Start: 2024-11-17 03:42:18 GMT [testing] Package: python3-mdanalysis Source: mdanalysis Version: 2.7.0-5 Installed-Size: 21924 Maintainer: Debichem Team Architecture: amd64 Depends: python3-duecredit, python3 (<< 3.13), python3 (>= 3.12~), python3-fasteners, python3-griddataformats, python3-joblib, python3-matplotlib, python3-mda-xdrlib, python3-mmtf, python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3-packaging, python3-scipy, python3-threadpoolctl, python3-tqdm, python3:any, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libstdc++6 (>= 11) Recommends: python3-sklearn Suggests: python-mdanalysis-doc Description: analyse molecular dynamics files and trajectories Homepage: https://www.mdanalysis.org/ Description-md5: 9d4e18df399b20b80dcfdf83cc426a35 Section: python Priority: optional Filename: pool/main/m/mdanalysis/python3-mdanalysis_2.7.0-5_amd64.deb Size: 1915332 MD5sum: be56f85c4e6f2853a6edbe0185aa173b SHA256: 6885f69e56f8ae24409c14c16f366f7397eca4754d515b6c889aa14c811a032c [sid] Package: python3-mdanalysis Source: mdanalysis (2.7.0-5) Version: 2.7.0-5+b1 Installed-Size: 25624 Maintainer: Debichem Team Architecture: amd64 Depends: python3-duecredit, python3 (<< 3.14), python3 (>= 3.12~), python3-fasteners, python3-griddataformats, python3-joblib, python3-matplotlib, python3-mda-xdrlib, python3-mmtf, python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3-packaging, python3-scipy, python3-threadpoolctl, python3-tqdm, python3:any, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libstdc++6 (>= 11) Recommends: python3-sklearn Suggests: python-mdanalysis-doc Description: analyse molecular dynamics files and trajectories Homepage: https://www.mdanalysis.org/ Description-md5: 9d4e18df399b20b80dcfdf83cc426a35 Section: python Priority: optional Filename: pool/main/m/mdanalysis/python3-mdanalysis_2.7.0-5+b1_amd64.deb Size: 2474304 MD5sum: ee73f66165222181998b2ddb8d8d9bfe SHA256: fdf71d75fda81311849af1437e8724936a7d3aaee689f6a65a9fa62457848841 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt python3-mdanalysis=2.7.0-5+b1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt python3-mdanalysis=2.7.0-5+b1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpnswz8fbc 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpnswz8fbc 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpnswz8fbc/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', 'update'] 0m1.5s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9365 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6257 kB] Fetched 15.8 MB in 1s (17.5 MB/s) Reading package lists... 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', 'update'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: bsdutils libblkid1 libmount1 libsmartcols1 libuuid1 login mount util-linux 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2097 kB of archives. After this operation, 22.5 kB disk space will be freed. Get:1 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.40.2-11 [105 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libuuid1 amd64 2.40.2-11 [35.9 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.40.2-11 [168 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libmount1 amd64 2.40.2-11 [199 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libsmartcols1 amd64 2.40.2-11 [139 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 util-linux amd64 2.40.2-11 [1213 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 mount amd64 2.40.2-11 [155 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 login amd64 1:4.16.0-2+really2.40.2-11 [81.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2097 kB in 0s (82.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5158 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.2-11_amd64.deb ... Unpacking bsdutils (1:2.40.2-11) over (1:2.40.2-9) ... Setting up bsdutils (1:2.40.2-11) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5158 files and directories currently installed.) Preparing to unpack .../libuuid1_2.40.2-11_amd64.deb ... Unpacking libuuid1:amd64 (2.40.2-11) over (2.40.2-9) ... Setting up libuuid1:amd64 (2.40.2-11) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5158 files and directories currently installed.) Preparing to unpack .../libblkid1_2.40.2-11_amd64.deb ... Unpacking libblkid1:amd64 (2.40.2-11) over (2.40.2-9) ... Setting up libblkid1:amd64 (2.40.2-11) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5158 files and directories currently installed.) Preparing to unpack .../libmount1_2.40.2-11_amd64.deb ... Unpacking libmount1:amd64 (2.40.2-11) over (2.40.2-9) ... Setting up libmount1:amd64 (2.40.2-11) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5158 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40.2-11_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40.2-11) over (2.40.2-9) ... Setting up libsmartcols1:amd64 (2.40.2-11) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5158 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.2-11_amd64.deb ... Unpacking util-linux (2.40.2-11) over (2.40.2-9) ... Setting up util-linux (2.40.2-11) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5155 files and directories currently installed.) Preparing to unpack .../mount_2.40.2-11_amd64.deb ... Unpacking mount (2.40.2-11) over (2.40.2-9) ... Preparing to unpack .../login_1%3a4.16.0-2+really2.40.2-11_amd64.deb ... Unpacking login (1:4.16.0-2+really2.40.2-11) over (1:4.16.0-2+really2.40.2-9) ... Setting up mount (2.40.2-11) ... Setting up login (1:4.16.0-2+really2.40.2-11) ... Processing triggers for libc-bin (2.40-3) ... 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s DUMP: 0500f7a100a3f2fa145e4b4e8673c3a8 - 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s INFO: Running scripts post_setup 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_setup_forbid_home'] 0m2.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_setup_forbid_home'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.9s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_setup_minimize'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_setup_minimize'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_setup_zz_backports'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_setup_zz_backports'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.9s DUMP: install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.10 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.1-3 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2+b1 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b2 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b3 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 256.7-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 256.7-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-11 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.40.0-7 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m2.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m3.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m3.1s INFO: Running scripts is_testable 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/is_testable_uninstallable'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/is_testable_uninstallable'] 0m3.1s INFO: Running scripts pre_test 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_test_exceptions'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_test_exceptions'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_test_root_password'] 0m3.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_test_root_password'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'show', '--no-all-versions', 'python3-mdanalysis'] 0m3.3s DUMP: Package: python3-mdanalysis Source: mdanalysis Version: 2.7.0-5 Installed-Size: 21924 Maintainer: Debichem Team Architecture: amd64 Depends: python3-duecredit, python3 (<< 3.13), python3 (>= 3.12~), python3-fasteners, python3-griddataformats, python3-joblib, python3-matplotlib, python3-mda-xdrlib, python3-mmtf, python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3-packaging, python3-scipy, python3-threadpoolctl, python3-tqdm, python3:any, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libstdc++6 (>= 11) Recommends: python3-sklearn Suggests: python-mdanalysis-doc Description-en: analyse molecular dynamics files and trajectories MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists. . MDAnalysis allows one to read particle-based trajectories (including individual coordinate frames such as biomolecules in the PDB format) and access the atomic coordinates through NumPy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. In addition, powerful atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out. . It works with a wide range of popular simulation packages including Gromacs, Amber, NAMD, CHARMM, DL_Poly, HooMD, LAMMPS and many others ?? see the lists of supported trajectory formats and topology formats. MDAnalysis also includes widely used analysis algorithms in the MDAnalysis.analysis module. . The MDAnalysis project uses an open governance model and is fiscally sponsored by NumFOCUS. . This package installs the library for Python 3. Description-md5: 9d4e18df399b20b80dcfdf83cc426a35 Homepage: https://www.mdanalysis.org/ Section: python Priority: optional Filename: pool/main/m/mdanalysis/python3-mdanalysis_2.7.0-5_amd64.deb Size: 1915332 MD5sum: be56f85c4e6f2853a6edbe0185aa173b SHA256: 6885f69e56f8ae24409c14c16f366f7397eca4754d515b6c889aa14c811a032c 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'show', '--no-all-versions', 'python3-mdanalysis'] 0m3.3s INFO: apt-cache knows about the following packages: python3-mdanalysis 0m3.3s INFO: Running scripts pre_install 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_database-server'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_database-server'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_exceptions'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_exceptions'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_extras'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_extras'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'policy'] 0m3.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'policy'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'policy', 'python3-mdanalysis'] 0m3.4s DUMP: python3-mdanalysis: Installed: (none) Candidate: 2.7.0-5 Version table: 2.7.0-5 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'policy', 'python3-mdanalysis'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', '-y', 'install', 'python3-mdanalysis'] 0m26.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: blt ca-certificates fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx libatomic1 libblas3 libbrotli1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libncursesw6 libnsl2 libopenjp2-7 libpng16-16t64 libproc2-0 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 libreadline8t64 libsharpyuv0 libsqlite3-0 libtcl8.6 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 media-types netbase openssl procps python-matplotlib-data python3 python3-appdirs python3-attr python3-autocommand python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-citeproc python3-contourpy python3-cycler python3-dateutil python3-decorator python3-duecredit python3-fasteners python3-fonttools python3-fs python3-griddataformats python3-idna python3-inflect python3-jaraco.context python3-jaraco.functools python3-joblib python3-kiwisolver python3-looseversion python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib python3-minimal python3-mmtf python3-monotonic python3-more-itertools python3-mpmath python3-mrcfile python3-msgpack python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pyparsing python3-requests python3-scipy python3-six python3-sympy python3-threadpoolctl python3-tk python3-tqdm python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3.12 python3.12-minimal python3.12-tk python3.13-tk readline-common sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data x11-common Suggested packages: blt-demo low-memory-monitor krb5-doc krb5-user libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python3-doc python3-venv python-attr-doc python-charset-normalizer-doc python-cycler-doc python-joblib-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mdanalysis-doc python-mpmath-doc python3-gmpy2 gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc python3-setuptools python-pyparsing-doc python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.12-venv python3.12-doc binutils binfmt-support readline-doc Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales libgpm2 psmisc linux-sysctl-defaults python3-pytest python3-simplejson python3-psutil python3-bs4 python3-cssselect python3-html5lib python3-sklearn python3-olefile g++ | c++-compiler isympy-common The following NEW packages will be installed: blt ca-certificates fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx libatomic1 libblas3 libbrotli1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libncursesw6 libnsl2 libopenjp2-7 libpng16-16t64 libproc2-0 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 libreadline8t64 libsharpyuv0 libsqlite3-0 libtcl8.6 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 media-types netbase openssl procps python-matplotlib-data python3 python3-appdirs python3-attr python3-autocommand python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-citeproc python3-contourpy python3-cycler python3-dateutil python3-decorator python3-duecredit python3-fasteners python3-fonttools python3-fs python3-griddataformats python3-idna python3-inflect python3-jaraco.context python3-jaraco.functools python3-joblib python3-kiwisolver python3-looseversion python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib python3-mdanalysis python3-minimal python3-mmtf python3-monotonic python3-more-itertools python3-mpmath python3-mrcfile python3-msgpack python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pyparsing python3-requests python3-scipy python3-six python3-sympy python3-threadpoolctl python3-tk python3-tqdm python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3.12 python3.12-minimal python3.12-tk python3.13-tk readline-common sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data x11-common 0 upgraded, 140 newly installed, 0 to remove and 0 not upgraded. Need to get 95.3 MB of archives. After this operation, 408 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 fonts-lato all 2.015-1 [2780 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get:23 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:49 http://deb.debian.org/debian trixie/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.2.1-1 [190 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Get:52 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get:88 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:93 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 python3-citeproc all 0.6.0-3 [96.7 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.3.0-2+b1 [264 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:102 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 python3-looseversion all 1.3.0-3 [8964 B] Get:105 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.8-2 [41.6 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 python3-duecredit all 0.10.2-2 [70.6 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 python3-monotonic all 1.6-2 [5728 B] Get:111 http://deb.debian.org/debian trixie/main amd64 python3-fasteners all 0.18-2 [14.0 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-7 [16.4 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b5 [25.6 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.13.1-5 [16.7 MB] Get:117 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [32.9 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b3 [299 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.54.1-4+b1 [1631 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1022 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 python3-mrcfile all 1.5.3-3 [119 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 python3-griddataformats all 1.0.2-2 [2048 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 python3-joblib all 1.3.2-5 [216 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.7-2+b1 [77.0 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.4.0-1+b1 [522 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 python3.12-tk amd64 3.12.7-3 [112 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 python3.13-tk amd64 3.13.0-2 [103 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.12.7-1 [9444 B] Get:132 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 10.4.0-1+b1 [79.8 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.8.3-3+b1 [5654 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 python3-mda-xdrlib all 0.2.0-3 [11.6 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 python3-msgpack amd64 1.0.3-3+b3 [112 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 python3-mmtf all 1.1.3-1 [17.0 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 python3-tqdm all 4.67.0-1 [90.2 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 python3-mdanalysis amd64 2.7.0-5 [1915 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 95.3 MB in 1s (78.1 MB/s) Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5159 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. 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Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../03-libncursesw6_6.5-2+b1_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2+b1) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../05-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../06-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../07-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../08-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../09-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../10-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../11-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../12-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../13-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../14-libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6063 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-6_amd64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../005-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../006-libbrotli1_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../007-libpng16-16t64_1.6.44-2_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../008-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../009-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../010-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../011-fontconfig-config_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../012-libfontconfig1_2.15.0-1.1+b1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1+b1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../013-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../014-libxdmcp6_1%3a1.1.2-3+b2_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3+b2) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../015-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../016-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../017-libx11-6_2%3a1.8.10-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.10-2) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../018-libxrender1_1%3a0.9.10-1.1+b2_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1+b2) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../019-libxft2_2.3.6-1+b2_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b2) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../020-libxext6_2%3a1.3.4-1+b2_amd64.deb ... 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Setting up media-types (10.1.0) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b2) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up fonts-lato (2.015-1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up fonts-lyx (2.4.2.1-1) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libdeflate0:amd64 (1.22-1) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b2) ... Setting up libgomp1:amd64 (14.2.0-8) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up unicode-data (15.1.0-1) ... Setting up libblas3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up libatomic1:amd64 (14.2.0-8) ... Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libncursesw6:amd64 (6.5-2+b1) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up procps (2:4.0.4-6) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b4) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.8.3-3) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:amd64 (1.4.0-0.1+b1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up liblapack3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libglib2.0-0t64:amd64 (2.82.2-2) ... No schema files found: doing nothing. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libxft2:amd64 (2.3.6-1+b2) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up python3.12-tk (3.12.7-3) ... Setting up python3.13-tk (3.13.0-2) ... Setting up libraqm0:amd64 (0.10.1-1+b2) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3.12 (3.12.7-3) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-mda-xdrlib (0.2.0-3) ... Setting up python3-tz (2024.1-2) ... Setting up python3-monotonic (1.6-2) ... Setting up python3-six (1.16.0-7) ... Setting up python3-pil:amd64 (10.4.0-1+b1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.1-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-brotli (1.1.0-2+b6) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.7-2+b1) ... Setting up python3-idna (3.8-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-fasteners (0.18-2) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up python3-looseversion (1.3.0-3) ... Setting up python3-lxml:amd64 (5.3.0-1+b1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-msgpack (1.0.3-3+b3) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b5) ... Setting up python3-citeproc (0.6.0-3) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b3) ... Setting up python3-tqdm (4.67.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-tk:amd64 (3.12.7-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pil.imagetk:amd64 (10.4.0-1+b1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-joblib (1.3.2-5) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-contourpy (1.3.0-2+b1) ... Setting up python3-mrcfile (1.5.3-3) ... Setting up python3-scipy (1.13.1-5) ... Setting up python3-duecredit (0.10.2-2) ... Setting up python3-mmtf (1.1.3-1) ... Setting up python3-griddataformats (1.0.2-2) ... Setting up python3-fonttools (4.54.1-4+b1) ... Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3+b1) ... Setting up python3-mdanalysis (2.7.0-5) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', '-y', 'install', 'python3-mdanalysis'] 0m26.2s INFO: Running scripts post_install 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_install_exceptions'] 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_install_exceptions'] 0m26.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m26.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m26.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpnswz8fbc to sid 0m26.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m26.8s INFO: Running scripts pre_distupgrade 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', 'update'] 0m28.7s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7332 kB] Fetched 17.6 MB in 1s (12.3 MB/s) Reading package lists... 0m28.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', 'update'] 0m28.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', '-yf', 'dist-upgrade'] 0m34.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt debianutils libapt-pkg6.0t64 libaudit-common libaudit1 libglib2.0-0t64 libgnutls30t64 libpcre2-8-0 libpython3-stdlib libsystemd0 libudev1 login.defs passwd python3 python3-attr python3-fonttools python3-mdanalysis python3-minimal python3-packaging python3-pkg-resources python3-scipy 21 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 32.5 MB of archives. After this operation, 45.8 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.21 [92.1 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 257~rc2-3 [447 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 257~rc2-3 [147 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.11 [1043 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get:6 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.11 [1362 kB] Get:7 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get:8 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get:10 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.0.2-2 [12.7 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.2-2 [54.9 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.44-4 [275 kB] Get:13 http://deb.debian.org/debian sid/main amd64 login.defs all 1:4.16.0-5 [185 kB] Get:14 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.16.0-5 [1232 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB] Get:16 http://deb.debian.org/debian sid/main amd64 python3-attr all 24.2.0-1 [68.4 kB] Get:17 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get:18 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.13.1-6 [20.2 MB] Get:19 http://deb.debian.org/debian sid/main amd64 python3-fonttools amd64 4.55.0-1 [1634 kB] Get:20 http://deb.debian.org/debian sid/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:21 http://deb.debian.org/debian sid/main amd64 python3-mdanalysis amd64 2.7.0-5+b1 [2474 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 32.5 MB in 0s (200 MB/s) (Reading database ... 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Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-attr (24.2.0-1) ... Setting up python3-scipy (1.13.1-6) ... Setting up python3-mdanalysis (2.7.0-5+b1) ... Setting up python3-fonttools (4.55.0-1) ... Processing triggers for libc-bin (2.40-3) ... 0m34.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', '-yf', 'dist-upgrade'] 0m34.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m35.3s DUMP: 26551649d51f8e4dde170a23cdb29c28 - 0m35.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m35.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'show', '--no-all-versions', 'python3-mdanalysis'] 0m35.4s DUMP: Package: python3-mdanalysis Source: mdanalysis (2.7.0-5) Version: 2.7.0-5+b1 Installed-Size: 25624 Maintainer: Debichem Team Architecture: amd64 Depends: python3-duecredit, python3 (<< 3.14), python3 (>= 3.12~), python3-fasteners, python3-griddataformats, python3-joblib, python3-matplotlib, python3-mda-xdrlib, python3-mmtf, python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3-packaging, python3-scipy, python3-threadpoolctl, python3-tqdm, python3:any, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libstdc++6 (>= 11) Recommends: python3-sklearn Suggests: python-mdanalysis-doc Description-en: analyse molecular dynamics files and trajectories MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists. . MDAnalysis allows one to read particle-based trajectories (including individual coordinate frames such as biomolecules in the PDB format) and access the atomic coordinates through NumPy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. In addition, powerful atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out. . It works with a wide range of popular simulation packages including Gromacs, Amber, NAMD, CHARMM, DL_Poly, HooMD, LAMMPS and many others ?? see the lists of supported trajectory formats and topology formats. MDAnalysis also includes widely used analysis algorithms in the MDAnalysis.analysis module. . The MDAnalysis project uses an open governance model and is fiscally sponsored by NumFOCUS. . This package installs the library for Python 3. Description-md5: 9d4e18df399b20b80dcfdf83cc426a35 Homepage: https://www.mdanalysis.org/ Section: python Priority: optional Filename: pool/main/m/mdanalysis/python3-mdanalysis_2.7.0-5+b1_amd64.deb Size: 2474304 MD5sum: ee73f66165222181998b2ddb8d8d9bfe SHA256: fdf71d75fda81311849af1437e8724936a7d3aaee689f6a65a9fa62457848841 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'show', '--no-all-versions', 'python3-mdanalysis'] 0m35.4s INFO: apt-cache knows about the following packages: python3-mdanalysis 0m35.4s INFO: Running scripts pre_install 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_database-server'] 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_database-server'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_exceptions'] 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_exceptions'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_extras'] 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_extras'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_foreign_architecture'] 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_foreign_architecture'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'policy'] 0m35.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'policy'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'policy', 'python3-mdanalysis'] 0m35.5s DUMP: python3-mdanalysis: Installed: 2.7.0-5+b1 Candidate: 2.7.0-5+b1 Version table: *** 2.7.0-5+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'policy', 'python3-mdanalysis'] 0m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', '-y', 'install', 'python3-mdanalysis'] 0m35.7s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-mdanalysis is already the newest version (2.7.0-5+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m35.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', '-y', 'install', 'python3-mdanalysis'] 0m35.7s INFO: Running scripts post_install 0m35.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_install_exceptions'] 0m35.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_install_exceptions'] 0m35.7s INFO: Running scripts post_distupgrade 0m35.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m35.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m35.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_distupgrade_exceptions'] 0m35.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_distupgrade_exceptions'] 0m35.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m35.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m35.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m35.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m35.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_distupgrade_zz_backports'] 0m35.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_distupgrade_zz_backports'] 0m35.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m36.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m36.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m37.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m37.0s INFO: Running scripts pre_install 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_database-server'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_database-server'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_exceptions'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_exceptions'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_extras'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_extras'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_foreign_architecture'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_foreign_architecture'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'policy'] 0m37.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'policy'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'policy', 'python3-mdanalysis'] 0m37.0s DUMP: python3-mdanalysis: Installed: 2.7.0-5+b1 Candidate: 2.7.0-5+b1 Version table: *** 2.7.0-5+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-cache', 'policy', 'python3-mdanalysis'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', '-y', 'install', 'python3-mdanalysis=2.7.0-5+b1'] 0m37.2s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-mdanalysis is already the newest version (2.7.0-5+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', '-y', 'install', 'python3-mdanalysis=2.7.0-5+b1'] 0m37.2s INFO: Running scripts post_install 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_install_exceptions'] 0m37.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_install_exceptions'] 0m37.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m37.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m38.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', '-ac', '--ignore-obsolete'] 0m39.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', '-ac', '--ignore-obsolete'] 0m39.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m39.7s DUMP: 0.15.6 0m39.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m39.7s INFO: Running adequate version 0.15.6 now. 0m39.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'python3-mdanalysis'] 0m39.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'python3-mdanalysis'] 0m39.8s INFO: Running scripts pre_remove 0m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m41.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m41.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m41.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m41.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m41.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m41.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_remove_exceptions'] 0m41.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/pre_remove_exceptions'] 0m41.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m41.1s DUMP: install ok installed apt apt 2.9.11 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1+b1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-font-awesome fonts-font-awesome 5.0.10+really4.7.0~dfsg-4.1 install ok installed fonts-lato fonts-lato 2.015-1 install ok installed fonts-lyx fonts-lyx 2.4.2.1-1 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.11 install ok installed libatomic1:amd64 libatomic1 14.2.0-8 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblas3:amd64 libblas3 3.12.0-3+b1 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b6 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libdeflate0:amd64 libdeflate0 1.22-1 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1+b1 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.15-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-8 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.82.2-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-8 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.0.1-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libicu72:amd64 libicu72 72.1-5+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1+b2 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3+b1 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 7.4.7-4 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3+b1 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b2 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libncursesw6:amd64 libncursesw6 6.5-2+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b3 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2+b4 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-4 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.44-2 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-6 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.7-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.7-3 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.7-3 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b2 install ok installed libraqm0:amd64 libraqm0 0.10.1-1+b2 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b3 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1+b1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc2-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.15+dfsg-2 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3+b1 install ok installed libtk8.6:amd64 libtk8.6 8.6.15-1 install ok installed libudev1:amd64 libudev1 257~rc2-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1+b1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.4.0-0.1+b1 install ok installed libwebpmux3:amd64 libwebpmux3 1.4.0-0.1+b1 install ok installed libx11-6:amd64 libx11-6 2:1.8.10-2 install ok installed libx11-data libx11-data 2:1.8.10-2 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3+b2 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b2 install ok installed libxft2:amd64 libxft2 2.3.6-1+b2 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.2+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b2 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1.1+b1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-11 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.3.2-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl-base perl-base 5.40.0-7 install ok installed procps procps 2:4.0.4-6 install ok installed python-matplotlib-data python-matplotlib-data 3.8.3-3 install ok installed python3 python3 3.12.7-1 install ok installed python3-appdirs python3-appdirs 1.4.4-4 install ok installed python3-attr python3-attr 24.2.0-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-brotli python3-brotli 1.1.0-2+b6 install ok installed python3-certifi python3-certifi 2024.8.30+dfsg-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-charset-normalizer python3-charset-normalizer 3.4.0-1+b1 install ok installed python3-citeproc python3-citeproc 0.6.0-3 install ok installed python3-contourpy python3-contourpy 1.3.0-2+b1 install ok installed python3-cycler python3-cycler 0.12.1-1 install ok installed python3-dateutil python3-dateutil 2.9.0-3 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-duecredit python3-duecredit 0.10.2-2 install ok installed python3-fasteners python3-fasteners 0.18-2 install ok installed python3-fonttools python3-fonttools 4.55.0-1 install ok installed python3-fs python3-fs 2.4.16-4 install ok installed python3-griddataformats python3-griddataformats 1.0.2-2 install ok installed python3-idna python3-idna 3.8-2 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-joblib python3-joblib 1.3.2-5 install ok installed python3-kiwisolver python3-kiwisolver 1.4.7-2+b1 install ok installed python3-looseversion python3-looseversion 1.3.0-3 install ok installed python3-lxml:amd64 python3-lxml 5.3.0-1+b1 install ok installed python3-lz4 python3-lz4 4.0.2+dfsg-1+b5 install ok installed python3-matplotlib python3-matplotlib 3.8.3-3+b1 install ok installed python3-mda-xdrlib python3-mda-xdrlib 0.2.0-3 install ok installed python3-mdanalysis python3-mdanalysis 2.7.0-5+b1 install ok installed python3-minimal python3-minimal 3.12.7-1 install ok installed python3-mmtf python3-mmtf 1.1.3-1 install ok installed python3-monotonic python3-monotonic 1.6-2 install ok installed python3-more-itertools python3-more-itertools 10.5.0-1 install ok installed python3-mpmath python3-mpmath 1.3.0-1 install ok installed python3-mrcfile python3-mrcfile 1.5.3-3 install ok installed python3-msgpack python3-msgpack 1.0.3-3+b3 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-12 install ok installed python3-packaging python3-packaging 24.2-1 install ok installed python3-pil:amd64 python3-pil 10.4.0-1+b1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 10.4.0-1+b1 install ok installed python3-pkg-resources python3-pkg-resources 75.2.0-1 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-requests python3-requests 2.32.3+dfsg-1 install ok installed python3-scipy python3-scipy 1.13.1-6 install ok installed python3-six python3-six 1.16.0-7 install ok installed python3-sympy python3-sympy 1.13.3-1 install ok installed python3-threadpoolctl python3-threadpoolctl 3.1.0-1 install ok installed python3-tk:amd64 python3-tk 3.12.7-1 install ok installed python3-tqdm python3-tqdm 4.67.0-1 install ok installed python3-typeguard python3-typeguard 4.4.1-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3-tz python3-tz 2024.1-2 install ok installed python3-ufolib2 python3-ufolib2 0.16.1+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b3 install ok installed python3-urllib3 python3-urllib3 2.0.7-2 install ok installed python3.12 python3.12 3.12.7-3 install ok installed python3.12-minimal python3.12-minimal 3.12.7-3 install ok installed python3.12-tk python3.12-tk 3.12.7-3 install ok installed python3.13-tk python3.13-tk 3.13.0-2 install ok installed readline-common readline-common 8.2-5 install ok installed sed sed 4.9-2 install ok installed sphinx-rtd-theme-common sphinx-rtd-theme-common 3.0.1+dfsg-1 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed tzdata tzdata 2024b-3 install ok installed unicode-data unicode-data 15.1.0-1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m41.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m41.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', 'remove', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-citeproc', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-duecredit', 'python3-fasteners', 'python3-fonttools', 'python3-fs', 'python3-griddataformats', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-joblib', 'python3-kiwisolver', 'python3-looseversion', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-mda-xdrlib', 'python3-minimal', 'python3-mmtf', 'python3-monotonic', 'python3-more-itertools', 'python3-mpmath', 'python3-mrcfile', 'python3-msgpack', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-requests', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tqdm', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'sphinx-rtd-theme-common', 'tk8.6-blt2.5', 'unicode-data', 'x11-common', 'python3-mdanalysis'] 0m44.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blt ca-certificates fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx libatomic1 libblas3 libbrotli1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libncursesw6 libnsl2 libopenjp2-7 libpng16-16t64 libproc2-0 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 libreadline8t64 libsharpyuv0 libsqlite3-0 libtcl8.6 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 media-types netbase openssl procps python-matplotlib-data python3 python3-appdirs python3-attr python3-autocommand python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-citeproc python3-contourpy python3-cycler python3-dateutil python3-decorator python3-duecredit python3-fasteners python3-fonttools python3-fs python3-griddataformats python3-idna python3-inflect python3-jaraco.context python3-jaraco.functools python3-joblib python3-kiwisolver python3-looseversion python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib python3-mdanalysis python3-minimal python3-mmtf python3-monotonic python3-more-itertools python3-mpmath python3-mrcfile python3-msgpack python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pyparsing python3-requests python3-scipy python3-six python3-sympy python3-threadpoolctl python3-tk python3-tqdm python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3.12 python3.12-minimal python3.12-tk python3.13-tk readline-common sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data x11-common 0 upgraded, 0 newly installed, 140 to remove and 0 not upgraded. After this operation, 454 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15954 files and directories currently installed.) Removing python3-mdanalysis (2.7.0-5+b1) ... Removing python3-matplotlib (3.8.3-3+b1) ... Removing python3-pil.imagetk:amd64 (10.4.0-1+b1) ... Removing python3-pil:amd64 (10.4.0-1+b1) ... Removing python3-tk:amd64 (3.12.7-1) ... Removing blt (2.5.3+dfsg-7) ... Removing python3-duecredit (0.10.2-2) ... Removing python3-requests (2.32.3+dfsg-1) ... Removing python3-certifi (2024.8.30+dfsg-1) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing python3.13-tk (3.13.0-2) ... Removing python-matplotlib-data (3.8.3-3) ... Removing python3-griddataformats (1.0.2-2) ... Removing python3-mrcfile (1.5.3-3) ... Removing sphinx-rtd-theme-common (3.0.1+dfsg-1) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing fonts-lato (2.015-1) ... Removing fonts-lyx (2.4.2.1-1) ... Removing libraqm0:amd64 (0.10.1-1+b2) ... Removing libharfbuzz0b:amd64 (10.0.1-1) ... Removing libglib2.0-0t64:amd64 (2.82.2-3) ... Removing libatomic1:amd64 (14.2.0-8) ... Removing python3-mmtf (1.1.3-1) ... Removing python3-contourpy (1.3.0-2+b1) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.22-1) ... Removing python3-tqdm (4.67.0-1) ... Removing python3-joblib (1.3.2-5) ... Removing python3-msgpack (1.0.3-3+b3) ... Removing libfribidi0:amd64 (1.0.15-1) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libgomp1:amd64 (14.2.0-8) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing python3-citeproc (0.6.0-3) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Removing libjs-sphinxdoc (7.4.7-4) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing procps (2:4.0.4-6) ... Removing libopenjp2-7:amd64 (2.5.0-2+b4) ... Removing libproc2-0:amd64 (2:4.0.4-6) ... Removing libqhull-r8.0:amd64 (2020.2-6+b2) ... Removing libwebpmux3:amd64 (1.4.0-0.1+b1) ... Removing libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Removing libwebp7:amd64 (1.4.0-0.1+b1) ... Removing libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Removing python3.12-tk (3.12.7-3) ... Removing openssl (3.3.2-2) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-charset-normalizer (3.4.0-1+b1) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-3) ... Removing python3-fasteners (0.18-2) ... Removing python3-idna (3.8-2) ... Removing python3-kiwisolver (1.4.7-2+b1) ... Removing python3-looseversion (1.3.0-3) ... Removing python3-mda-xdrlib (0.2.0-3) ... Removing python3-monotonic (1.6-2) ... Removing python3-packaging (24.2-1) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-threadpoolctl (3.1.0-1) ... Removing python3-urllib3 (2.0.7-2) ... Removing libtk8.6:amd64 (8.6.15-1) ... Removing libxft2:amd64 (2.3.6-1+b2) ... Removing libfontconfig1:amd64 (2.15.0-1.1+b1) ... Removing fontconfig-config (2.15.0-1.1+b1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing libpng16-16t64:amd64 (1.6.44-2) ... Removing libtcl8.6:amd64 (8.6.15+dfsg-2) ... Removing libxss1:amd64 (1:1.2.3-1+b2) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b2) ... Removing libxext6:amd64 (2:1.3.4-1+b2) ... Removing x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libx11-6:amd64 (2:1.8.10-2) ... Removing libx11-data (2:1.8.10-2) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3+b2) ... Removing python3-ufolib2 (0.16.1+dfsg1-1) ... Removing python3-attr (24.2.0-1) ... Removing python3-fonttools (4.55.0-1) ... Removing python3-scipy (1.13.1-6) ... Removing python3-numpy (1:1.26.4+ds-12) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Removing liblapack3:amd64 (3.12.0-3+b1) ... Removing libblas3:amd64 (3.12.0-3+b1) ... Removing python3-unicodedata2 (15.1.0+ds-1+b3) ... Removing python3-fs (2.4.16-4) ... Removing python3-pkg-resources (75.2.0-1) ... Removing python3-sympy (1.13.3-1) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.1-1) ... Removing libgfortran5:amd64 (14.2.0-8) ... Removing python3-lxml:amd64 (5.3.0-1+b1) ... Removing libxslt1.1:amd64 (1.1.35-1.1+b1) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Removing libicu72:amd64 (72.1-5+b1) ... Removing python3-appdirs (1.4.4-4) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-brotli (1.1.0-2+b6) ... Removing python3-decorator (5.1.1-5) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-lz4 (4.0.2+dfsg-1+b5) ... Removing python3-more-itertools (10.5.0-1) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-six (1.16.0-7) ... Removing python3-typing-extensions (4.12.2-2) ... Removing python3-tz (2024.1-2) ... Removing unicode-data (15.1.0-1) ... Removing python3 (3.12.7-1) ... Removing python3.12 (3.12.7-3) ... Removing python3-minimal (3.12.7-1) ... Removing python3.12-minimal (3.12.7-3) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libpython3-stdlib:amd64 (3.12.7-1) ... Removing libpython3.12-stdlib:amd64 (3.12.7-3) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b3) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libncursesw6:amd64 (6.5-2+b1) ... Removing libpython3.12-minimal:amd64 (3.12.7-3) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-5) ... Processing triggers for libc-bin (2.40-3) ... 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', 'remove', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-citeproc', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-duecredit', 'python3-fasteners', 'python3-fonttools', 'python3-fs', 'python3-griddataformats', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-joblib', 'python3-kiwisolver', 'python3-looseversion', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-mda-xdrlib', 'python3-minimal', 'python3-mmtf', 'python3-monotonic', 'python3-more-itertools', 'python3-mpmath', 'python3-mrcfile', 'python3-msgpack', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-requests', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tqdm', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'sphinx-rtd-theme-common', 'tk8.6-blt2.5', 'unicode-data', 'x11-common', 'python3-mdanalysis'] 0m44.8s INFO: Running scripts post_remove 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_remove_exceptions'] 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_remove_exceptions'] 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-citeproc', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-duecredit', 'python3-fasteners', 'python3-fonttools', 'python3-fs', 'python3-griddataformats', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-joblib', 'python3-kiwisolver', 'python3-looseversion', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-mda-xdrlib', 'python3-minimal', 'python3-mmtf', 'python3-monotonic', 'python3-more-itertools', 'python3-mpmath', 'python3-mrcfile', 'python3-msgpack', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-requests', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tqdm', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'sphinx-rtd-theme-common', 'tk8.6-blt2.5', 'unicode-data', 'x11-common'] 0m44.9s DUMP: dpkg: warning: ignoring request to remove blt which isn't installed (Reading database ... 5205 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fontconfig-config (2.15.0-1.1+b1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed Purging configuration files for fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... dpkg: warning: ignoring request to remove fonts-lato which isn't installed dpkg: warning: ignoring request to remove fonts-lyx which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.82.2-3) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblbfgsb0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.7-3) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.3.2-2) ... Purging configuration files for procps (2:4.0.4-6) ... Purging configuration files for python-matplotlib-data (3.8.3-3) ... Purging configuration files for python3 (3.12.7-1) ... dpkg: warning: ignoring request to remove python3-appdirs which isn't installed dpkg: warning: ignoring request to remove python3-attr which isn't installed dpkg: warning: ignoring request to remove python3-autocommand which isn't installed dpkg: warning: ignoring request to remove python3-brotli which isn't installed dpkg: warning: ignoring request to remove python3-certifi which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-charset-normalizer which isn't installed dpkg: warning: ignoring request to remove python3-citeproc which isn't installed dpkg: warning: ignoring request to remove python3-contourpy which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-duecredit which isn't installed dpkg: warning: ignoring request to remove python3-fasteners which isn't installed dpkg: warning: ignoring request to remove python3-fonttools which isn't installed dpkg: warning: ignoring request to remove python3-fs which isn't installed dpkg: warning: ignoring request to remove python3-griddataformats which isn't installed dpkg: warning: ignoring request to remove python3-idna which isn't installed dpkg: warning: ignoring request to remove python3-inflect which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.context which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.functools which isn't installed dpkg: warning: ignoring request to remove python3-joblib which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-looseversion which isn't installed dpkg: warning: ignoring request to remove python3-lxml which isn't installed dpkg: warning: ignoring request to remove python3-lz4 which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python3-mda-xdrlib which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-mmtf which isn't installed dpkg: warning: ignoring request to remove python3-monotonic which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools which isn't installed dpkg: warning: ignoring request to remove python3-mpmath which isn't installed dpkg: warning: ignoring request to remove python3-mrcfile which isn't installed dpkg: warning: ignoring request to remove python3-msgpack which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pil.imagetk which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-requests which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed Purging configuration files for python3-sympy (1.13.3-1) ... dpkg: warning: ignoring request to remove python3-threadpoolctl which isn't installed dpkg: warning: ignoring request to remove python3-tk which isn't installed dpkg: warning: ignoring request to remove python3-tqdm which isn't installed dpkg: warning: ignoring request to remove python3-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-ufolib2 which isn't installed dpkg: warning: ignoring request to remove python3-unicodedata2 which isn't installed dpkg: warning: ignoring request to remove python3-urllib3 which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.7-3) ... dpkg: warning: ignoring request to remove python3.12-tk which isn't installed dpkg: warning: ignoring request to remove python3.13-tk which isn't installed Purging configuration files for readline-common (8.2-5) ... dpkg: warning: ignoring request to remove sphinx-rtd-theme-common which isn't installed dpkg: warning: ignoring request to remove tk8.6-blt2.5 which isn't installed dpkg: warning: ignoring request to remove unicode-data which isn't installed Purging configuration files for x11-common (1:7.7+23.1) ... 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-citeproc', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-duecredit', 'python3-fasteners', 'python3-fonttools', 'python3-fs', 'python3-griddataformats', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-joblib', 'python3-kiwisolver', 'python3-looseversion', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-mda-xdrlib', 'python3-minimal', 'python3-mmtf', 'python3-monotonic', 'python3-more-itertools', 'python3-mpmath', 'python3-mrcfile', 'python3-msgpack', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-requests', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tqdm', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'sphinx-rtd-theme-common', 'tk8.6-blt2.5', 'unicode-data', 'x11-common'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg', '--purge', 'python3-mdanalysis'] 0m44.9s DUMP: dpkg: warning: ignoring request to remove python3-mdanalysis which isn't installed 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg', '--purge', 'python3-mdanalysis'] 0m44.9s INFO: Running scripts post_purge 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_purge_exceptions'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_purge_exceptions'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg', '--purge', '--pending'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg', '--purge', '--pending'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg', '--remove', '--pending'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg', '--remove', '--pending'] 0m44.9s INFO: Running scripts post_test 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_test_exceptions'] 0m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'tmp/scripts/post_test_exceptions'] 0m45.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m45.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m45.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg-divert', '--list'] 0m45.2s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m45.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'dpkg-divert', '--list'] 0m45.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', 'clean'] 0m45.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc', 'apt-get', 'clean'] 0m45.2s DEBUG: Recording chroot state 0m45.5s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned 0m45.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/shm'] 0m45.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/shm'] 0m45.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/console'] 0m45.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/console'] 0m45.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/ptmx'] 0m45.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/ptmx'] 0m45.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/pts'] 0m45.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/dev/pts'] 0m45.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/proc'] 0m45.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc/proc'] 0m45.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m45.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnswz8fbc'] 0m45.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpnswz8fbc 0m45.8s INFO: PASS: Upgrading between Debian distributions. 0m45.8s INFO: PASS: All tests. 0m45.8s INFO: piuparts run ends. ret=0 End: 2024-11-17 03:43:04 GMT