1.7.0-5). python3-typeguard is already the newest version (4.4.4-1). python3-typeguard set to manually installed. liblz4-1 is already the newest version (1.10.0-6). liblz4-1 set to manually installed. python3-inflect is already the newest version (7.5.0-1). python3-inflect set to manually installed. dh-strip-nondeterminism is already the newest version (1.15.0-1). dh-strip-nondeterminism set to manually installed. po-debconf is already the newest version (1.0.22). po-debconf set to manually installed. dwz is already the newest version (0.16-2). dwz set to manually installed. libc6-dev is already the newest version (2.42-5). libc6-dev set to manually installed. libtsan2 is already the newest version (15.2.0-10). libtsan2 set to manually installed. python3-jupyterlab-pygments is already the newest version (0.2.2-3). python3-jupyterlab-pygments set to manually installed. openssl-provider-legacy is already the newest version (3.5.4-1). python3-iniconfig is already the newest version (2.1.0-1). python3-iniconfig set to manually installed. init-system-helpers is already the newest version (1.69). libblosc2-4 is already the newest version (2.17.1+ds-2). libblosc2-4 set to manually installed. python3-nbformat is already the newest version (5.9.1-1). python3-nbformat set to manually installed. gettext-base is already the newest version (0.23.2-1). gettext-base set to manually installed. libpam-modules-bin is already the newest version (1.7.0-5). libmpc3 is already the newest version (1.3.1-2). libmpc3 set to manually installed. python3-snowballstemmer is already the newest version (3.0.1-1). python3-snowballstemmer set to manually installed. libisl23 is already the newest version (0.27-1). libisl23 set to manually installed. libldap2 is already the newest version (2.6.10+dfsg-1). libldap2 set to manually installed. libpcre2-8-0 is already the newest version (10.46-1). ncurses-bin is already the newest version (6.5+20251123-1). python3-babel is already the newest version (2.17.0-2). python3-babel set to manually installed. libtool is already the newest version (2.5.4-9). libtool set to manually installed. python3-jsonschema is already the newest version (4.25.1-2). python3-jsonschema set to manually installed. libmagic1t64 is already the newest version (1:5.46-5). libmagic1t64 set to manually installed. groff-base is already the newest version (1.23.0-10). groff-base set to manually installed. util-linux is already the newest version (2.41.2-4). python3-decorator is already the newest version (5.2.1-2). python3-decorator set to manually installed. libcap-ng0 is already the newest version (0.8.5-4+b2). python3-traitlets is already the newest version (5.14.3+really5.14.3-2). python3-traitlets set to manually installed. python3-cftime is already the newest version (1.6.5-1+b1). python3-cftime set to manually installed. libctf-nobfd0 is already the newest version (2.45.50.20251201-1). libctf-nobfd0 set to manually installed. python3-pygments is already the newest version (2.18.0+dfsg-2). python3-pygments set to manually installed. libpython3-all-dev is already the newest version (3.13.9-2). libpython3-all-dev set to manually installed. tzdata is already the newest version (2025b-5). tzdata set to manually installed. libpython3.13-minimal is already the newest version (3.13.11-1+b1). libpython3.13-minimal set to manually installed. python3-referencing is already the newest version (0.36.2-2). python3-referencing set to manually installed. findutils is already the newest version (4.10.0-3). python3-dateutil is already the newest version (2.9.0-4). python3-dateutil set to manually installed. openssl is already the newest version (3.5.4-1). openssl set to manually installed. libxxhash0 is already the newest version (0.8.3-2). libxxhash0 set to manually installed. libpipeline1 is already the newest version (1.5.8-2). libpipeline1 set to manually installed. zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). zlib1g-dev set to manually installed. make is already the newest version (4.4.1-3). make set to manually installed. python3-rpds-py is already the newest version (0.28.0-1). python3-rpds-py set to manually installed. python3-jsonschema-specifications is already the newest version (2023.12.1-4). python3-jsonschema-specifications set to manually installed. libk5crypto3 is already the newest version (1.22.1-2). libk5crypto3 set to manually installed. libc-dev-bin is already the newest version (2.42-5). libc-dev-bin set to manually installed. libunistring5 is already the newest version (1.3-2). libunistring5 set to manually installed. python3-netcdf4 is already the newest version (1.7.3-1+b1). python3-netcdf4 set to manually installed. coreutils is already the newest version (9.7-3). libc6 is already the newest version (2.42-5). cpp-15-aarch64-linux-gnu is already the newest version (15.2.0-10). cpp-15-aarch64-linux-gnu set to manually installed. libqhull-r8.0 is already the newest version (2020.2-7). libqhull-r8.0 set to manually installed. libdb5.3t64 is already the newest version (5.3.28+dfsg2-11). python-tinycss2-common is already the newest version (1.4.0-2). python-tinycss2-common set to manually installed. sphinx-common is already the newest version (8.2.3-11). sphinx-common set to manually installed. python3-tables is already the newest version (3.10.2-3). python3-tables set to manually installed. libpsl5t64 is already the newest version (0.21.2-1.1+b1). libpsl5t64 set to manually installed. python3-pyproject-hooks is already the newest version (1.2.0-1). python3-pyproject-hooks set to manually installed. gzip is already the newest version (1.13-1). python3-all is already the newest version (3.13.9-2). python3-all set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libmd0 is already the newest version (1.1.0-2+b1). libhwasan0 is already the newest version (15.2.0-10). libhwasan0 set to manually installed. libkeyutils1 is already the newest version (1.6.3-6). libkeyutils1 set to manually installed. python3-scipy is already the newest version (1.16.3-2). python3-scipy set to manually installed. python3-bleach is already the newest version (6.3.0-1). python3-bleach set to manually installed. libacl1 is already the newest version (2.3.2-2+b1). python3.13-dev is already the newest version (3.13.11-1+b1). python3.13-dev set to manually installed. libjson-perl is already the newest version (4.10000-1). libjson-perl set to manually installed. libblosc1 is already the newest version (1.21.5+ds-2). libblosc1 set to manually installed. libctf0 is already the newest version (2.45.50.20251201-1). libctf0 set to manually installed. libubsan1 is already the newest version (15.2.0-10). libubsan1 set to manually installed. python3-packaging is already the newest version (25.0-1). python3-packaging set to manually installed. libuuid1 is already the newest version (2.41.2-4). python3.14 is already the newest version (3.14.2-1+b1). python3.14 set to manually installed. python3-nbsphinx is already the newest version (0.9.5+ds-1). python3-nbsphinx set to manually installed. python3-zipp is already the newest version (3.23.0-1). python3-zipp set to manually installed. libkrb5support0 is already the newest version (1.22.1-2). libkrb5support0 set to manually installed. xz-utils is already the newest version (5.8.1-2). xz-utils set to manually installed. libpgm-5.3-0t64 is already the newest version (5.3.128~dfsg-2.1+b1). libpgm-5.3-0t64 set to manually installed. libhogweed6t64 is already the newest version (3.10.2-1). libhogweed6t64 set to manually installed. python3-all-dev is already the newest version (3.13.9-2). python3-all-dev set to manually installed. libstdc++-15-dev is already the newest version (15.2.0-10). libstdc++-15-dev set to manually installed. python3-psutil is already the newest version (7.1.0-1). python3-psutil set to manually installed. python3-versioneer is already the newest version (0.29-1). python3-versioneer set to manually installed. libblas3 is already the newest version (3.12.1-7). libblas3 set to manually installed. libc-bin is already the newest version (2.42-5). libitm1 is already the newest version (15.2.0-10). libitm1 set to manually installed. python3-pluggy is already the newest version (1.6.0-1). python3-pluggy set to manually installed. python3-charset-normalizer is already the newest version (3.4.4-2). python3-charset-normalizer set to manually installed. libselinux1 is already the newest version (3.9-4+b1). libfile-stripnondeterminism-perl is already the newest version (1.15.0-1). libfile-stripnondeterminism-perl set to manually installed. libpython3.14-dev is already the newest version (3.14.2-1+b1). libpython3.14-dev set to manually installed. libnghttp2-14 is already the newest version (1.64.0-1.1+b1). libnghttp2-14 set to manually installed. python3-typing-extensions is already the newest version (4.15.0-1). python3-typing-extensions set to manually installed. libidn2-0 is already the newest version (2.3.8-4). libidn2-0 set to manually installed. libpython3.13 is already the newest version (3.13.11-1+b1). libpython3.13 set to manually installed. libzmq5 is already the newest version (4.3.5-1+b3). libzmq5 set to manually installed. libcrypt-dev is already the newest version (1:4.5.1-1). libcrypt-dev set to manually installed. autoconf is already the newest version (2.72-3.1). autoconf set to manually installed. automake is already the newest version (1:1.18.1-3). automake set to manually installed. python3-numpy is already the newest version (1:2.3.5+ds-2+b1). python3-numpy set to manually installed. gcc-15-base is already the newest version (15.2.0-10). libnetcdf22 is already the newest version (1:4.9.3-1+b1). libnetcdf22 set to manually installed. gcc-15 is already the newest version (15.2.0-10). gcc-15 set to manually installed. python3-installer is already the newest version (0.7.0+dfsg1-3). python3-installer set to manually installed. libsmartcols1 is already the newest version (2.41.2-4). python3-fastjsonschema is already the newest version (2.21.1-1). python3-fastjsonschema set to manually installed. python3-html5lib is already the newest version (1.2-2). python3-html5lib set to manually installed. python3-cpuinfo is already the newest version (9.0.0+git20221119-3). python3-cpuinfo set to manually installed. libhdf5-310 is already the newest version (1.14.5+repack-4). libhdf5-310 set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-5). python3-wheel is already the newest version (0.46.1-2). python3-wheel set to manually installed. perl is already the newest version (5.40.1-7). perl set to manually installed. libmpfr6 is already the newest version (4.2.2-2). libmpfr6 set to manually installed. libbsd0 is already the newest version (0.12.2-2). libbsd0 set to manually installed. libngtcp2-16 is already the newest version (1.16.0-1). libngtcp2-16 set to manually installed. libsystemd0 is already the newest version (259~rc2-1). libc-gconv-modules-extra is already the newest version (2.42-5). libattr1 is already the newest version (1:2.5.2-3). cython3 is already the newest version (3.1.6+dfsg-2+b1). cython3 set to manually installed. libelf1t64 is already the newest version (0.194-1). libelf1t64 set to manually installed. dpkg is already the newest version (1.22.21). binutils is already the newest version (2.45.50.20251201-1). binutils set to manually installed. python3-pytz is already the newest version (2025.2-5). python3-pytz set to manually installed. libdebhelper-perl is already the newest version (13.28). libdebhelper-perl set to manually installed. libssh2-1t64 is already the newest version (1.11.1-1). libssh2-1t64 set to manually installed. libsodium23 is already the newest version (1.0.18-1+b2). libsodium23 set to manually installed. libcap2 is already the newest version (1:2.75-10+b2). perl-base is already the newest version (5.40.1-7). python3-numpy-dev is already the newest version (1:2.3.5+ds-2+b1). python3-numpy-dev set to manually installed. python3-markupsafe is already the newest version (3.0.3-1+b1). python3-markupsafe set to manually installed. libatomic1 is already the newest version (15.2.0-10). libatomic1 set to manually installed. libpython3-stdlib is already the newest version (3.13.9-2). libpython3-stdlib set to manually installed. python3-pandas is already the newest version (2.3.3+dfsg-2). python3-pandas set to manually installed. binutils-common is already the newest version (2.45.50.20251201-1). binutils-common set to manually installed. python3-jinja2 is already the newest version (3.1.6-1). python3-jinja2 set to manually installed. python3-numexpr is already the newest version (2.14.1-1+b1). python3-numexpr set to manually installed. python3-pytest is already the newest version (8.4.2-1). python3-pytest set to manually installed. patch is already the newest version (2.8-2). patch set to manually installed. python3-soupsieve is already the newest version (2.7-2). python3-soupsieve set to manually installed. python3-tinycss2 is already the newest version (1.4.0-2). python3-tinycss2 set to manually installed. python3.13 is already the newest version (3.13.11-1+b1). python3.13 set to manually installed. libtasn1-6 is already the newest version (4.20.0-2). libtasn1-6 set to manually installed. python3-build is already the newest version (1.2.2-4). python3-build set to manually installed. python3-jupyter-client is already the newest version (8.6.3-3). python3-jupyter-client set to manually installed. libhdf5-hl-310 is already the newest version (1.14.5+repack-4). libhdf5-hl-310 set to manually installed. dh-autoreconf is already the newest version (21). dh-autoreconf set to manually installed. file is already the newest version (1:5.46-5). file set to manually installed. libnghttp3-9 is already the newest version (1.12.0-1). libnghttp3-9 set to manually installed. python3-pkg-resources is already the newest version (78.1.1-0.1). python3-pkg-resources set to manually installed. autopoint is already the newest version (0.23.2-1). autopoint set to manually installed. libcc1-0 is already the newest version (15.2.0-10). libcc1-0 set to manually installed. python3-gsd is already the newest version (4.2.0-1). python3-gsd set to manually installed. python3-more-itertools is already the newest version (10.8.0-1). python3-more-itertools set to manually installed. libseccomp2 is already the newest version (2.6.0-2+b1). libseccomp2 set to manually installed. librtmp1 is already the newest version (2.4+20151223.gitfa8646d.1-3). librtmp1 set to manually installed. libngtcp2-crypto-gnutls8 is already the newest version (1.16.0-1). libngtcp2-crypto-gnutls8 set to manually installed. g++ is already the newest version (4:15.2.0-4). g++ set to manually installed. base-passwd is already the newest version (3.6.8). libjs-mathjax is already the newest version (2.7.9+dfsg-1). libjs-mathjax set to manually installed. cpp is already the newest version (4:15.2.0-4). cpp set to manually installed. gcc is already the newest version (4:15.2.0-4). gcc set to manually installed. mawk is already the newest version (1.3.4.20250131-1). libmagic-mgc is already the newest version (1:5.46-5). libmagic-mgc set to manually installed. python3-roman-numerals is already the newest version (3.1.0-2). python3-roman-numerals set to manually installed. netbase is already the newest version (6.5). netbase set to manually installed. libgprofng0 is already the newest version (2.45.50.20251201-1). libgprofng0 set to manually installed. python3-minimal is already the newest version (3.13.9-2). python3-minimal set to manually installed. python3.14-minimal is already the newest version (3.14.2-1+b1). python3.14-minimal set to manually installed. libasan8 is already the newest version (15.2.0-10). libasan8 set to manually installed. sysvinit-utils is already the newest version (3.15-6). debhelper is already the newest version (13.28). debhelper set to manually installed. diffutils is already the newest version (1:3.12-1). libssl3t64 is already the newest version (3.5.4-1). libffi8 is already the newest version (3.5.2-3). libffi8 set to manually installed. sed is already the newest version (4.9-2+b1). python3-jaraco.functools is already the newest version (4.1.0-1). python3-jaraco.functools set to manually installed. libbinutils is already the newest version (2.45.50.20251201-1). libbinutils set to manually installed. libbrotli1 is already the newest version (1.1.0-2+b9). libbrotli1 set to manually installed. libstdc++6 is already the newest version (15.2.0-10). libstdc++6 set to manually installed. g++-15 is already the newest version (15.2.0-10). g++-15 set to manually installed. libgnutls30t64 is already the newest version (3.8.11-3). libgnutls30t64 set to manually installed. libcurl3t64-gnutls is already the newest version (8.17.0-3). libcurl3t64-gnutls set to manually installed. docutils-common is already the newest version (0.22.3+dfsg-1). docutils-common set to manually installed. dpkg-dev is already the newest version (1.22.21). dpkg-dev set to manually installed. libpam-runtime is already the newest version (1.7.0-5). libxml2-16 is already the newest version (2.15.1+dfsg-2+b1). libxml2-16 set to manually installed. libsqlite3-0 is already the newest version (3.46.1-8). libsqlite3-0 set to manually installed. python3-jaraco.context is already the newest version (6.0.1-1). python3-jaraco.context set to manually installed. libgdbm-compat4t64 is already the newest version (1.26-1). libgdbm-compat4t64 set to manually installed. media-types is already the newest version (14.0.0). media-types set to manually installed. libpython3.14-minimal is already the newest version (3.14.2-1+b1). libpython3.14-minimal set to manually installed. libnettle8t64 is already the newest version (3.10.2-1). libnettle8t64 set to manually installed. python3-mistune is already the newest version (3.1.4-1). python3-mistune set to manually installed. cpp-15 is already the newest version (15.2.0-10). cpp-15 set to manually installed. python3-idna is already the newest version (3.10-1). python3-idna set to manually installed. libpython3-dev is already the newest version (3.13.9-2). libpython3-dev set to manually installed. libpam-modules is already the newest version (1.7.0-5). libreadline8t64 is already the newest version (8.3-3). libreadline8t64 set to manually installed. ca-certificates is already the newest version (20250419). ca-certificates set to manually installed. libblkid1 is already the newest version (2.41.2-4). python3-attr is already the newest version (25.4.0-1). python3-attr set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. gcc-15-aarch64-linux-gnu is already the newest version (15.2.0-10). gcc-15-aarch64-linux-gnu set to manually installed. python3-certifi is already the newest version (2025.11.12+ds-1). python3-certifi set to manually installed. python3-jupyter-core is already the newest version (5.7.2-5). python3-jupyter-core set to manually installed. python3-networkx is already the newest version (3.4.2-4). python3-networkx set to manually installed. hostname is already the newest version (3.25). python3-tables-lib is already the newest version (3.10.2-3+b1). python3-tables-lib set to manually installed. grep is already the newest version (3.12-1). python3-pytest-rerunfailures is already the newest version (16.1-1). python3-pytest-rerunfailures set to manually installed. libtinfo6 is already the newest version (6.5+20251123-1). python3-imagesize is already the newest version (1.4.1-1). python3-imagesize set to manually installed. gcc-aarch64-linux-gnu is already the newest version (4:15.2.0-4). gcc-aarch64-linux-gnu set to manually installed. libexpat1 is already the newest version (2.7.3-1). libexpat1 set to manually installed. libpython3.14-stdlib is already the newest version (3.14.2-1+b1). libpython3.14-stdlib set to manually installed. python3-dev is already the newest version (3.13.9-2). python3-dev set to manually installed. debianutils is already the newest version (5.23.2). python3-autocommand is already the newest version (2.2.2-3). python3-autocommand set to manually installed. dh-python is already the newest version (6.20251204.1). dh-python set to manually installed. dash is already the newest version (0.5.12-12). python3-zmq is already the newest version (27.1.0-1+b1). python3-zmq set to manually installed. libaudit1 is already the newest version (1:4.1.2-1+b1). libjansson4 is already the newest version (2.14-2+b3). libjansson4 set to manually installed. python3-nbconvert is already the newest version (7.16.6-1). python3-nbconvert set to manually installed. python3-sphinx is already the newest version (8.2.3-11). python3-sphinx set to manually installed. libgcc-s1 is already the newest version (15.2.0-10). intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. m4 is already the newest version (1.4.20-2). m4 set to manually installed. libdpkg-perl is already the newest version (1.22.21). libdpkg-perl set to manually installed. python3-bs4 is already the newest version (4.14.3-1). python3-bs4 set to manually installed. binutils-aarch64-linux-gnu is already the newest version (2.45.50.20251201-1). binutils-aarch64-linux-gnu set to manually installed. readline-common is already the newest version (8.3-3). readline-common set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). libsasl2-2 is already the newest version (2.1.28+dfsg1-10). libsasl2-2 set to manually installed. bzip2 is already the newest version (1.0.8-6). bzip2 set to manually installed. libzstd1 is already the newest version (1.5.7+dfsg-2). autotools-dev is already the newest version (20240727.1). autotools-dev set to manually installed. g++-15-aarch64-linux-gnu is already the newest version (15.2.0-10). g++-15-aarch64-linux-gnu set to manually installed. cpp-aarch64-linux-gnu is already the newest version (4:15.2.0-4). cpp-aarch64-linux-gnu set to manually installed. libkrb5-3 is already the newest version (1.22.1-2). libkrb5-3 set to manually installed. libgomp1 is already the newest version (15.2.0-10). libgomp1 set to manually installed. libsz2 is already the newest version (1.1.4-2). libsz2 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-requests is already the newest version (2.32.5+dfsg-1). python3-requests set to manually installed. python3-setuptools is already the newest version (78.1.1-0.1). python3-setuptools set to manually installed. libsframe2 is already the newest version (2.45.50.20251201-1). libsframe2 set to manually installed. ncurses-base is already the newest version (6.5+20251123-1). python3-chardet is already the newest version (5.2.0+dfsg-2). python3-chardet set to manually installed. python3-pyparsing is already the newest version (3.1.3-1). python3-pyparsing set to manually installed. bsdextrautils is already the newest version (2.41.2-4). bsdextrautils set to manually installed. python3-jaraco.text is already the newest version (4.0.0-1). python3-jaraco.text set to manually installed. python3.13-minimal is already the newest version (3.13.11-1+b1). python3.13-minimal set to manually installed. python3-alabaster is already the newest version (0.7.16-0.1). python3-alabaster set to manually installed. xml-core is already the newest version (0.19). xml-core set to manually installed. libngtcp2-crypto-ossl0 is already the newest version (1.16.0-1). libngtcp2-crypto-ossl0 set to manually installed. python3.14-dev is already the newest version (3.14.2-1+b1). python3.14-dev set to manually installed. libcrypt1 is already the newest version (1:4.5.1-1). libpython3.14 is already the newest version (3.14.2-1+b1). libpython3.14 set to manually installed. libgssapi-krb5-2 is already the newest version (1.22.1-2). libgssapi-krb5-2 set to manually installed. man-db is already the newest version (2.13.1-1). man-db set to manually installed. libmount1 is already the newest version (2.41.2-4). pybuild-plugin-pyproject is already the newest version (6.20251204.1). pybuild-plugin-pyproject set to manually installed. linux-libc-dev is already the newest version (6.17.10-1). linux-libc-dev set to manually installed. libncursesw6 is already the newest version (6.5+20251123-1). libncursesw6 set to manually installed. libpython3.13-dev is already the newest version (3.13.11-1+b1). libpython3.13-dev set to manually installed. libgcc-15-dev is already the newest version (15.2.0-10). libgcc-15-dev set to manually installed. libsasl2-modules-db is already the newest version (2.1.28+dfsg1-10). libsasl2-modules-db set to manually installed. python3-nbclient is already the newest version (0.8.0-3). python3-nbclient set to manually installed. python-tables-data is already the newest version (3.10.2-3). python-tables-data set to manually installed. python3-webencodings is already the newest version (0.5.1-5). python3-webencodings set to manually installed. liblzma5 is already the newest version (5.8.1-2). python3 is already the newest version (3.13.9-2). python3 set to manually installed. libp11-kit0 is already the newest version (0.25.10-1). libp11-kit0 set to manually installed. libgfortran5 is already the newest version (15.2.0-10). libgfortran5 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.aQNLsBTZ4a (Reading database ... 35635 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.aQNLsBTZ4a I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.aQNLsBTZ4a 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.aQNLsBTZ4a... I: success in 147.6094 seconds Downloading dependency 257 of 317: libexpat1:arm64=2.7.3-1 Downloading dependency 258 of 317: libpython3.14-stdlib:arm64=3.14.2-1+b1 Downloading dependency 259 of 317: python3-dev:arm64=3.13.9-2 Downloading dependency 260 of 317: debianutils:arm64=5.23.2 Downloading dependency 261 of 317: python3-autocommand:arm64=2.2.2-3 Downloading dependency 262 of 317: dh-python:arm64=6.20251204.1 Downloading dependency 263 of 317: dash:arm64=0.5.12-12 Downloading dependency 264 of 317: python3-zmq:arm64=27.1.0-1+b1 Downloading dependency 265 of 317: libaudit1:arm64=1:4.1.2-1+b1 Downloading dependency 266 of 317: libjansson4:arm64=2.14-2+b3 Downloading dependency 267 of 317: python3-nbconvert:arm64=7.16.6-1 Downloading dependency 268 of 317: python3-sphinx:arm64=8.2.3-11 Downloading dependency 269 of 317: libgcc-s1:arm64=15.2.0-10 Downloading dependency 270 of 317: intltool-debian:arm64=0.35.0+20060710.6 Downloading dependency 271 of 317: m4:arm64=1.4.20-2 Downloading dependency 272 of 317: libdpkg-perl:arm64=1.22.21 Downloading dependency 273 of 317: python3-bs4:arm64=4.14.3-1 Downloading dependency 274 of 317: binutils-aarch64-linux-gnu:arm64=2.45.50.20251201-1 Downloading dependency 275 of 317: readline-common:arm64=8.3-3 Downloading dependency 276 of 317: zlib1g:arm64=1:1.3.dfsg+really1.3.1-1+b1 Downloading dependency 277 of 317: libsasl2-2:arm64=2.1.28+dfsg1-10 Downloading dependency 278 of 317: bzip2:arm64=1.0.8-6 Downloading dependency 279 of 317: libzstd1:arm64=1.5.7+dfsg-2 Downloading dependency 280 of 317: autotools-dev:arm64=20240727.1 Downloading dependency 281 of 317: g++-15-aarch64-linux-gnu:arm64=15.2.0-10 Downloading dependency 282 of 317: cpp-aarch64-linux-gnu:arm64=4:15.2.0-4 Downloading dependency 283 of 317: libkrb5-3:arm64=1.22.1-2 Downloading dependency 284 of 317: libgomp1:arm64=15.2.0-10 Downloading dependency 285 of 317: libsz2:arm64=1.1.4-2 Downloading dependency 286 of 317: python3-pandas-lib:arm64=2.3.3+dfsg-3 Downloading dependency 287 of 317: python3-requests:arm64=2.32.5+dfsg-1 Downloading dependency 288 of 317: python3-setuptools:arm64=78.1.1-0.1 Downloading dependency 289 of 317: libsframe2:arm64=2.45.50.20251201-1 Downloading dependency 290 of 317: ncurses-base:arm64=6.5+20251123-1 Downloading dependency 291 of 317: python3-chardet:arm64=5.2.0+dfsg-2 Downloading dependency 292 of 317: python3-pyparsing:arm64=3.1.3-1 Downloading dependency 293 of 317: bsdextrautils:arm64=2.41.2-4 Downloading dependency 294 of 317: python3-jaraco.text:arm64=4.0.0-1 Downloading dependency 295 of 317: python3.13-minimal:arm64=3.13.11-1+b1 Downloading dependency 296 of 317: python3-alabaster:arm64=0.7.16-0.1 Downloading dependency 297 of 317: xml-core:arm64=0.19 Downloading dependency 298 of 317: libngtcp2-crypto-ossl0:arm64=1.16.0-1 Downloading dependency 299 of 317: python3.14-dev:arm64=3.14.2-1+b1 Downloading dependency 300 of 317: libcrypt1:arm64=1:4.5.1-1 Downloading dependency 301 of 317: libpython3.14:arm64=3.14.2-1+b1 Downloading dependency 302 of 317: libgssapi-krb5-2:arm64=1.22.1-2 Downloading dependency 303 of 317: man-db:arm64=2.13.1-1 Downloading dependency 304 of 317: libmount1:arm64=2.41.2-4 Downloading dependency 305 of 317: pybuild-plugin-pyproject:arm64=6.20251204.1 Downloading dependency 306 of 317: linux-libc-dev:arm64=6.17.10-1 Downloading dependency 307 of 317: libncursesw6:arm64=6.5+20251123-1 Downloading dependency 308 of 317: libpython3.13-dev:arm64=3.13.11-1+b1 Downloading dependency 309 of 317: libgcc-15-dev:arm64=15.2.0-10 Downloading dependency 310 of 317: libsasl2-modules-db:arm64=2.1.28+dfsg1-10 Downloading dependency 311 of 317: python3-nbclient:arm64=0.8.0-3 Downloading dependency 312 of 317: python-tables-data:arm64=3.10.2-3 Downloading dependency 313 of 317: python3-webencodings:arm64=0.5.1-5 Downloading dependency 314 of 317: liblzma5:arm64=5.8.1-2 Downloading dependency 315 of 317: python3:arm64=3.13.9-2 Downloading dependency 316 of 317: libp11-kit0:arm64=0.25.10-1 Downloading dependency 317 of 317: libgfortran5:arm64=15.2.0-10 env --chdir=/srv/rebuilderd/tmp/rebuilderdekgDYI/out DEB_BUILD_OPTIONS=parallel=8 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1765286939 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildlRPV6v/debrebuild.sbuildrc.C8iTHUagLzNP sbuild --build=arm64 --host=arm64 --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 arm64; no source changes. * Rebuild with Python 3.14 as supported -- arm Build Daemon (arm-conova-03) Tue, 09 Dec 2025 13:28:59 +0000 --chroot=/srv/rebuilderd/tmp/debrebuildlRPV6v/debrebuild.tar.cE5ykLGECQzq --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/rebuilderdekgDYI/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 codethink02-arm64 +==============================================================================+ | mdtraj 1.11.0-2+b1 (arm64) Fri, 26 Dec 2025 07:00:36 +0000 | +==============================================================================+ Package: mdtraj Version: 1.11.0-2+b1 Source Version: 1.11.0-2 Distribution: unstable Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuildlRPV6v/debrebuild.tar.cE5ykLGECQzq to /srv/rebuilderd/tmp/tmp.sbuild.rNSd10D5Uv... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Fri, 26 Dec 2025 07:00:45 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdekgDYI/inputs/mdtraj_1.11.0-2.dsc exists in /srv/rebuilderd/tmp/rebuilderdekgDYI/inputs; copying to chroot sbuild: warning: descr(l1): found blank line where expected first heading +------------------------------------------------------------------------------+ | Install package build dependencies Fri, 26 Dec 2025 07:00:48 +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-zlZNI7/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Fri, 26 Dec 2025 07:00:55 +0000 | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any-amd64 arm64 i386 all) +------------------------------------------------------------------------------+ | Build environment Fri, 26 Dec 2025 07:00:56 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.57+deb13-cloud-arm64 #1 SMP Debian 6.12.57-1 (2025-11-05) arm64 (aarch64) 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-aarch64-linux-gnu_2.45.50.20251201-1 binutils-common_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-aarch64-linux-gnu_15.2.0-10 cpp-aarch64-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-aarch64-linux-gnu_15.2.0-10 g++-aarch64-linux-gnu_4:15.2.0-4 gcc_4:15.2.0-4 gcc-15_15.2.0-10 gcc-15-aarch64-linux-gnu_15.2.0-10 gcc-15-base_15.2.0-10 gcc-aarch64-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 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-2 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+b1 sed_4.9-2+b1 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 Fri, 26 Dec 2025 07:00:56 +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=8 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=1765286939 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 arm Build Daemon (arm-conova-03) dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/15/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-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=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-15-15.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 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... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 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-aarch64-cpython-314/mdtraj copying mdtraj/io.py -> build/lib.linux-aarch64-cpython-314/mdtraj copying mdtraj/__init__.py -> build/lib.linux-aarch64-cpython-314/mdtraj copying mdtraj/_version.py -> build/lib.linux-aarch64-cpython-314/mdtraj creating build/lib.linux-aarch64-cpython-314/mdtraj/nmr copying mdtraj/nmr/__init__.py -> build/lib.linux-aarch64-cpython-314/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-aarch64-cpython-314/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-aarch64-cpython-314/mdtraj/nmr creating build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/pi_stacking.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/distance.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/order.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/contact.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/alignment.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/internal.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/rdf.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/rg.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/hbond.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/__init__.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/shape.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/sasa.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/dssp.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry copying mdtraj/geometry/angle.py -> build/lib.linux-aarch64-cpython-314/mdtraj/geometry creating build/lib.linux-aarch64-cpython-314/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> build/lib.linux-aarch64-cpython-314/mdtraj/scripts copying mdtraj/scripts/__init__.py -> build/lib.linux-aarch64-cpython-314/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> build/lib.linux-aarch64-cpython-314/mdtraj/scripts creating build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/lh5.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/netcdf.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/prmtop.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/arc.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/gsd.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/amberrst.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/openmmxml.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/__init__.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/xyzfile.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/mol2.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/registry.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/psf.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/gro.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/mdcrd.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats copying mdtraj/formats/hdf5.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats creating build/lib.linux-aarch64-cpython-314/mdtraj/utils copying mdtraj/utils/delay_import.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils copying mdtraj/utils/singleton.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils copying mdtraj/utils/zipped.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils copying mdtraj/utils/__init__.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils copying mdtraj/utils/validation.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils copying mdtraj/utils/unitcell.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils copying mdtraj/utils/rotation.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils creating build/lib.linux-aarch64-cpython-314/mdtraj/core copying mdtraj/core/topology.py -> build/lib.linux-aarch64-cpython-314/mdtraj/core copying mdtraj/core/selection.py -> build/lib.linux-aarch64-cpython-314/mdtraj/core copying mdtraj/core/residue_names.py -> build/lib.linux-aarch64-cpython-314/mdtraj/core copying mdtraj/core/element.py -> build/lib.linux-aarch64-cpython-314/mdtraj/core copying mdtraj/core/__init__.py -> build/lib.linux-aarch64-cpython-314/mdtraj/core copying mdtraj/core/trajectory.py -> build/lib.linux-aarch64-cpython-314/mdtraj/core creating build/lib.linux-aarch64-cpython-314/mdtraj/testing copying mdtraj/testing/docstrings.py -> build/lib.linux-aarch64-cpython-314/mdtraj/testing copying mdtraj/testing/testing.py -> build/lib.linux-aarch64-cpython-314/mdtraj/testing copying mdtraj/testing/__init__.py -> build/lib.linux-aarch64-cpython-314/mdtraj/testing copying mdtraj/testing/docscrape.py -> build/lib.linux-aarch64-cpython-314/mdtraj/testing creating build/lib.linux-aarch64-cpython-314/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> build/lib.linux-aarch64-cpython-314/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-aarch64-cpython-314/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-aarch64-cpython-314/mdtraj/reporters copying mdtraj/reporters/__init__.py -> build/lib.linux-aarch64-cpython-314/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-aarch64-cpython-314/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-aarch64-cpython-314/mdtraj/reporters creating build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/pdbx.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/PdbxReader.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/PdbxContainers.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/__init__.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/pdbxfile.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdbx creating build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdb creating build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit creating build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdb/data UPDATING build/lib.linux-aarch64-cpython-314/mdtraj/_version.py set build/lib.linux-aarch64-cpython-314/mdtraj/_version.py to '1.11.0' running build_ext building 'mdtraj.formats.xtc' extension creating build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/src aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/mdtraj/formats/xtc.cpython-314-aarch64-linux-gnu.so /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.formats.trr' extension aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-314/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/mdtraj/formats/trr.cpython-314-aarch64-linux-gnu.so /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.formats.dcd' extension creating build/temp.linux-aarch64-cpython-314/mdtraj/formats/dcd creating build/temp.linux-aarch64-cpython-314/mdtraj/formats/dcd/src aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-314/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-314/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-314/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-314/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/mdtraj/formats/dcd.cpython-314-aarch64-linux-gnu.so /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.formats.dtr' extension creating build/temp.linux-aarch64-cpython-314/mdtraj/formats/dtr creating build/temp.linux-aarch64-cpython-314/mdtraj/formats/dtr/src aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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 ()); | ~~~~~~~~~~~~~~~~~ aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-314/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-314/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/mdtraj/formats/dtr.cpython-314-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj._rmsd' extension creating build/temp.linux-aarch64-cpython-314/mdtraj/rmsd creating build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o build/lib.linux-aarch64-cpython-314/mdtraj/_rmsd.cpython-314-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj._lprmsd' extension aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o build/lib.linux-aarch64-cpython-314/mdtraj/_lprmsd.cpython-314-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.core.lib.libtheobald' extension aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 aarch64-linux-gnu-gcc-ar rcs build/lib.linux-aarch64-cpython-314/mdtraj/core/lib/libtheobald.a build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-aarch64-cpython-314/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o build/lib.linux-aarch64-cpython-314/mdtraj/geometry/_geometry.cpython-314-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.geometry.drid' extension aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-314/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o build/lib.linux-aarch64-cpython-314/mdtraj/geometry/drid.cpython-314-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.geometry.neighbors' extension aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-314/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o build/lib.linux-aarch64-cpython-314/mdtraj/geometry/neighbors.cpython-314-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.geometry.neighborlist' extension aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-314/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-314/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o build/lib.linux-aarch64-cpython-314/mdtraj/geometry/neighborlist.cpython-314-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. installing to build/bdist.linux-aarch64/wheel running install running install_lib creating build/bdist.linux-aarch64/wheel creating build/bdist.linux-aarch64/wheel/mdtraj creating build/bdist.linux-aarch64/wheel/mdtraj/nmr copying build/lib.linux-aarch64-cpython-314/mdtraj/nmr/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/nmr copying build/lib.linux-aarch64-cpython-314/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-aarch64/wheel/./mdtraj/nmr copying build/lib.linux-aarch64-cpython-314/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-aarch64/wheel/./mdtraj/nmr copying build/lib.linux-aarch64-cpython-314/mdtraj/_lprmsd.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj creating build/bdist.linux-aarch64/wheel/mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/pi_stacking.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/distance.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/order.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/drid.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/contact.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/alignment.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/internal.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/neighborlist.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/rdf.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/dihedral.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/rg.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/hbond.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/shape.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/sasa.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/neighbors.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/dssp.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/_geometry.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-314/mdtraj/geometry/angle.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry creating build/bdist.linux-aarch64/wheel/mdtraj/scripts copying build/lib.linux-aarch64-cpython-314/mdtraj/scripts/mdconvert.py -> build/bdist.linux-aarch64/wheel/./mdtraj/scripts copying build/lib.linux-aarch64-cpython-314/mdtraj/scripts/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/scripts copying build/lib.linux-aarch64-cpython-314/mdtraj/scripts/mdinspect.py -> build/bdist.linux-aarch64/wheel/./mdtraj/scripts creating build/bdist.linux-aarch64/wheel/mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/lh5.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats creating build/bdist.linux-aarch64/wheel/mdtraj/formats/pdbx copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdbx/pdbx.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdbx/PdbxReader.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdbx/PdbxContainers.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdbx/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdbx/pdbxfile.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/netcdf.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/prmtop.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/trr.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/arc.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/hoomdxml.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/xtc.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/gsd.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/amberrst.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/openmmxml.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/dcd.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/formats creating build/bdist.linux-aarch64/wheel/mdtraj/formats/pdb copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdb copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdb creating build/bdist.linux-aarch64/wheel/mdtraj/formats/pdb/data copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdb/data copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdb/data copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdb copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/dtr.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/xyzfile.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/mol2.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/registry.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/psf.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/gro.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/mdcrd.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/lammpstrj.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/formats/hdf5.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-314/mdtraj/io.py -> build/bdist.linux-aarch64/wheel/./mdtraj copying build/lib.linux-aarch64-cpython-314/mdtraj/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj copying build/lib.linux-aarch64-cpython-314/mdtraj/_rmsd.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj copying build/lib.linux-aarch64-cpython-314/mdtraj/_version.py -> build/bdist.linux-aarch64/wheel/./mdtraj creating build/bdist.linux-aarch64/wheel/mdtraj/utils copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/delay_import.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/singleton.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/zipped.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils creating build/bdist.linux-aarch64/wheel/mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit/prefix.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit/quantity.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit/doctests.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit/unit.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit/constants.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/validation.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/unitcell.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/rotation.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils copying build/lib.linux-aarch64-cpython-314/mdtraj/utils/contextmanagers.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils creating build/bdist.linux-aarch64/wheel/mdtraj/core copying build/lib.linux-aarch64-cpython-314/mdtraj/core/topology.py -> build/bdist.linux-aarch64/wheel/./mdtraj/core copying build/lib.linux-aarch64-cpython-314/mdtraj/core/selection.py -> build/bdist.linux-aarch64/wheel/./mdtraj/core copying build/lib.linux-aarch64-cpython-314/mdtraj/core/residue_names.py -> build/bdist.linux-aarch64/wheel/./mdtraj/core copying build/lib.linux-aarch64-cpython-314/mdtraj/core/element.py -> build/bdist.linux-aarch64/wheel/./mdtraj/core copying build/lib.linux-aarch64-cpython-314/mdtraj/core/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/core copying build/lib.linux-aarch64-cpython-314/mdtraj/core/trajectory.py -> build/bdist.linux-aarch64/wheel/./mdtraj/core creating build/bdist.linux-aarch64/wheel/mdtraj/core/lib copying build/lib.linux-aarch64-cpython-314/mdtraj/core/lib/center.h -> build/bdist.linux-aarch64/wheel/./mdtraj/core/lib copying build/lib.linux-aarch64-cpython-314/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-aarch64/wheel/./mdtraj/core/lib copying build/lib.linux-aarch64-cpython-314/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-aarch64/wheel/./mdtraj/core/lib creating build/bdist.linux-aarch64/wheel/mdtraj/testing copying build/lib.linux-aarch64-cpython-314/mdtraj/testing/docstrings.py -> build/bdist.linux-aarch64/wheel/./mdtraj/testing copying build/lib.linux-aarch64-cpython-314/mdtraj/testing/testing.py -> build/bdist.linux-aarch64/wheel/./mdtraj/testing copying build/lib.linux-aarch64-cpython-314/mdtraj/testing/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/testing copying build/lib.linux-aarch64-cpython-314/mdtraj/testing/docscrape.py -> build/bdist.linux-aarch64/wheel/./mdtraj/testing creating build/bdist.linux-aarch64/wheel/mdtraj/reporters copying build/lib.linux-aarch64-cpython-314/mdtraj/reporters/basereporter.py -> build/bdist.linux-aarch64/wheel/./mdtraj/reporters copying build/lib.linux-aarch64-cpython-314/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-aarch64/wheel/./mdtraj/reporters copying build/lib.linux-aarch64-cpython-314/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-aarch64/wheel/./mdtraj/reporters copying build/lib.linux-aarch64-cpython-314/mdtraj/reporters/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/reporters copying build/lib.linux-aarch64-cpython-314/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-aarch64/wheel/./mdtraj/reporters copying build/lib.linux-aarch64-cpython-314/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-aarch64/wheel/./mdtraj/reporters 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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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-aarch64/wheel/./mdtraj-1.11.0.egg-info running install_scripts creating build/bdist.linux-aarch64/wheel/mdtraj-1.11.0.dist-info/WHEEL creating '/build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.14_mdtraj/.tmp-s067aii7/mdtraj-1.11.0-cp314-cp314-linux_aarch64.whl' and adding 'build/bdist.linux-aarch64/wheel' to it adding 'mdtraj/__init__.py' adding 'mdtraj/_lprmsd.cpython-314-aarch64-linux-gnu.so' adding 'mdtraj/_rmsd.cpython-314-aarch64-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-aarch64-linux-gnu.so' adding 'mdtraj/formats/dtr.cpython-314-aarch64-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-aarch64-linux-gnu.so' adding 'mdtraj/formats/xtc.cpython-314-aarch64-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-aarch64-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-aarch64-linux-gnu.so' adding 'mdtraj/geometry/dssp.py' adding 'mdtraj/geometry/hbond.py' adding 'mdtraj/geometry/internal.py' adding 'mdtraj/geometry/neighborlist.cpython-314-aarch64-linux-gnu.so' adding 'mdtraj/geometry/neighbors.cpython-314-aarch64-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-aarch64/wheel Successfully built mdtraj-1.11.0-cp314-cp314-linux_aarch64.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/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/15/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-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=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-15-15.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 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... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 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-aarch64-cpython-313/mdtraj copying mdtraj/io.py -> build/lib.linux-aarch64-cpython-313/mdtraj copying mdtraj/__init__.py -> build/lib.linux-aarch64-cpython-313/mdtraj copying mdtraj/_version.py -> build/lib.linux-aarch64-cpython-313/mdtraj creating build/lib.linux-aarch64-cpython-313/mdtraj/nmr copying mdtraj/nmr/__init__.py -> build/lib.linux-aarch64-cpython-313/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-aarch64-cpython-313/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-aarch64-cpython-313/mdtraj/nmr creating build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/pi_stacking.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/distance.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/order.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/contact.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/alignment.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/internal.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/rdf.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/rg.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/hbond.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/__init__.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/shape.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/sasa.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/dssp.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry copying mdtraj/geometry/angle.py -> build/lib.linux-aarch64-cpython-313/mdtraj/geometry creating build/lib.linux-aarch64-cpython-313/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> build/lib.linux-aarch64-cpython-313/mdtraj/scripts copying mdtraj/scripts/__init__.py -> build/lib.linux-aarch64-cpython-313/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> build/lib.linux-aarch64-cpython-313/mdtraj/scripts creating build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/lh5.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/netcdf.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/prmtop.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/arc.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/gsd.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/amberrst.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/openmmxml.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/__init__.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/xyzfile.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/mol2.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/registry.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/psf.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/gro.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/mdcrd.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats copying mdtraj/formats/hdf5.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats creating build/lib.linux-aarch64-cpython-313/mdtraj/utils copying mdtraj/utils/delay_import.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils copying mdtraj/utils/singleton.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils copying mdtraj/utils/zipped.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils copying mdtraj/utils/__init__.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils copying mdtraj/utils/validation.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils copying mdtraj/utils/unitcell.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils copying mdtraj/utils/rotation.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils creating build/lib.linux-aarch64-cpython-313/mdtraj/core copying mdtraj/core/topology.py -> build/lib.linux-aarch64-cpython-313/mdtraj/core copying mdtraj/core/selection.py -> build/lib.linux-aarch64-cpython-313/mdtraj/core copying mdtraj/core/residue_names.py -> build/lib.linux-aarch64-cpython-313/mdtraj/core copying mdtraj/core/element.py -> build/lib.linux-aarch64-cpython-313/mdtraj/core copying mdtraj/core/__init__.py -> build/lib.linux-aarch64-cpython-313/mdtraj/core copying mdtraj/core/trajectory.py -> build/lib.linux-aarch64-cpython-313/mdtraj/core creating build/lib.linux-aarch64-cpython-313/mdtraj/testing copying mdtraj/testing/docstrings.py -> build/lib.linux-aarch64-cpython-313/mdtraj/testing copying mdtraj/testing/testing.py -> build/lib.linux-aarch64-cpython-313/mdtraj/testing copying mdtraj/testing/__init__.py -> build/lib.linux-aarch64-cpython-313/mdtraj/testing copying mdtraj/testing/docscrape.py -> build/lib.linux-aarch64-cpython-313/mdtraj/testing creating build/lib.linux-aarch64-cpython-313/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> build/lib.linux-aarch64-cpython-313/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-aarch64-cpython-313/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-aarch64-cpython-313/mdtraj/reporters copying mdtraj/reporters/__init__.py -> build/lib.linux-aarch64-cpython-313/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-aarch64-cpython-313/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-aarch64-cpython-313/mdtraj/reporters creating build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/pdbx.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/PdbxReader.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/PdbxContainers.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/__init__.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/pdbxfile.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdbx creating build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdb creating build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit creating build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdb/data UPDATING build/lib.linux-aarch64-cpython-313/mdtraj/_version.py set build/lib.linux-aarch64-cpython-313/mdtraj/_version.py to '1.11.0' running build_ext building 'mdtraj.formats.xtc' extension creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.formats.trr' extension aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.formats.dcd' extension creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/src aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.formats.dtr' extension creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/src aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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 ()); | ~~~~~~~~~~~~~~~~~ aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj._rmsd' extension creating build/temp.linux-aarch64-cpython-313/mdtraj/rmsd creating build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o build/lib.linux-aarch64-cpython-313/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj._lprmsd' extension aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o build/lib.linux-aarch64-cpython-313/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.core.lib.libtheobald' extension aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 aarch64-linux-gnu-gcc-ar rcs build/lib.linux-aarch64-cpython-313/mdtraj/core/lib/libtheobald.a build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o build/lib.linux-aarch64-cpython-313/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.geometry.drid' extension aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o build/lib.linux-aarch64-cpython-313/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.geometry.neighbors' extension aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o build/lib.linux-aarch64-cpython-313/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. building 'mdtraj.geometry.neighborlist' extension aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o build/lib.linux-aarch64-cpython-313/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. installing to build/bdist.linux-aarch64/wheel running install running install_lib creating build/bdist.linux-aarch64/wheel creating build/bdist.linux-aarch64/wheel/mdtraj creating build/bdist.linux-aarch64/wheel/mdtraj/nmr copying build/lib.linux-aarch64-cpython-313/mdtraj/nmr/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/nmr copying build/lib.linux-aarch64-cpython-313/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-aarch64/wheel/./mdtraj/nmr copying build/lib.linux-aarch64-cpython-313/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-aarch64/wheel/./mdtraj/nmr creating build/bdist.linux-aarch64/wheel/mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/pi_stacking.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/distance.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/order.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/contact.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/alignment.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/internal.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/rdf.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/dihedral.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/rg.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/hbond.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/shape.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/sasa.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/dssp.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry copying build/lib.linux-aarch64-cpython-313/mdtraj/geometry/angle.py -> build/bdist.linux-aarch64/wheel/./mdtraj/geometry creating build/bdist.linux-aarch64/wheel/mdtraj/scripts copying build/lib.linux-aarch64-cpython-313/mdtraj/scripts/mdconvert.py -> build/bdist.linux-aarch64/wheel/./mdtraj/scripts copying build/lib.linux-aarch64-cpython-313/mdtraj/scripts/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/scripts copying build/lib.linux-aarch64-cpython-313/mdtraj/scripts/mdinspect.py -> build/bdist.linux-aarch64/wheel/./mdtraj/scripts creating build/bdist.linux-aarch64/wheel/mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/lh5.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats creating build/bdist.linux-aarch64/wheel/mdtraj/formats/pdbx copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdbx/pdbx.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdbx/PdbxReader.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdbx/PdbxContainers.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdbx/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdbx/pdbxfile.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdbx copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/netcdf.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/prmtop.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/arc.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/hoomdxml.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/gsd.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/amberrst.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/openmmxml.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats creating build/bdist.linux-aarch64/wheel/mdtraj/formats/pdb copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdb copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdb creating build/bdist.linux-aarch64/wheel/mdtraj/formats/pdb/data copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdb/data copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdb/data copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats/pdb copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/xyzfile.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/mol2.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/registry.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/psf.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/gro.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/mdcrd.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/lammpstrj.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/formats/hdf5.py -> build/bdist.linux-aarch64/wheel/./mdtraj/formats copying build/lib.linux-aarch64-cpython-313/mdtraj/io.py -> build/bdist.linux-aarch64/wheel/./mdtraj copying build/lib.linux-aarch64-cpython-313/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj copying build/lib.linux-aarch64-cpython-313/mdtraj/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj copying build/lib.linux-aarch64-cpython-313/mdtraj/_version.py -> build/bdist.linux-aarch64/wheel/./mdtraj creating build/bdist.linux-aarch64/wheel/mdtraj/utils copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/delay_import.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/singleton.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/zipped.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils creating build/bdist.linux-aarch64/wheel/mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit/prefix.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit/quantity.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit/doctests.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit/unit.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit/constants.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils/unit copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/validation.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/unitcell.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/rotation.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils copying build/lib.linux-aarch64-cpython-313/mdtraj/utils/contextmanagers.py -> build/bdist.linux-aarch64/wheel/./mdtraj/utils creating build/bdist.linux-aarch64/wheel/mdtraj/core copying build/lib.linux-aarch64-cpython-313/mdtraj/core/topology.py -> build/bdist.linux-aarch64/wheel/./mdtraj/core copying build/lib.linux-aarch64-cpython-313/mdtraj/core/selection.py -> build/bdist.linux-aarch64/wheel/./mdtraj/core copying build/lib.linux-aarch64-cpython-313/mdtraj/core/residue_names.py -> build/bdist.linux-aarch64/wheel/./mdtraj/core copying build/lib.linux-aarch64-cpython-313/mdtraj/core/element.py -> build/bdist.linux-aarch64/wheel/./mdtraj/core copying build/lib.linux-aarch64-cpython-313/mdtraj/core/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/core copying build/lib.linux-aarch64-cpython-313/mdtraj/core/trajectory.py -> build/bdist.linux-aarch64/wheel/./mdtraj/core creating build/bdist.linux-aarch64/wheel/mdtraj/core/lib copying build/lib.linux-aarch64-cpython-313/mdtraj/core/lib/center.h -> build/bdist.linux-aarch64/wheel/./mdtraj/core/lib copying build/lib.linux-aarch64-cpython-313/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-aarch64/wheel/./mdtraj/core/lib copying build/lib.linux-aarch64-cpython-313/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-aarch64/wheel/./mdtraj/core/lib creating build/bdist.linux-aarch64/wheel/mdtraj/testing copying build/lib.linux-aarch64-cpython-313/mdtraj/testing/docstrings.py -> build/bdist.linux-aarch64/wheel/./mdtraj/testing copying build/lib.linux-aarch64-cpython-313/mdtraj/testing/testing.py -> build/bdist.linux-aarch64/wheel/./mdtraj/testing copying build/lib.linux-aarch64-cpython-313/mdtraj/testing/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/testing copying build/lib.linux-aarch64-cpython-313/mdtraj/testing/docscrape.py -> build/bdist.linux-aarch64/wheel/./mdtraj/testing copying build/lib.linux-aarch64-cpython-313/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./mdtraj creating build/bdist.linux-aarch64/wheel/mdtraj/reporters copying build/lib.linux-aarch64-cpython-313/mdtraj/reporters/basereporter.py -> build/bdist.linux-aarch64/wheel/./mdtraj/reporters copying build/lib.linux-aarch64-cpython-313/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-aarch64/wheel/./mdtraj/reporters copying build/lib.linux-aarch64-cpython-313/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-aarch64/wheel/./mdtraj/reporters copying build/lib.linux-aarch64-cpython-313/mdtraj/reporters/__init__.py -> build/bdist.linux-aarch64/wheel/./mdtraj/reporters copying build/lib.linux-aarch64-cpython-313/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-aarch64/wheel/./mdtraj/reporters copying build/lib.linux-aarch64-cpython-313/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-aarch64/wheel/./mdtraj/reporters 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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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-aarch64/wheel/./mdtraj-1.11.0.egg-info running install_scripts creating build/bdist.linux-aarch64/wheel/mdtraj-1.11.0.dist-info/WHEEL creating '/build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/.tmp-xitft55f/mdtraj-1.11.0-cp313-cp313-linux_aarch64.whl' and adding 'build/bdist.linux-aarch64/wheel' to it adding 'mdtraj/__init__.py' adding 'mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so' adding 'mdtraj/_rmsd.cpython-313-aarch64-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-aarch64-linux-gnu.so' adding 'mdtraj/formats/dtr.cpython-313-aarch64-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-aarch64-linux-gnu.so' adding 'mdtraj/formats/xtc.cpython-313-aarch64-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-aarch64-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-aarch64-linux-gnu.so' adding 'mdtraj/geometry/dssp.py' adding 'mdtraj/geometry/hbond.py' adding 'mdtraj/geometry/internal.py' adding 'mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so' adding 'mdtraj/geometry/neighbors.cpython-313-aarch64-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-aarch64/wheel Successfully built mdtraj-1.11.0-cp313-cp313-linux_aarch64.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%] 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[ 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 (...) 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[ 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...) 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[ 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...) 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[ 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 140.34s (0:02:20) = 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 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[ 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 144.87s (0:02:24) = 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-V2T9lMRV 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.arm64 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/mdinspect.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 chmod 0644 -- 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 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/ I: dh_python3 tools:114: replacing shebang in debian/python3-mdtraj/usr/bin/mdconvert-mdtraj I: dh_python3 tools:114: replacing shebang in debian/python3-mdtraj/usr/bin/mdinspect 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 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 (>= 3.13~)', 'python3-packaging', 'python3-scipy', 'python3-pyparsing', 'python3 (<< 3.15)', 'python3:any', '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.arm64 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.arm64 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/aarch64-linux-gnu dwz -mdebian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug -- debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-314-aarch64-linux-gnu.so objcopy --compress-debug-sections debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug chmod 0644 -- debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-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/e3 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-314-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e3/578402d73de1c498327b566e2251e4d1d36723.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e3/578402d73de1c498327b566e2251e4d1d36723.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-314-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e3/578402d73de1c498327b566e2251e4d1d36723.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-314-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/42 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/42/092736eded3012c66b5ea9a3181a23ebd6c291.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/42/092736eded3012c66b5ea9a3181a23ebd6c291.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/42/092736eded3012c66b5ea9a3181a23ebd6c291.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/7a objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-314-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/7a/04b1200a9fbc09a01929d6a7291c6285fdaa27.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/7a/04b1200a9fbc09a01929d6a7291c6285fdaa27.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-314-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/7a/04b1200a9fbc09a01929d6a7291c6285fdaa27.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-314-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3b objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3b/2b51812cd64f4516e15a238898511d52429425.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3b/2b51812cd64f4516e15a238898511d52429425.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3b/2b51812cd64f4516e15a238898511d52429425.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3b objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3b/790b6efa9947577258775feac56ab82088850d.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3b/790b6efa9947577258775feac56ab82088850d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3b/790b6efa9947577258775feac56ab82088850d.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/82 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-314-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/82/c2683a2ebe82b5c012b7c85889a15d8b2e471d.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/82/c2683a2ebe82b5c012b7c85889a15d8b2e471d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-314-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/82/c2683a2ebe82b5c012b7c85889a15d8b2e471d.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-314-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d5 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d5/afef57475b79e8fca084d6ffea2935c40a3898.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d5/afef57475b79e8fca084d6ffea2935c40a3898.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d5/afef57475b79e8fca084d6ffea2935c40a3898.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/db objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-314-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/db/d379fb1511722656d27b613216f10d717484a9.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/db/d379fb1511722656d27b613216f10d717484a9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-314-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/db/d379fb1511722656d27b613216f10d717484a9.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-314-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d8 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d8/d2c4c1b1f7f17e30622dbb477c25331e0ca160.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d8/d2c4c1b1f7f17e30622dbb477c25331e0ca160.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d8/d2c4c1b1f7f17e30622dbb477c25331e0ca160.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/85 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/85/9d16a5a2ef2427bfe2edc7cd01baf362962bba.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/85/9d16a5a2ef2427bfe2edc7cd01baf362962bba.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/85/9d16a5a2ef2427bfe2edc7cd01baf362962bba.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/eb objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-314-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/eb/196277f6dbef408199d996cecedffa8fc8d88b.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/eb/196277f6dbef408199d996cecedffa8fc8d88b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-314-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/eb/196277f6dbef408199d996cecedffa8fc8d88b.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-314-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/16 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-314-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/16/aea72bb675eb9bb35a352f5d88104e56821edd.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/16/aea72bb675eb9bb35a352f5d88104e56821edd.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-314-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/16/aea72bb675eb9bb35a352f5d88104e56821edd.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-314-aarch64-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/formats/trr.cpython-314-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d7/fa400f971cff9a4ee4f42aed02742b062a71d4.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d7/fa400f971cff9a4ee4f42aed02742b062a71d4.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-314-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d7/fa400f971cff9a4ee4f42aed02742b062a71d4.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-314-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a1 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-314-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a1/9536adfc823a0c24968ef0c74088df58613f19.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a1/9536adfc823a0c24968ef0c74088df58613f19.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-314-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a1/9536adfc823a0c24968ef0c74088df58613f19.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-314-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6e objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6e/2c5b850cdf9960a46213875072b53d95aff27a.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6e/2c5b850cdf9960a46213875072b53d95aff27a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6e/2c5b850cdf9960a46213875072b53d95aff27a.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4a objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-314-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4a/aeebbc3d4f9a9af7697ff1175c2ff2d8d0ae1c.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4a/aeebbc3d4f9a9af7697ff1175c2ff2d8d0ae1c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-314-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4a/aeebbc3d4f9a9af7697ff1175c2ff2d8d0ae1c.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-314-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/27 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-314-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/27/7cbf2df566ad30ec8580a2f69a66965544cf5c.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/27/7cbf2df566ad30ec8580a2f69a66965544cf5c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-314-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/27/7cbf2df566ad30ec8580a2f69a66965544cf5c.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-314-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2f objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2f/1d9a6b4b4689ba26f14e9856c56a62738747b1.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2f/1d9a6b4b4689ba26f14e9856c56a62738747b1.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2f/1d9a6b4b4689ba26f14e9856c56a62738747b1.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e7 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e7/4b333f9f876347854006a7e204ed6d0a895842.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e7/4b333f9f876347854006a7e204ed6d0a895842.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e7/4b333f9f876347854006a7e204ed6d0a895842.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fe objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fe/a9f0c3ec5ceba721e02c26e6efad2d6982ce08.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fe/a9f0c3ec5ceba721e02c26e6efad2d6982ce08.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fe/a9f0c3ec5ceba721e02c26e6efad2d6982ce08.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-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/aarch64-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-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-314-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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="16aea72bb675eb9bb35a352f5d88104e56821edd 277cbf2df566ad30ec8580a2f69a66965544cf5c 2f1d9a6b4b4689ba26f14e9856c56a62738747b1 3b2b51812cd64f4516e15a238898511d52429425 3b790b6efa9947577258775feac56ab82088850d 42092736eded3012c66b5ea9a3181a23ebd6c291 4aaeebbc3d4f9a9af7697ff1175c2ff2d8d0ae1c 6e2c5b850cdf9960a46213875072b53d95aff27a 7a04b1200a9fbc09a01929d6a7291c6285fdaa27 82c2683a2ebe82b5c012b7c85889a15d8b2e471d 859d16a5a2ef2427bfe2edc7cd01baf362962bba a19536adfc823a0c24968ef0c74088df58613f19 d5afef57475b79e8fca084d6ffea2935c40a3898 d7fa400f971cff9a4ee4f42aed02742b062a71d4 d8d2c4c1b1f7f17e30622dbb477c25331e0ca160 dbd379fb1511722656d27b613216f10d717484a9 e3578402d73de1c498327b566e2251e4d1d36723 e74b333f9f876347854006a7e204ed6d0a895842 eb196277f6dbef408199d996cecedffa8fc8d88b fea9f0c3ec5ceba721e02c26e6efad2d6982ce08" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/python3-mdtraj chmod 0644 -- debian/python3-mdtraj/DEBIAN/control dh_md5sums -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN cd debian/python3-mdtraj >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python3-mdtraj/DEBIAN/md5sums install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN cd debian/.debhelper/python3-mdtraj/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/md5sums dh_builddeb -a -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/python3-mdtraj .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-mdtraj/dbgsym-root .. dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.11.0-2+b1_arm64.deb'. dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.11.0-2+b1_arm64.deb'. dpkg-genbuildinfo --build=any -O../mdtraj_1.11.0-2+b1_arm64.buildinfo dpkg-genchanges --build=any -O../mdtraj_1.11.0-2+b1_arm64.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 2025-12-26T07:11:47Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Fri, 26 Dec 2025 07:11:48 +0000 | +------------------------------------------------------------------------------+ mdtraj_1.11.0-2+b1_arm64.changes: --------------------------------- Format: 1.8 Date: Tue, 09 Dec 2025 13:28:59 +0000 Source: mdtraj (1.11.0-2) Binary: python3-mdtraj python3-mdtraj-dbgsym Binary-Only: yes Architecture: arm64 Version: 1.11.0-2+b1 Distribution: unstable Urgency: low Maintainer: Debichem Team Changed-By: arm Build Daemon (arm-conova-03) 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 arm64; no source changes. * Rebuild with Python 3.14 as supported Checksums-Sha1: c7fba72459f69456d7a4361fd252d2443890f67a 10901 mdtraj_1.11.0-2+b1_arm64.buildinfo ba9de7ce7645dc61755ab2772812e9974ad84ef9 11119068 python3-mdtraj-dbgsym_1.11.0-2+b1_arm64.deb 346d9df8d862a420db09ec1478bd301e32a029d8 1337744 python3-mdtraj_1.11.0-2+b1_arm64.deb Checksums-Sha256: 38079a8778ac4b1c6bea47c0d66ea54311c186f6b113e6d11f88742dd1ff122a 10901 mdtraj_1.11.0-2+b1_arm64.buildinfo 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Rebuild with Python 3.14 as supported . -- arm Build Daemon (arm-conova-03) Tue, 09 Dec 2025 13:28:59 +0000 Checksums-Md5: 6d319a50e298bb0cc07ab9d269eef2ca 11119068 python3-mdtraj-dbgsym_1.11.0-2+b1_arm64.deb de183c2f1dd4466ab8d7c60a71554aa3 1337744 python3-mdtraj_1.11.0-2+b1_arm64.deb Checksums-Sha1: ba9de7ce7645dc61755ab2772812e9974ad84ef9 11119068 python3-mdtraj-dbgsym_1.11.0-2+b1_arm64.deb 346d9df8d862a420db09ec1478bd301e32a029d8 1337744 python3-mdtraj_1.11.0-2+b1_arm64.deb Checksums-Sha256: 59d6be267106f2e97663fd9c2cf27cf7bbedd179740335c5555a362f19561e3a 11119068 python3-mdtraj-dbgsym_1.11.0-2+b1_arm64.deb 1e89b236d1fe14343b2c8541234431537edc27c1c516112fbe7d9d215245ca3c 1337744 python3-mdtraj_1.11.0-2+b1_arm64.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Fri, 26 Dec 2025 07:11:47 +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), 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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-2), 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+b1), sed (= 4.9-2+b1), sensible-utils (= 0.0.26), sgml-base (= 1.31+nmu1), sphinx-common (= 8.2.3-11), sysvinit-utils (= 3.15-6), tar (= 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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. . 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Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Fri, 26 Dec 2025 07:11:53 +0000 | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: 298092 Build-Time: 647 Distribution: unstable Host Architecture: arm64 Install-Time: 7 Job: /srv/rebuilderd/tmp/rebuilderdekgDYI/inputs/mdtraj_1.11.0-2.dsc Machine Architecture: arm64 Package: mdtraj Package-Time: 671 Source-Version: 1.11.0-2 Space: 298092 Status: successful Version: 1.11.0-2+b1 -------------------------------------------------------------------------------- Finished at 2025-12-26T07:11:47Z Build needed 00:11:11, 298092k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderdekgDYI/out checking python3-mdtraj-dbgsym_1.11.0-2+b1_arm64.deb: size differs for python3-mdtraj-dbgsym_1.11.0-2+b1_arm64.deb