Start: 2025-02-23 03:33:51 GMT [testing] Package: python3-mdanalysis Source: mdanalysis Version: 2.8.0-4 Installed-Size: 28378 Maintainer: Debichem Team Architecture: amd64 Depends: python3-duecredit, python3-biopython (>= 1.80), python3 (<< 3.14), python3 (>= 3.12~), python3-fasteners, python3-griddataformats, python3-joblib, python3-matplotlib, python3-mda-xdrlib, python3-mmtf, python3-numpy, python3-numpy2-abi0 | 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_2.8.0-4_amd64.deb Size: 4766368 MD5sum: 2963247719573cc5023a2d5cbea09c13 SHA256: 20e68d613e1bc27ca3f0d615f609eceba48b7542427c9eca5f77c8dc8fec16b3 [sid] Package: python3-mdanalysis Source: mdanalysis Version: 2.8.0-4 Installed-Size: 28378 Maintainer: Debichem Team Architecture: amd64 Depends: python3-duecredit, python3-biopython (>= 1.80), python3 (<< 3.14), python3 (>= 3.12~), python3-fasteners, python3-griddataformats, python3-joblib, python3-matplotlib, python3-mda-xdrlib, python3-mmtf, python3-numpy, python3-numpy2-abi0 | 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_2.8.0-4_amd64.deb Size: 4766368 MD5sum: 2963247719573cc5023a2d5cbea09c13 SHA256: 20e68d613e1bc27ca3f0d615f609eceba48b7542427c9eca5f77c8dc8fec16b3 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=2.8.0-4 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=2.8.0-4 0m0.0s INFO: Running on: Linux piu-slave-conova-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/tmpu3o6eah3 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpu3o6eah3 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpu3o6eah3/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', 'update'] 0m2.4s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [175 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9485 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6360 kB] Fetched 16.0 MB in 1s (14.4 MB/s) Reading package lists... 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', 'update'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', '-yf', 'dist-upgrade'] 0m5.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following NEW packages will be installed: libapt-pkg7.0 The following packages will be upgraded: apt libc-bin libc6 login.defs passwd 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 7409 kB of archives. After this operation, 3982 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libc6 amd64 2.40-7 [2815 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libapt-pkg7.0 amd64 2.9.30 [1104 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.30 [1440 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libc-bin amd64 2.40-7 [631 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 login.defs all 1:4.17.2-5 [186 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 passwd amd64 1:4.17.2-5 [1234 kB] Preconfiguring packages ... Fetched 7409 kB in 0s (80.9 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 ... 5026 files and directories currently installed.) Preparing to unpack .../libc6_2.40-7_amd64.deb ... Unpacking libc6:amd64 (2.40-7) over (2.40-6) ... Setting up libc6:amd64 (2.40-7) ... Selecting previously unselected package libapt-pkg7.0:amd64. (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 ... 5026 files and directories currently installed.) Preparing to unpack .../libapt-pkg7.0_2.9.30_amd64.deb ... Unpacking libapt-pkg7.0:amd64 (2.9.30) ... Setting up libapt-pkg7.0:amd64 (2.9.30) ... (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 ... 5075 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.30_amd64.deb ... Unpacking apt (2.9.30) over (2.9.29) ... Setting up apt (2.9.30) ... (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 ... 5075 files and directories currently installed.) Preparing to unpack .../libc-bin_2.40-7_amd64.deb ... Unpacking libc-bin (2.40-7) over (2.40-6) ... Setting up libc-bin (2.40-7) ... (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 ... 5075 files and directories currently installed.) Preparing to unpack .../login.defs_1%3a4.17.2-5_all.deb ... Unpacking login.defs (1:4.17.2-5) over (1:4.16.0-7) ... Preparing to unpack .../passwd_1%3a4.17.2-5_amd64.deb ... Unpacking passwd (1:4.17.2-5) over (1:4.16.0-7) ... Setting up login.defs (1:4.17.2-5) ... Setting up passwd (1:4.17.2-5) ... 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', '-yf', 'dist-upgrade'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.1s DUMP: 50a0ba5478ab1fc853dfb977de326e86 - 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.1s INFO: Running scripts post_setup 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_setup_dummy_users'] 0m7.1s 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 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_setup_dummy_users'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_setup_forbid_home'] 0m7.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_setup_forbid_home'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.1s 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' 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_setup_minimize'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_setup_minimize'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_setup_zz_backports'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_setup_zz_backports'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.2s DUMP: install ok installed apt apt 2.9.30 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.6 install ok installed bash bash 5.2.37-1 install ok installed bsdutils bsdutils 1:2.40.4-3 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.89 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-2 install ok installed dpkg dpkg 1.22.15 install ok installed e2fsprogs e2fsprogs 1.47.2-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-16 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.29 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 2.9.30 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+b1 install ok installed libblkid1:amd64 libblkid1 2.40.4-3 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 2.40-7 install ok installed libc6:amd64 libc6 2.40-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-16 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-3 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 2.40.4-3 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3.1 install ok installed libsemanage-common libsemanage-common 3.7-2.1 install ok installed libsemanage2:amd64 libsemanage2 3.7-2.1+b1 install ok installed libsepol2:amd64 libsepol2 3.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-3 install ok installed libss2:amd64 libss2 1.47.2-1 install ok installed libssl3t64:amd64 libssl3t64 3.4.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-16 install ok installed libsystemd0:amd64 libsystemd0 257.3-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250125-2 install ok installed libudev1:amd64 libudev1 257.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.4-3 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed login login 1:4.16.0-2+really2.40.4-3 install ok installed login.defs login.defs 1:4.17.2-5 install ok installed logsave logsave 1.47.2-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.40.4-3 install ok installed ncurses-base ncurses-base 6.5+20250125-2 install ok installed ncurses-bin ncurses-bin 6.5+20250125-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.1-1 install ok installed passwd passwd 1:4.17.2-5 install ok installed perl-base perl-base 5.40.1-2 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.2.1-6+b1 install ok installed sysvinit-utils sysvinit-utils 3.14-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025a-2 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.4-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.2s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m7.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 0m7.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 0m7.5s INFO: Running scripts is_testable 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/is_testable_uninstallable'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/is_testable_uninstallable'] 0m7.5s INFO: Running scripts pre_test 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_test_exceptions'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_test_exceptions'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_test_root_password'] 0m7.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_test_root_password'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'show', '--no-all-versions', 'python3-mdanalysis'] 0m7.8s DUMP: Package: python3-mdanalysis Source: mdanalysis Version: 2.8.0-4 Installed-Size: 28378 Maintainer: Debichem Team Architecture: amd64 Depends: python3-duecredit, python3-biopython (>= 1.80), python3 (<< 3.14), python3 (>= 3.12~), python3-fasteners, python3-griddataformats, python3-joblib, python3-matplotlib, python3-mda-xdrlib, python3-mmtf, python3-numpy, python3-numpy2-abi0 | 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_2.8.0-4_amd64.deb Size: 4766368 MD5sum: 2963247719573cc5023a2d5cbea09c13 SHA256: 20e68d613e1bc27ca3f0d615f609eceba48b7542427c9eca5f77c8dc8fec16b3 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'show', '--no-all-versions', 'python3-mdanalysis'] 0m7.8s INFO: apt-cache knows about the following packages: python3-mdanalysis 0m7.8s INFO: Running scripts pre_install 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_database-server'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_database-server'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_exceptions'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_exceptions'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_extras'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_extras'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'policy'] 0m8.0s 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: 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'policy'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'policy', 'python3-mdanalysis'] 0m8.0s DUMP: python3-mdanalysis: Installed: (none) Candidate: 2.8.0-4 Version table: 2.8.0-4 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'policy', 'python3-mdanalysis'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', '-y', 'install', 'python3-mdanalysis'] 1m22.6s 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 fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libdeflate0 libexpat1 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgfortran5 libglib2.0-0t64 libgomp1 libgpg-error0 libgraphite2-3 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libncursesw6 libopenjp2-7 libpixman-1-0 libpng16-16t64 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 libsharpyuv0 libsqlite3-0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 media-types netbase openssl procps python-matplotlib-data python3 python3-attr python3-biopython python3-brotli python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-citeproc python3-contourpy python3-cycler python3-dateutil python3-decorator python3-duecredit python3-fasteners python3-fonttools python3-freetype python3-fs python3-griddataformats python3-idna python3-joblib python3-kiwisolver python3-looseversion python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib python3-minimal python3-mmtf python3-monotonic python3-mpmath python3-mrcfile python3-msgpack python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-platformdirs python3-pyparsing python3-pytz python3-reportlab python3-requests python3-rlpycairo python3-scipy python3-sympy python3-threadpoolctl python3-tk python3-tqdm python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3.12-tk python3.13 python3.13-minimal python3.13-tk readline-common sgml-base sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core Suggested packages: blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre rng-tools low-memory-monitor libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python3-doc python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-rdflib python3-psycopg2 python3-igraph raxml samtools t-coffee wise 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 python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.13-venv python3.13-doc binutils binfmt-support readline-doc sgml-base-doc debhelper Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs libgpg-error-l10n javascript-common libgpm2 psmisc linux-sysctl-defaults python-biopython-doc ncbi-blast+ python3-psutil python3-pytest python3-bs4 python3-cssselect python3-html5lib python3-sklearn python3-olefile fonts-dejavu-extra g++ | c++-compiler python3-pooch 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 fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libdeflate0 libexpat1 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgfortran5 libglib2.0-0t64 libgomp1 libgpg-error0 libgraphite2-3 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libncursesw6 libopenjp2-7 libpixman-1-0 libpng16-16t64 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 libsharpyuv0 libsqlite3-0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 media-types netbase openssl procps python-matplotlib-data python3 python3-attr python3-biopython python3-brotli python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-citeproc python3-contourpy python3-cycler python3-dateutil python3-decorator python3-duecredit python3-fasteners python3-fonttools python3-freetype python3-fs python3-griddataformats python3-idna python3-joblib python3-kiwisolver python3-looseversion python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib python3-mdanalysis python3-minimal python3-mmtf python3-monotonic python3-mpmath python3-mrcfile python3-msgpack python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-platformdirs python3-pyparsing python3-pytz python3-reportlab python3-requests python3-rlpycairo python3-scipy python3-sympy python3-threadpoolctl python3-tk python3-tqdm python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3.12-tk python3.13 python3.13-minimal python3.13-tk readline-common sgml-base sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 143 newly installed, 0 to remove and 0 not upgraded. Need to get 118 MB of archives. After this operation, 500 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 libpython3.13-minimal amd64 3.13.2-1 [859 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 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 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 libffi8 amd64 3.4.7-1 [23.9 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5+20250125-2 [135 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get:16 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:33 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:47 http://deb.debian.org/debian trixie/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.3-1 [190 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-16 [9296 B] Get:50 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.83.3-2 [1511 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-16 [137 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.3-1 [204 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 python3-attr all 25.1.0-1 [68.7 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [4736 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 python3.12-tk amd64 3.12.9-1 [113 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 python3.13-tk amd64 3.13.2-1 [103 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.13.1-1 [9464 B] Get:93 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 11.1.0-5 [81.5 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 11.1.0-5 [531 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.26.1-2+b1 [130 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:98 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.3.1-1 [1158 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.85+dfsg-2 [1674 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get:104 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.1-1 [142 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.3.1-1 [1683 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 python3-citeproc all 0.7.0-1 [98.3 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.3.1-1 [264 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:109 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 python3-looseversion all 1.3.0-3 [8964 B] Get:112 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.10-1 [42.0 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.3.0-1 [114 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 python3-duecredit all 0.10.2-2 [70.6 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 python3-monotonic all 1.6-3 [5340 B] Get:118 http://deb.debian.org/debian trixie/main amd64 python3-fasteners all 0.18-2 [14.0 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 python3-pytz all 2025.1-3 [150 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2025.1-3 [4004 B] Get:121 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-6 [95.1 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.4.0+dfsg-1 [25.5 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.14.1-4 [20.5 MB] Get:125 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b3 [299 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.55.3-2 [1633 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 python3-mrcfile all 1.5.4-2 [118 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 python3-griddataformats all 1.0.2-2 [2048 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 python3-joblib all 1.4.2-2 [216 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.7-3 [76.9 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.8.3-3+b3 [5650 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 python3-mda-xdrlib all 0.2.0-3 [11.6 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 python3-msgpack amd64 1.0.3-3+b3 [112 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 python3-mmtf all 1.1.3-1 [17.0 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 python3-tqdm all 4.67.1-2 [91.1 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 python3-mdanalysis amd64 2.8.0-4 [4766 kB] Preconfiguring packages ... Fetched 118 MB in 1s (172 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 ... 5076 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 libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_amd64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:amd64 (3.13.2-1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (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 ... 5436 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.13.1-2_amd64.deb ... Unpacking python3-minimal (3.13.1-2) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../03-libffi8_3.4.7-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.7-1) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../04-libncursesw6_6.5+20250125-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.5+20250125-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../05-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../06-libreadline8t64_8.2-6_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 (8.2-6) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../07-libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../08-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../09-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../10-libpython3-stdlib_3.13.1-2_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.1-2) ... Setting up python3-minimal (3.13.1-2) ... 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 ... 5948 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.1-2_amd64.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-7_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-7) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-7_amd64.deb ... Unpacking procps (2:4.0.4-7) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.4.1-1_amd64.deb ... Unpacking openssl (3.4.1-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20241223_all.deb ... Unpacking ca-certificates (20241223) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../006-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../007-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 .../008-libpng16-16t64_1.6.46-4_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.46-4) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../009-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 .../010-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 .../011-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:amd64. Preparing to unpack .../012-libfontenc1_1%3a1.1.8-1+b2_amd64.deb ... Unpacking libfontenc1:amd64 (1:1.1.8-1+b2) ... Selecting previously unselected package x11-common. Preparing to unpack .../013-x11-common_1%3a7.7+24_all.deb ... Unpacking x11-common (1:7.7+24) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../014-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../015-xfonts-utils_1%3a7.7+7_amd64.deb ... Unpacking xfonts-utils (1:7.7+7) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../016-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../017-fontconfig-config_2.15.0-2_amd64.deb ... Unpacking fontconfig-config (2.15.0-2) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../018-libfontconfig1_2.15.0-2_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-2) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../019-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 .../020-libxdmcp6_1%3a1.1.5-1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../021-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 .../022-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 .../023-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 .../024-libxrender1_1%3a0.9.10-1.1+b4_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1+b4) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../025-libxft2_2.3.6-1+b4_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b4) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../026-libxext6_2%3a1.3.4-1+b3_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b3) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../027-libxss1_1%3a1.2.3-1+b3_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../028-libtk8.6_8.6.16-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.16-1) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../029-tk8.6-blt2.5_2.5.3+dfsg-7_amd64.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... Selecting previously unselected package blt. Preparing to unpack .../030-blt_2.5.3+dfsg-7_amd64.deb ... Unpacking blt (2.5.3+dfsg-7) ... Selecting previously unselected package fonts-font-awesome. Preparing to unpack .../031-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Selecting previously unselected package fonts-lyx. Preparing to unpack .../032-fonts-lyx_2.4.3-1_all.deb ... Unpacking fonts-lyx (2.4.3-1) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../033-libatomic1_14.2.0-16_amd64.deb ... Unpacking libatomic1:amd64 (14.2.0-16) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../034-libblas3_3.12.1-2_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-2) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../035-libpixman-1-0_0.44.0-3_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.44.0-3) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../036-libxcb-render0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-render0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../037-libxcb-shm0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../038-libcairo2_1.18.2-2_amd64.deb ... Unpacking libcairo2:amd64 (1.18.2-2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../039-libdeflate0_1.23-1+b1_amd64.deb ... Unpacking libdeflate0:amd64 (1.23-1+b1) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../040-libfribidi0_1.0.16-1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.16-1) ... Selecting previously unselected package libgpg-error0:amd64. Preparing to unpack .../041-libgpg-error0_1.51-3_amd64.deb ... Unpacking libgpg-error0:amd64 (1.51-3) ... Selecting previously unselected package libgcrypt20:amd64. Preparing to unpack .../042-libgcrypt20_1.11.0-7_amd64.deb ... Unpacking libgcrypt20:amd64 (1.11.0-7) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../043-libgfortran5_14.2.0-16_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-16) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../044-libglib2.0-0t64_2.83.3-2_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.83.3-2) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../045-libgomp1_14.2.0-16_amd64.deb ... Unpacking libgomp1:amd64 (14.2.0-16) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../046-libgraphite2-3_1.3.14-2+b1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../047-libharfbuzz0b_10.2.0-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../048-libicu72_72.1-6_amd64.deb ... Unpacking libicu72:amd64 (72.1-6) ... Selecting previously unselected package libimagequant0:amd64. Preparing to unpack .../049-libimagequant0_2.18.0-1+b2_amd64.deb ... Unpacking libimagequant0:amd64 (2.18.0-1+b2) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../050-libjbig0_2.1-6.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../051-libjpeg62-turbo_1%3a2.1.5-3+b1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../052-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../053-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../054-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../055-libjs-sphinxdoc_8.1.3-4_all.deb ... Unpacking libjs-sphinxdoc (8.1.3-4) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../056-liblapack3_3.12.1-2_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-2) ... Selecting previously unselected package liblbfgsb0:amd64. Preparing to unpack .../057-liblbfgsb0_3.0+dfsg.4-1+b2_amd64.deb ... Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../058-liblcms2-2_2.16-2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.16-2) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../059-liblerc4_4.0.0+ds-5_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-5) ... Selecting previously unselected package libopenjp2-7:amd64. Preparing to unpack .../060-libopenjp2-7_2.5.3-1_amd64.deb ... Unpacking libopenjp2-7:amd64 (2.5.3-1) ... Selecting previously unselected package libqhull-r8.0:amd64. Preparing to unpack .../061-libqhull-r8.0_2020.2-6+b2_amd64.deb ... Unpacking libqhull-r8.0:amd64 (2020.2-6+b2) ... Selecting previously unselected package libraqm0:amd64. Preparing to unpack .../062-libraqm0_0.10.2-1_amd64.deb ... Unpacking libraqm0:amd64 (0.10.2-1) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../063-libsharpyuv0_1.5.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../064-libwebp7_1.5.0-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../065-libtiff6_4.5.1+git230720-5_amd64.deb ... Unpacking libtiff6:amd64 (4.5.1+git230720-5) ... Selecting previously unselected package libwebpdemux2:amd64. Preparing to unpack .../066-libwebpdemux2_1.5.0-0.1_amd64.deb ... Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../067-libwebpmux3_1.5.0-0.1_amd64.deb ... Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../068-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libxslt1.1:amd64. Preparing to unpack .../069-libxslt1.1_1.1.35-1.1+b1_amd64.deb ... Unpacking libxslt1.1:amd64 (1.1.35-1.1+b1) ... Selecting previously unselected package python-matplotlib-data. Preparing to unpack .../070-python-matplotlib-data_3.8.3-3_all.deb ... Unpacking python-matplotlib-data (3.8.3-3) ... Selecting previously unselected package python3-attr. Preparing to unpack .../071-python3-attr_25.1.0-1_all.deb ... Unpacking python3-attr (25.1.0-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../072-python3-numpy_1%3a1.26.4+ds-13_amd64.deb ... Unpacking python3-numpy (1:1.26.4+ds-13) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../073-python3-chardet_5.2.0+dfsg-2_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-2) ... Selecting previously unselected package python3.12-tk. Preparing to unpack .../074-python3.12-tk_3.12.9-1_amd64.deb ... Unpacking python3.12-tk (3.12.9-1) ... Selecting previously unselected package python3.13-tk. Preparing to unpack .../075-python3.13-tk_3.13.2-1_amd64.deb ... Unpacking python3.13-tk (3.13.2-1) ... Selecting previously unselected package python3-tk:amd64. Preparing to unpack .../076-python3-tk_3.13.1-1_amd64.deb ... Unpacking python3-tk:amd64 (3.13.1-1) ... Selecting previously unselected package python3-pil.imagetk:amd64. Preparing to unpack .../077-python3-pil.imagetk_11.1.0-5_amd64.deb ... Unpacking python3-pil.imagetk:amd64 (11.1.0-5) ... Selecting previously unselected package python3-pil:amd64. Preparing to unpack .../078-python3-pil_11.1.0-5_amd64.deb ... Unpacking python3-pil:amd64 (11.1.0-5) ... Selecting previously unselected package python3-cairo. Preparing to unpack .../079-python3-cairo_1.26.1-2+b1_amd64.deb ... Unpacking python3-cairo (1.26.1-2+b1) ... Selecting previously unselected package python3-freetype. Preparing to unpack .../080-python3-freetype_2.5.1-1_all.deb ... Unpacking python3-freetype (2.5.1-1) ... Selecting previously unselected package python3-rlpycairo. Preparing to unpack .../081-python3-rlpycairo_0.3.0-3_all.deb ... Unpacking python3-rlpycairo (0.3.0-3) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../082-python3-reportlab_4.3.1-1_all.deb ... Unpacking python3-reportlab (4.3.1-1) ... Selecting previously unselected package xml-core. Preparing to unpack .../083-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package w3c-sgml-lib. Preparing to unpack .../084-w3c-sgml-lib_1.3-3_all.deb ... Unpacking w3c-sgml-lib (1.3-3) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../085-python3-biopython_1.85+dfsg-2_amd64.deb ... Unpacking python3-biopython (1.85+dfsg-2) ... Selecting previously unselected package python3-brotli. Preparing to unpack .../086-python3-brotli_1.1.0-2+b6_amd64.deb ... Unpacking python3-brotli (1.1.0-2+b6) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../087-python3-certifi_2025.1.31+ds-1_all.deb ... Unpacking python3-certifi (2025.1.31+ds-1) ... Selecting previously unselected package python3-charset-normalizer. Preparing to unpack .../088-python3-charset-normalizer_3.4.1-1_amd64.deb ... Unpacking python3-charset-normalizer (3.4.1-1) ... Selecting previously unselected package python3-lxml:amd64. Preparing to unpack .../089-python3-lxml_5.3.1-1_amd64.deb ... Unpacking python3-lxml:amd64 (5.3.1-1) ... Selecting previously unselected package python3-citeproc. Preparing to unpack .../090-python3-citeproc_0.7.0-1_all.deb ... Unpacking python3-citeproc (0.7.0-1) ... Selecting previously unselected package python3-contourpy. Preparing to unpack .../091-python3-contourpy_1.3.1-1_amd64.deb ... Unpacking python3-contourpy (1.3.1-1) ... Selecting previously unselected package python3-cycler. Preparing to unpack .../092-python3-cycler_0.12.1-1_all.deb ... Unpacking python3-cycler (0.12.1-1) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../093-python3-dateutil_2.9.0-3_all.deb ... Unpacking python3-dateutil (2.9.0-3) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../094-python3-decorator_5.1.1-5_all.deb ... Unpacking python3-decorator (5.1.1-5) ... Selecting previously unselected package python3-looseversion. Preparing to unpack .../095-python3-looseversion_1.3.0-3_all.deb ... Unpacking python3-looseversion (1.3.0-3) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../096-python3-packaging_24.2-1_all.deb ... Unpacking python3-packaging (24.2-1) ... Selecting previously unselected package python3-idna. Preparing to unpack .../097-python3-idna_3.10-1_all.deb ... Unpacking python3-idna (3.10-1) ... Selecting previously unselected package python3-urllib3. Preparing to unpack .../098-python3-urllib3_2.3.0-1_all.deb ... Unpacking python3-urllib3 (2.3.0-1) ... Selecting previously unselected package python3-requests. Preparing to unpack .../099-python3-requests_2.32.3+dfsg-4_all.deb ... Unpacking python3-requests (2.32.3+dfsg-4) ... Selecting previously unselected package python3-duecredit. Preparing to unpack .../100-python3-duecredit_0.10.2-2_all.deb ... Unpacking python3-duecredit (0.10.2-2) ... Selecting previously unselected package python3-monotonic. Preparing to unpack .../101-python3-monotonic_1.6-3_all.deb ... Unpacking python3-monotonic (1.6-3) ... Selecting previously unselected package python3-fasteners. Preparing to unpack .../102-python3-fasteners_0.18-2_all.deb ... Unpacking python3-fasteners (0.18-2) ... Selecting previously unselected package python3-pytz. Preparing to unpack .../103-python3-pytz_2025.1-3_all.deb ... Unpacking python3-pytz (2025.1-3) ... Selecting previously unselected package python3-tz. Preparing to unpack .../104-python3-tz_2025.1-3_all.deb ... Unpacking python3-tz (2025.1-3) ... Selecting previously unselected package python3-platformdirs. Preparing to unpack .../105-python3-platformdirs_4.3.6-1_all.deb ... Unpacking python3-platformdirs (4.3.6-1) ... Selecting previously unselected package python3-fs. Preparing to unpack .../106-python3-fs_2.4.16-6_all.deb ... Unpacking python3-fs (2.4.16-6) ... Selecting previously unselected package python3-lz4. Preparing to unpack .../107-python3-lz4_4.4.0+dfsg-1_amd64.deb ... Unpacking python3-lz4 (4.4.0+dfsg-1) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../108-python3-scipy_1.14.1-4_amd64.deb ... Unpacking python3-scipy (1.14.1-4) ... Selecting previously unselected package python3-mpmath. Preparing to unpack .../109-python3-mpmath_1.3.0-1_all.deb ... Unpacking python3-mpmath (1.3.0-1) ... Selecting previously unselected package python3-sympy. Preparing to unpack .../110-python3-sympy_1.13.3-1_all.deb ... Unpacking python3-sympy (1.13.3-1) ... Selecting previously unselected package python3-ufolib2. Preparing to unpack .../111-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... Selecting previously unselected package python3-unicodedata2. Preparing to unpack .../112-python3-unicodedata2_15.1.0+ds-1+b3_amd64.deb ... Unpacking python3-unicodedata2 (15.1.0+ds-1+b3) ... Selecting previously unselected package unicode-data. Preparing to unpack .../113-unicode-data_15.1.0-1_all.deb ... Unpacking unicode-data (15.1.0-1) ... Selecting previously unselected package python3-fonttools. Preparing to unpack .../114-python3-fonttools_4.55.3-2_amd64.deb ... Unpacking python3-fonttools (4.55.3-2) ... Selecting previously unselected package sphinx-rtd-theme-common. Preparing to unpack .../115-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... Selecting previously unselected package python3-mrcfile. Preparing to unpack .../116-python3-mrcfile_1.5.4-2_all.deb ... Unpacking python3-mrcfile (1.5.4-2) ... Selecting previously unselected package python3-griddataformats. Preparing to unpack .../117-python3-griddataformats_1.0.2-2_all.deb ... Unpacking python3-griddataformats (1.0.2-2) ... Selecting previously unselected package python3-joblib. Preparing to unpack .../118-python3-joblib_1.4.2-2_all.deb ... Unpacking python3-joblib (1.4.2-2) ... Selecting previously unselected package python3-kiwisolver. Preparing to unpack .../119-python3-kiwisolver_1.4.7-3_amd64.deb ... Unpacking python3-kiwisolver (1.4.7-3) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../120-python3-pyparsing_3.1.2-1_all.deb ... Unpacking python3-pyparsing (3.1.2-1) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../121-python3-matplotlib_3.8.3-3+b3_amd64.deb ... Unpacking python3-matplotlib (3.8.3-3+b3) ... Selecting previously unselected package python3-mda-xdrlib. Preparing to unpack .../122-python3-mda-xdrlib_0.2.0-3_all.deb ... Unpacking python3-mda-xdrlib (0.2.0-3) ... Selecting previously unselected package python3-msgpack. Preparing to unpack .../123-python3-msgpack_1.0.3-3+b3_amd64.deb ... Unpacking python3-msgpack (1.0.3-3+b3) ... Selecting previously unselected package python3-mmtf. Preparing to unpack .../124-python3-mmtf_1.1.3-1_all.deb ... Unpacking python3-mmtf (1.1.3-1) ... Selecting previously unselected package python3-threadpoolctl. Preparing to unpack .../125-python3-threadpoolctl_3.1.0-1_all.deb ... Unpacking python3-threadpoolctl (3.1.0-1) ... Selecting previously unselected package python3-tqdm. Preparing to unpack .../126-python3-tqdm_4.67.1-2_all.deb ... Unpacking python3-tqdm (4.67.1-2) ... Selecting previously unselected package python3-mdanalysis. Preparing to unpack .../127-python3-mdanalysis_2.8.0-4_amd64.deb ... Unpacking python3-mdanalysis (2.8.0-4) ... 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 libpixman-1-0:amd64 (0.44.0-3) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up fonts-lato (2.015-1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up libgpg-error0:amd64 (1.51-3) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up fonts-lyx (2.4.3-1) ... 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+24) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up libgcrypt20:amd64 (1.11.0-7) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b2) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libgomp1:amd64 (14.2.0-16) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up unicode-data (15.1.0-1) ... Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up libblas3:amd64 (3.12.1-2) ... 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 xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libproc2-0:amd64 (2:4.0.4-7) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.46-4) ... Setting up libatomic1:amd64 (14.2.0-16) ... Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libncursesw6:amd64 (6.5+20250125-2) ... Setting up libgfortran5:amd64 (14.2.0-16) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up procps (2:4.0.4-7) ... Setting up libopenjp2-7:amd64 (2.5.3-1) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.8.3-3) ... Setting up openssl (3.4.1-1) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up readline-common (8.2-6) ... 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 (3.0.2+dfsg-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up liblapack3:amd64 (3.12.1-2) ... 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+b4) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libglib2.0-0t64:amd64 (2.83.3-2) ... 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 libjs-sphinxdoc (8.1.3-4) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:amd64 (10.2.0-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up python3.13 (3.13.2-1) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up python3.12-tk (3.12.9-1) ... Setting up python3 (3.13.1-2) ... Setting up python3-freetype (2.5.1-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up python3.13-tk (3.13.2-1) ... Setting up python3-mda-xdrlib (0.2.0-3) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-monotonic (1.6-3) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up python3-brotli (1.1.0-2+b6) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.7-3) ... Setting up python3-idna (3.10-1) ... Setting up python3-fasteners (0.18-2) ... Setting up python3-numpy (1:1.26.4+ds-13) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up python3-looseversion (1.3.0-3) ... Setting up python3-lxml:amd64 (5.3.1-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-contourpy (1.3.1-1) ... Setting up python3-msgpack (1.0.3-3+b3) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-mrcfile (1.5.4-2) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (25.1.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up python3-scipy (1.14.1-4) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-joblib (1.4.2-2) ... Setting up python3-lz4 (4.4.0+dfsg-1) ... Setting up python3-citeproc (0.7.0-1) ... Setting up python3-charset-normalizer (3.4.1-1) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b3) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-tqdm (4.67.1-2) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-tk:amd64 (3.13.1-1) ... Setting up python3-pytz (2025.1-3) ... Setting up python3-mmtf (1.1.3-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-tz (2025.1-3) ... Setting up python3-fs (2.4.16-6) ... Setting up python3-pil:amd64 (11.1.0-5) ... Setting up python3-griddataformats (1.0.2-2) ... Setting up python3-pil.imagetk:amd64 (11.1.0-5) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-requests (2.32.3+dfsg-4) ... Setting up python3-reportlab (4.3.1-1) ... Setting up python3-duecredit (0.10.2-2) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-fonttools (4.55.3-2) ... Setting up python3-matplotlib (3.8.3-3+b3) ... Processing triggers for libc-bin (2.40-7) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-2) ... Setting up python3-mdanalysis (2.8.0-4) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 1m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', '-y', 'install', 'python3-mdanalysis'] 1m22.6s INFO: Running scripts post_install 1m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_install_exceptions'] 1m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_install_exceptions'] 1m22.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 1m23.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 1m23.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpu3o6eah3 to sid 1m23.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 1m23.5s INFO: Running scripts pre_distupgrade 1m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_distupgrade_exceptions'] 1m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_distupgrade_exceptions'] 1m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', 'update'] 1m26.4s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7379 kB] Fetched 17.7 MB in 2s (9107 kB/s) Reading package lists... 1m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', 'update'] 1m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', '-yf', 'dist-upgrade'] 1m38.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: python3-numpy-dev The following packages will be upgraded: bash bsdutils gcc-14-base libatomic1 libattr1 libblkid1 libcap2 libgcc-s1 libgfortran5 libglib2.0-0t64 libgomp1 libhogweed6t64 libjpeg62-turbo libjs-sphinxdoc libmount1 libncursesw6 libnettle8t64 libpcre2-8-0 libpng16-16t64 libselinux1 libsemanage-common libsemanage2 libsmartcols1 libstdc++6 libtinfo6 libuuid1 login media-types mount ncurses-base ncurses-bin python3-numpy python3-sympy util-linux 34 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 21.6 MB of archives. After this operation, 7562 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.37-1.1 [1500 kB] Get:2 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.4-4 [106 kB] Get:3 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.5+20250216-1 [439 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.4-4 [36.5 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.4-4 [169 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.4-4 [200 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.4-4 [140 kB] Get:8 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.4-4 [1206 kB] Get:9 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.4-4 [156 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.45-1 [298 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.8-3 [84.6 kB] Get:12 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.5+20250216-1 [273 kB] Get:13 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.4-4 [88.7 kB] Get:14 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:2.2.3+ds-2 [7517 kB] Get:15 http://deb.debian.org/debian sid/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-2 [138 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-17 [9316 B] Get:17 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-17 [137 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB] Get:19 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-17 [49.1 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-17 [72.7 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-17 [713 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-3 [22.9 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.73-4 [27.3 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libnettle8t64 amd64 3.10.1-1 [305 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libhogweed6t64 amd64 3.10.1-1 [335 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5+20250216-1 [136 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.5+20250216-1 [348 kB] Get:28 http://deb.debian.org/debian sid/main amd64 media-types all 12.0.0 [28.9 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.83.4-1 [1512 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.47-1 [282 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.8-1 [7720 B] Get:34 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.8-1 [94.4 kB] Get:35 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.13.3-3 [4148 kB] Fetched 21.6 MB in 0s (124 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 ... 18484 files and directories currently installed.) Preparing to unpack .../bash_5.2.37-1.1_amd64.deb ... Unpacking bash (5.2.37-1.1) over (5.2.37-1) ... Setting up bash (5.2.37-1.1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (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 ... 18484 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.4-4_amd64.deb ... Unpacking bsdutils (1:2.40.4-4) over (1:2.40.4-3) ... Setting up bsdutils (1:2.40.4-4) ... (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 ... 18484 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.5+20250216-1_amd64.deb ... Unpacking ncurses-bin (6.5+20250216-1) over (6.5+20250125-2) ... Setting up ncurses-bin (6.5+20250216-1) ... (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 ... 18484 files and directories currently installed.) Preparing to unpack .../libuuid1_2.40.4-4_amd64.deb ... Unpacking libuuid1:amd64 (2.40.4-4) over (2.40.4-3) ... Setting up libuuid1:amd64 (2.40.4-4) ... (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 ... 18484 files and directories currently installed.) Preparing to unpack .../libblkid1_2.40.4-4_amd64.deb ... Unpacking libblkid1:amd64 (2.40.4-4) over (2.40.4-3) ... Setting up libblkid1:amd64 (2.40.4-4) ... (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 ... 18484 files and directories currently installed.) Preparing to unpack .../libmount1_2.40.4-4_amd64.deb ... Unpacking libmount1:amd64 (2.40.4-4) over (2.40.4-3) ... Setting up libmount1:amd64 (2.40.4-4) ... (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 ... 18484 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40.4-4_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40.4-4) over (2.40.4-3) ... Setting up libsmartcols1:amd64 (2.40.4-4) ... (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 ... 18484 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.4-4_amd64.deb ... Unpacking util-linux (2.40.4-4) over (2.40.4-3) ... Setting up util-linux (2.40.4-4) ... (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 ... 18481 files and directories currently installed.) Preparing to unpack .../mount_2.40.4-4_amd64.deb ... Unpacking mount (2.40.4-4) over (2.40.4-3) ... Preparing to unpack .../libpcre2-8-0_10.45-1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.45-1) over (10.44-5) ... Setting up libpcre2-8-0:amd64 (10.45-1) ... (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 ... 18481 files and directories currently installed.) Preparing to unpack .../libselinux1_3.8-3_amd64.deb ... Unpacking libselinux1:amd64 (3.8-3) over (3.7-3.1) ... Setting up libselinux1:amd64 (3.8-3) ... /var/lib/dpkg/info/libselinux1:amd64.postinst: 6: sestatus: not found (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 ... 18481 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.5+20250216-1_all.deb ... Unpacking ncurses-base (6.5+20250216-1) over (6.5+20250125-2) ... Setting up ncurses-base (6.5+20250216-1) ... (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 ... 18481 files and directories currently installed.) Preparing to unpack .../0-login_1%3a4.16.0-2+really2.40.4-4_amd64.deb ... Unpacking login (1:4.16.0-2+really2.40.4-4) over (1:4.16.0-2+really2.40.4-3) ... Preparing to unpack .../1-python3-numpy_1%3a2.2.3+ds-2_amd64.deb ... Unpacking python3-numpy (1:2.2.3+ds-2) over (1:1.26.4+ds-13) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../2-python3-numpy-dev_1%3a2.2.3+ds-2_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-2) ... Preparing to unpack .../3-libatomic1_14.2.0-17_amd64.deb ... Unpacking libatomic1:amd64 (14.2.0-17) over (14.2.0-16) ... Preparing to unpack .../4-libgomp1_14.2.0-17_amd64.deb ... Unpacking libgomp1:amd64 (14.2.0-17) over (14.2.0-16) ... Preparing to unpack .../5-libgfortran5_14.2.0-17_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-17) over (14.2.0-16) ... Preparing to unpack .../6-gcc-14-base_14.2.0-17_amd64.deb ... Unpacking gcc-14-base:amd64 (14.2.0-17) over (14.2.0-16) ... Setting up gcc-14-base:amd64 (14.2.0-17) ... (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 ... 18557 files and directories currently installed.) Preparing to unpack .../libgcc-s1_14.2.0-17_amd64.deb ... Unpacking libgcc-s1:amd64 (14.2.0-17) over (14.2.0-16) ... Setting up libgcc-s1:amd64 (14.2.0-17) ... (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 ... 18557 files and directories currently installed.) Preparing to unpack .../libstdc++6_14.2.0-17_amd64.deb ... Unpacking libstdc++6:amd64 (14.2.0-17) over (14.2.0-16) ... Setting up libstdc++6:amd64 (14.2.0-17) ... (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 ... 18557 files and directories currently installed.) Preparing to unpack .../libattr1_1%3a2.5.2-3_amd64.deb ... Unpacking libattr1:amd64 (1:2.5.2-3) over (1:2.5.2-2) ... Setting up libattr1:amd64 (1:2.5.2-3) ... (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 ... 18557 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.73-4_amd64.deb ... Unpacking libcap2:amd64 (1:2.73-4) over (1:2.66-5+b1) ... Setting up libcap2:amd64 (1:2.73-4) ... (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 ... 18556 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.10.1-1_amd64.deb ... Unpacking libnettle8t64:amd64 (3.10.1-1) over (3.10-1+b1) ... Setting up libnettle8t64:amd64 (3.10.1-1) ... (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 ... 18555 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.10.1-1_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.10.1-1) over (3.10-1+b1) ... Setting up libhogweed6t64:amd64 (3.10.1-1) ... (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 ... 18554 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.5+20250216-1_amd64.deb ... Unpacking libncursesw6:amd64 (6.5+20250216-1) over (6.5+20250125-2) ... Preparing to unpack .../libtinfo6_6.5+20250216-1_amd64.deb ... Unpacking libtinfo6:amd64 (6.5+20250216-1) over (6.5+20250125-2) ... Setting up libtinfo6:amd64 (6.5+20250216-1) ... (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 ... 18554 files and directories currently installed.) Preparing to unpack .../0-media-types_12.0.0_all.deb ... Unpacking media-types (12.0.0) over (10.1.0) ... Preparing to unpack .../1-libglib2.0-0t64_2.83.4-1_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.83.4-1) over (2.83.3-2) ... Preparing to unpack .../2-libjpeg62-turbo_1%3a2.1.5-3.1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3.1) over (1:2.1.5-3+b1) ... Preparing to unpack .../3-libjs-sphinxdoc_8.1.3-5_all.deb ... Unpacking libjs-sphinxdoc (8.1.3-5) over (8.1.3-4) ... Preparing to unpack .../4-libpng16-16t64_1.6.47-1_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.47-1) over (1.6.46-4) ... Preparing to unpack .../5-libsemanage-common_3.8-1_all.deb ... Unpacking libsemanage-common (3.8-1) over (3.7-2.1) ... Preparing to unpack .../6-libsemanage2_3.8-1_amd64.deb ... Unpacking libsemanage2:amd64 (3.8-1) over (3.7-2.1+b1) ... Preparing to unpack .../7-python3-sympy_1.13.3-3_all.deb ... Unpacking python3-sympy (1.13.3-3) over (1.13.3-1) ... Setting up media-types (12.0.0) ... Installing new version of config file /etc/mime.types ... Setting up python3-sympy (1.13.3-3) ... Setting up libgomp1:amd64 (14.2.0-17) ... Setting up libsemanage-common (3.8-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3.1) ... Setting up libpng16-16t64:amd64 (1.6.47-1) ... Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-2) ... Setting up libatomic1:amd64 (14.2.0-17) ... Setting up libncursesw6:amd64 (6.5+20250216-1) ... Setting up python3-numpy (1:2.2.3+ds-2) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up libgfortran5:amd64 (14.2.0-17) ... Setting up mount (2.40.4-4) ... Setting up libsemanage2:amd64 (3.8-1) ... Setting up login (1:4.16.0-2+really2.40.4-4) ... Setting up libglib2.0-0t64:amd64 (2.83.4-1) ... No schema files found: doing nothing. Processing triggers for libc-bin (2.40-7) ... Processing triggers for debianutils (5.21) ... 1m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', '-yf', 'dist-upgrade'] 1m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m38.9s DUMP: 2a13980d1c4a1b2288ce4adf6a534849 - 1m38.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m38.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'show', '--no-all-versions', 'python3-mdanalysis'] 1m39.2s DUMP: Package: python3-mdanalysis Source: mdanalysis Version: 2.8.0-4 Installed-Size: 28378 Maintainer: Debichem Team Architecture: amd64 Depends: python3-duecredit, python3-biopython (>= 1.80), python3 (<< 3.14), python3 (>= 3.12~), python3-fasteners, python3-griddataformats, python3-joblib, python3-matplotlib, python3-mda-xdrlib, python3-mmtf, python3-numpy, python3-numpy2-abi0 | 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_2.8.0-4_amd64.deb Size: 4766368 MD5sum: 2963247719573cc5023a2d5cbea09c13 SHA256: 20e68d613e1bc27ca3f0d615f609eceba48b7542427c9eca5f77c8dc8fec16b3 1m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'show', '--no-all-versions', 'python3-mdanalysis'] 1m39.2s INFO: apt-cache knows about the following packages: python3-mdanalysis 1m39.2s INFO: Running scripts pre_install 1m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_database-server'] 1m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_database-server'] 1m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_exceptions'] 1m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_exceptions'] 1m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_extras'] 1m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_extras'] 1m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_foreign_architecture'] 1m39.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_foreign_architecture'] 1m39.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m39.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m39.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'policy'] 1m39.4s 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: 1m39.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'policy'] 1m39.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'policy', 'python3-mdanalysis'] 1m39.4s DUMP: python3-mdanalysis: Installed: 2.8.0-4 Candidate: 2.8.0-4 Version table: *** 2.8.0-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m39.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'policy', 'python3-mdanalysis'] 1m39.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', '-y', 'install', 'python3-mdanalysis'] 1m40.0s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-mdanalysis is already the newest version (2.8.0-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', '-y', 'install', 'python3-mdanalysis'] 1m40.0s INFO: Running scripts post_install 1m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_install_exceptions'] 1m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_install_exceptions'] 1m40.0s INFO: Running scripts post_distupgrade 1m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_distupgrade_exceptions'] 1m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_distupgrade_exceptions'] 1m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_distupgrade_zz_backports'] 1m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_distupgrade_zz_backports'] 1m40.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 1m41.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 1m41.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 1m42.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 1m42.4s INFO: Running scripts pre_install 1m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_database-server'] 1m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_database-server'] 1m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_exceptions'] 1m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_exceptions'] 1m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_extras'] 1m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_extras'] 1m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_foreign_architecture'] 1m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_foreign_architecture'] 1m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'policy'] 1m42.5s 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: 1m42.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'policy'] 1m42.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'policy', 'python3-mdanalysis'] 1m42.5s DUMP: python3-mdanalysis: Installed: 2.8.0-4 Candidate: 2.8.0-4 Version table: *** 2.8.0-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m42.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-cache', 'policy', 'python3-mdanalysis'] 1m42.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', '-y', 'install', 'python3-mdanalysis=2.8.0-4'] 1m43.0s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-mdanalysis is already the newest version (2.8.0-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', '-y', 'install', 'python3-mdanalysis=2.8.0-4'] 1m43.0s INFO: Running scripts post_install 1m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_install_exceptions'] 1m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_install_exceptions'] 1m43.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 1m44.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 1m45.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', '-ac', '--ignore-obsolete'] 1m47.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', '-ac', '--ignore-obsolete'] 1m47.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m47.6s DUMP: 0.15.6 1m47.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m47.6s INFO: Running adequate version 0.15.6 now. 1m47.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'python3-mdanalysis'] 1m47.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'python3-mdanalysis'] 1m47.7s INFO: Running scripts pre_remove 1m47.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m47.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m47.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m47.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m47.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m49.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m49.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m50.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m50.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_remove_exceptions'] 1m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/pre_remove_exceptions'] 1m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m50.1s DUMP: install ok installed apt apt 2.9.30 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.6 install ok installed bash bash 5.2.37-1.1 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bsdutils bsdutils 1:2.40.4-4 install ok installed ca-certificates ca-certificates 20241223 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.89 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-2 install ok installed dpkg dpkg 1.22.15 install ok installed e2fsprogs e2fsprogs 1.47.2-1 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig-config fontconfig-config 2.15.0-2 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 2.4.3-1 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-17 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.29 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 2.9.30 install ok installed libatomic1:amd64 libatomic1 14.2.0-17 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b1 install ok installed libblas3:amd64 libblas3 3.12.1-2 install ok installed libblkid1:amd64 libblkid1 2.40.4-4 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 2.40-7 install ok installed libc6:amd64 libc6 2.40-7 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.73-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277 install ok installed libdeflate0:amd64 libdeflate0 1.23-1+b1 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1 install ok installed libffi8:amd64 libffi8 3.4.7-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-2 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1+b2 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-17 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-7 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-17 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.83.4-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgomp1:amd64 libgomp1 14.2.0-17 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.2.0-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed libicu72:amd64 libicu72 72.1-6 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 1:2.1.5-3.1 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 8.1.3-5 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed liblapack3:amd64 liblapack3 3.12.1-2 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 1.10.0-3 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 2.40.4-4 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.3-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.47-1 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-7 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.1-2 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.2-1 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.2-1 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b2 install ok installed libraqm0:amd64 libraqm0 0.10.2-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.8-3 install ok installed libsemanage-common libsemanage-common 3.8-1 install ok installed libsemanage2:amd64 libsemanage2 3.8-1 install ok installed libsepol2:amd64 libsepol2 3.8-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.5.0-0.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-4 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.2-1 install ok installed libssl3t64:amd64 libssl3t64 3.4.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-17 install ok installed libsystemd0:amd64 libsystemd0 257.3-1 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.16+dfsg-1 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.16-1 install ok installed libudev1:amd64 libudev1 257.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.4-4 install ok installed libwebp7:amd64 libwebp7 1.5.0-0.1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.5.0-0.1 install ok installed libwebpmux3:amd64 libwebpmux3 1.5.0-0.1 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 libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3 install ok installed libxft2:amd64 libxft2 2.3.6-1+b4 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+b4 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+b3 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed login login 1:4.16.0-2+really2.40.4-4 install ok installed login.defs login.defs 1:4.17.2-5 install ok installed logsave logsave 1.47.2-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed media-types media-types 12.0.0 install ok installed mount mount 2.40.4-4 install ok installed ncurses-base ncurses-base 6.5+20250216-1 install ok installed ncurses-bin ncurses-bin 6.5+20250216-1 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.4.1-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.1-1 install ok installed passwd passwd 1:4.17.2-5 install ok installed perl-base perl-base 5.40.1-2 install ok installed procps procps 2:4.0.4-7 install ok installed python-matplotlib-data python-matplotlib-data 3.8.3-3 install ok installed python3 python3 3.13.1-2 install ok installed python3-attr python3-attr 25.1.0-1 install ok installed python3-biopython python3-biopython 1.85+dfsg-2 install ok installed python3-brotli python3-brotli 1.1.0-2+b6 install ok installed python3-cairo python3-cairo 1.26.1-2+b1 install ok installed python3-certifi python3-certifi 2025.1.31+ds-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-2 install ok installed python3-charset-normalizer python3-charset-normalizer 3.4.1-1 install ok installed python3-citeproc python3-citeproc 0.7.0-1 install ok installed python3-contourpy python3-contourpy 1.3.1-1 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 4.55.3-2 install ok installed python3-freetype python3-freetype 2.5.1-1 install ok installed python3-fs python3-fs 2.4.16-6 install ok installed python3-griddataformats python3-griddataformats 1.0.2-2 install ok installed python3-idna python3-idna 3.10-1 install ok installed python3-joblib python3-joblib 1.4.2-2 install ok installed python3-kiwisolver python3-kiwisolver 1.4.7-3 install ok installed python3-looseversion python3-looseversion 1.3.0-3 install ok installed python3-lxml:amd64 python3-lxml 5.3.1-1 install ok installed python3-lz4 python3-lz4 4.4.0+dfsg-1 install ok installed python3-matplotlib python3-matplotlib 3.8.3-3+b3 install ok installed python3-mda-xdrlib python3-mda-xdrlib 0.2.0-3 install ok installed python3-mdanalysis python3-mdanalysis 2.8.0-4 install ok installed python3-minimal python3-minimal 3.13.1-2 install ok installed python3-mmtf python3-mmtf 1.1.3-1 install ok installed python3-monotonic python3-monotonic 1.6-3 install ok installed python3-mpmath python3-mpmath 1.3.0-1 install ok installed python3-mrcfile python3-mrcfile 1.5.4-2 install ok installed python3-msgpack python3-msgpack 1.0.3-3+b3 install ok installed python3-numpy python3-numpy 1:2.2.3+ds-2 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.3+ds-2 install ok installed python3-packaging python3-packaging 24.2-1 install ok installed python3-pil:amd64 python3-pil 11.1.0-5 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 11.1.0-5 install ok installed python3-platformdirs python3-platformdirs 4.3.6-1 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-pytz python3-pytz 2025.1-3 install ok installed python3-reportlab python3-reportlab 4.3.1-1 install ok installed python3-requests python3-requests 2.32.3+dfsg-4 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-scipy python3-scipy 1.14.1-4 install ok installed python3-sympy python3-sympy 1.13.3-3 install ok installed python3-threadpoolctl python3-threadpoolctl 3.1.0-1 install ok installed python3-tk:amd64 python3-tk 3.13.1-1 install ok installed python3-tqdm python3-tqdm 4.67.1-2 install ok installed python3-tz python3-tz 2025.1-3 install ok installed python3-ufolib2 python3-ufolib2 0.17.0+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b3 install ok installed python3-urllib3 python3-urllib3 2.3.0-1 install ok installed python3.12-tk python3.12-tk 3.12.9-1 install ok installed python3.13 python3.13 3.13.2-1 install ok installed python3.13-minimal python3.13-minimal 3.13.2-1 install ok installed python3.13-tk python3.13-tk 3.13.2-1 install ok installed readline-common readline-common 8.2-6 install ok installed sed sed 4.9-2 install ok installed sgml-base sgml-base 1.31 install ok installed sphinx-rtd-theme-common sphinx-rtd-theme-common 3.0.2+dfsg-2 install ok installed sqv sqv 1.2.1-6+b1 install ok installed sysvinit-utils sysvinit-utils 3.14-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed tzdata tzdata 2025a-2 install ok installed unicode-data unicode-data 15.1.0-1 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.4-4 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+24 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+7 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 1m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', 'remove', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libopenjp2-7:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0: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-attr', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-citeproc', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-duecredit', 'python3-fasteners', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-griddataformats', 'python3-idna', 'python3-joblib', 'python3-kiwisolver', 'python3-looseversion', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-mda-xdrlib', 'python3-minimal', 'python3-mmtf', 'python3-monotonic', 'python3-mpmath', 'python3-mrcfile', 'python3-msgpack', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-platformdirs', 'python3-pyparsing', 'python3-pytz', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-scipy', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tqdm', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3.12-tk', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'readline-common', 'sgml-base', 'sphinx-rtd-theme-common', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'python3-mdanalysis'] 2m30.8s 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 fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libdeflate0 libexpat1 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgfortran5 libglib2.0-0t64 libgomp1 libgpg-error0 libgraphite2-3 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libncursesw6 libopenjp2-7 libpixman-1-0 libpng16-16t64 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 libsharpyuv0 libsqlite3-0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 media-types netbase openssl procps python-matplotlib-data python3 python3-attr python3-biopython python3-brotli python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-citeproc python3-contourpy python3-cycler python3-dateutil python3-decorator python3-duecredit python3-fasteners python3-fonttools python3-freetype python3-fs python3-griddataformats python3-idna python3-joblib python3-kiwisolver python3-looseversion python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib python3-mdanalysis python3-minimal python3-mmtf python3-monotonic python3-mpmath python3-mrcfile python3-msgpack python3-numpy python3-numpy-dev python3-packaging python3-pil python3-pil.imagetk python3-platformdirs python3-pyparsing python3-pytz python3-reportlab python3-requests python3-rlpycairo python3-scipy python3-sympy python3-threadpoolctl python3-tk python3-tqdm python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3.12-tk python3.13 python3.13-minimal python3.13-tk readline-common sgml-base sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 144 to remove and 0 not upgraded. After this operation, 508 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 ... 18552 files and directories currently installed.) Removing python3-mdanalysis (2.8.0-4) ... Removing python3-biopython (1.85+dfsg-2) ... Removing python3-reportlab (4.3.1-1) ... Removing python3-matplotlib (3.8.3-3+b3) ... Removing python3-pil.imagetk:amd64 (11.1.0-5) ... Removing python3-pil:amd64 (11.1.0-5) ... Removing python3-tk:amd64 (3.13.1-1) ... Removing blt (2.5.3+dfsg-7) ... Removing python3-duecredit (0.10.2-2) ... Removing python3-requests (2.32.3+dfsg-4) ... Removing python3-certifi (2025.1.31+ds-1) ... Removing ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing python3.13-tk (3.13.2-1) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.26.1-2+b1) ... Removing libcairo2:amd64 (1.18.2-2) ... Removing python-matplotlib-data (3.8.3-3) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing python3-griddataformats (1.0.2-2) ... Removing python3-mrcfile (1.5.4-2) ... Removing sphinx-rtd-theme-common (3.0.2+dfsg-2) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing fonts-lato (2.015-1) ... Removing fonts-lyx (2.4.3-1) ... Removing libraqm0:amd64 (0.10.2-1) ... Removing libharfbuzz0b:amd64 (10.2.0-1) ... Removing libglib2.0-0t64:amd64 (2.83.4-1) ... Removing libatomic1:amd64 (14.2.0-17) ... Removing python3-mmtf (1.1.3-1) ... Removing python3-contourpy (1.3.1-1) ... Removing python3-freetype (2.5.1-1) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.23-1+b1) ... Removing python3-tqdm (4.67.1-2) ... Removing python3-msgpack (1.0.3-3+b3) ... Removing libfribidi0:amd64 (1.0.16-1) ... Removing python3-citeproc (0.7.0-1) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libgomp1:amd64 (14.2.0-17) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3.1) ... Removing libjs-sphinxdoc (8.1.3-5) ... 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 python3-joblib (1.4.2-2) ... Removing procps (2:4.0.4-7) ... Removing libopenjp2-7:amd64 (2.5.3-1) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libproc2-0:amd64 (2:4.0.4-7) ... Removing libqhull-r8.0:amd64 (2020.2-6+b2) ... Removing libwebpmux3:amd64 (1.5.0-0.1) ... Removing libwebpdemux2:amd64 (1.5.0-0.1) ... Removing libwebp7:amd64 (1.5.0-0.1) ... Removing libsharpyuv0:amd64 (1.5.0-0.1) ... Removing python3.12-tk (3.12.9-1) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing openssl (3.4.1-1) ... Removing python3-chardet (5.2.0+dfsg-2) ... Removing python3-charset-normalizer (3.4.1-1) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-3) ... Removing python3-fasteners (0.18-2) ... Removing python3-idna (3.10-1) ... Removing python3-kiwisolver (1.4.7-3) ... Removing python3-looseversion (1.3.0-3) ... Removing python3-mda-xdrlib (0.2.0-3) ... Removing python3-monotonic (1.6-3) ... Removing python3-packaging (24.2-1) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-threadpoolctl (3.1.0-1) ... Removing python3-urllib3 (2.3.0-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing libtk8.6:amd64 (8.6.16-1) ... Removing libxft2:amd64 (2.3.6-1+b4) ... Removing libfontconfig1:amd64 (2.15.0-2) ... Removing fontconfig-config (2.15.0-2) ... Removing fonts-urw-base35 (20200910-8) ... Removing xfonts-utils (1:7.7+7) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing libfontenc1:amd64 (1:1.1.8-1+b2) ... Removing libpng16-16t64:amd64 (1.6.47-1) ... Removing libtcl8.6:amd64 (8.6.16+dfsg-1) ... Removing libxss1:amd64 (1:1.2.3-1+b3) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b4) ... Removing libxext6:amd64 (2:1.3.4-1+b3) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+24) ... 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 (1:1.1.5-1) ... Removing python3-ufolib2 (0.17.0+dfsg1-1) ... Removing python3-attr (25.1.0-1) ... Removing python3-fonttools (4.55.3-2) ... Removing python3-scipy (1.14.1-4) ... Removing python3-numpy (1:2.2.3+ds-2) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Removing liblapack3:amd64 (3.12.1-2) ... Removing libblas3:amd64 (3.12.1-2) ... Removing python3-unicodedata2 (15.1.0+ds-1+b3) ... Removing python3-sympy (1.13.3-3) ... Removing python3-lxml:amd64 (5.3.1-1) ... Removing libxslt1.1:amd64 (1.1.35-1.1+b1) ... Removing libgcrypt20:amd64 (1.11.0-7) ... Removing libgfortran5:amd64 (14.2.0-17) ... Removing libgpg-error0:amd64 (1.51-3) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Removing libicu72:amd64 (72.1-6) ... Removing python3-brotli (1.1.0-2+b6) ... Removing python3-decorator (5.1.1-5) ... Removing python3-fs (2.4.16-6) ... Removing python3-lz4 (4.4.0+dfsg-1) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-numpy-dev:amd64 (1:2.2.3+ds-2) ... Removing python3-platformdirs (4.3.6-1) ... Removing python3-tz (2025.1-3) ... Removing python3-pytz (2025.1-3) ... Removing unicode-data (15.1.0-1) ... Removing python3 (3.13.1-2) ... Removing python3.13 (3.13.2-1) ... Removing python3-minimal (3.13.1-2) ... Removing python3.13-minimal (3.13.2-1) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libpython3-stdlib:amd64 (3.13.1-2) ... Removing libpython3.13-stdlib:amd64 (3.13.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libffi8:amd64 (3.4.7-1) ... Removing libncursesw6:amd64 (6.5+20250216-1) ... Removing libpython3.13-minimal:amd64 (3.13.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-6) ... 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 media-types (12.0.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.40-7) ... 2m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', 'remove', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libopenjp2-7:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0: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-attr', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-citeproc', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-duecredit', 'python3-fasteners', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-griddataformats', 'python3-idna', 'python3-joblib', 'python3-kiwisolver', 'python3-looseversion', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-mda-xdrlib', 'python3-minimal', 'python3-mmtf', 'python3-monotonic', 'python3-mpmath', 'python3-mrcfile', 'python3-msgpack', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-platformdirs', 'python3-pyparsing', 'python3-pytz', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-scipy', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tqdm', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3.12-tk', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'readline-common', 'sgml-base', 'sphinx-rtd-theme-common', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'python3-mdanalysis'] 2m30.8s INFO: Running scripts post_remove 2m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_remove_exceptions'] 2m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_remove_exceptions'] 2m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libopenjp2-7:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0: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-attr', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-citeproc', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-duecredit', 'python3-fasteners', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-griddataformats', 'python3-idna', 'python3-joblib', 'python3-kiwisolver', 'python3-looseversion', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-mda-xdrlib', 'python3-minimal', 'python3-mmtf', 'python3-monotonic', 'python3-mpmath', 'python3-mrcfile', 'python3-msgpack', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-platformdirs', 'python3-pyparsing', 'python3-pytz', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-scipy', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tqdm', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3.12-tk', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'readline-common', 'sgml-base', 'sphinx-rtd-theme-common', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 2m31.2s DUMP: dpkg: warning: ignoring request to remove blt which isn't installed (Reading database ... 5133 files and directories currently installed.) Purging configuration files for ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fontconfig-config (2.15.0-2) ... 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 Purging configuration files for fonts-urw-base35 (20200910-8) ... 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 libcairo2 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 libffi8 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 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 libgcrypt20 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.83.4-1) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgpg-error0 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed 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 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 libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 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 libpython3.13-minimal:amd64 (3.13.2-1) ... dpkg: warning: ignoring request to remove libpython3.13-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 (8.2-6) ... 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 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 libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 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 (12.0.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.4.1-1) ... Purging configuration files for procps (2:4.0.4-7) ... Purging configuration files for python-matplotlib-data (3.8.3-3) ... Purging configuration files for python3 (3.13.1-2) ... dpkg: warning: ignoring request to remove python3-attr which isn't installed dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-brotli which isn't installed dpkg: warning: ignoring request to remove python3-cairo 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-freetype 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-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-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 Purging configuration files for python3-numpy (1:2.2.3+ds-2) ... dpkg: warning: ignoring request to remove python3-numpy-dev 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-platformdirs which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pytz which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-requests which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed Purging configuration files for python3-sympy (1.13.3-3) ... 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-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-tk which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.2-1) ... dpkg: warning: ignoring request to remove python3.13-tk which isn't installed Purging configuration files for readline-common (8.2-6) ... Purging configuration files for sgml-base (1.31) ... 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 w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+24) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+7) ... Purging configuration files for xml-core (0.19) ... 2m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libopenjp2-7:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0: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-attr', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-citeproc', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-duecredit', 'python3-fasteners', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-griddataformats', 'python3-idna', 'python3-joblib', 'python3-kiwisolver', 'python3-looseversion', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-mda-xdrlib', 'python3-minimal', 'python3-mmtf', 'python3-monotonic', 'python3-mpmath', 'python3-mrcfile', 'python3-msgpack', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-platformdirs', 'python3-pyparsing', 'python3-pytz', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-scipy', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tqdm', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3.12-tk', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'readline-common', 'sgml-base', 'sphinx-rtd-theme-common', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 2m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg', '--purge', 'python3-mdanalysis'] 2m31.3s DUMP: dpkg: warning: ignoring request to remove python3-mdanalysis which isn't installed 2m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg', '--purge', 'python3-mdanalysis'] 2m31.3s INFO: Running scripts post_purge 2m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_purge_exceptions'] 2m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_purge_exceptions'] 2m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg', '--purge', '--pending'] 2m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg', '--purge', '--pending'] 2m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg', '--remove', '--pending'] 2m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg', '--remove', '--pending'] 2m31.3s INFO: Running scripts post_test 2m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_test_exceptions'] 2m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'tmp/scripts/post_test_exceptions'] 2m31.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 2m31.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 2m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg-divert', '--list'] 2m31.8s 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 2m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'dpkg-divert', '--list'] 2m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', 'clean'] 2m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3', 'apt-get', 'clean'] 2m31.8s DEBUG: Recording chroot state 2m32.3s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-urw-base35, 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 2m32.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/shm'] 2m32.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/shm'] 2m32.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/console'] 2m32.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/console'] 2m32.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/ptmx'] 2m32.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/ptmx'] 2m32.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/pts'] 2m32.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/dev/pts'] 2m32.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/proc'] 2m32.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3/proc'] 2m32.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 2m32.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpu3o6eah3'] 2m32.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpu3o6eah3 2m32.8s INFO: PASS: Upgrading between Debian distributions. 2m32.8s INFO: PASS: All tests. 2m32.8s INFO: piuparts run ends. ret=0 End: 2025-02-23 03:36:24 GMT