Start: 2025-02-05 09:09:01 GMT [testing] Package: python3-pdbfixer Source: python-pdbfixer Version: 1.9-6 Installed-Size: 2411 Maintainer: Debian Python Team Architecture: all Depends: python3-pkg-resources, python3-legacy-cgi, python3-numpy, python3-openmm, python3:any Description: Fix problems in Protein Data Bank files (Python 3) Homepage: https://github.com/openmm/pdbfixer Description-md5: de2ea7573d40aeeb33dde41eadef7ef0 Section: python Priority: optional Filename: pool/main/p/python-pdbfixer/python3-pdbfixer_1.9-6_all.deb Size: 434416 MD5sum: 8a5922ca53974f8063935c22c8afd9d8 SHA256: 090674a5f9ee8c5a1d770fa67153b5b30ace4900220185b65b1af2561edb75a2 [sid] Package: python3-pdbfixer Source: python-pdbfixer Version: 1.9-7 Installed-Size: 2411 Maintainer: Debian Python Team Architecture: all Depends: python3-legacy-cgi, python3-numpy, python3-openmm, python3:any Description: Fix problems in Protein Data Bank files (Python 3) Homepage: https://github.com/openmm/pdbfixer Description-md5: de2ea7573d40aeeb33dde41eadef7ef0 Section: python Priority: optional Filename: pool/main/p/python-pdbfixer/python3-pdbfixer_1.9-7_all.deb Size: 435260 MD5sum: ab31bbdda8207c89271ce414c5746e4f SHA256: 97d7b555accd80b97cc857b46bc1474f9af7997c41d00c8db60818b007917882 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-pdbfixer=1.9-7 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-pdbfixer=1.9-7 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/tmpb_q2w9ig 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpb_q2w9ig 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', '--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/tmpb_q2w9ig', '--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/tmpb_q2w9ig/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/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/tmpb_q2w9ig/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/shm'] 0m0.3s 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/tmpb_q2w9ig/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', 'update'] 0m2.5s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [175 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9424 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6319 kB] Fetched 15.9 MB in 1s (12.2 MB/s) Reading package lists... 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', 'update'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', '-yf', 'dist-upgrade'] 0m6.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: apt bsdutils dpkg libapt-pkg6.0t64 libblkid1 liblz4-1 libmount1 libpam-modules libpam-modules-bin libpam-runtime libpam0g libselinux1 libsemanage-common libsemanage2 libsmartcols1 libuuid1 login mount util-linux 19 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6974 kB of archives. After this operation, 327 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.40.4-2 [106 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 liblz4-1 amd64 1.10.0-3 [63.8 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libapt-pkg6.0t64 amd64 2.9.26 [1115 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 dpkg amd64 1.22.14 [1537 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libuuid1 amd64 2.40.4-2 [36.3 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.40.4-2 [169 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libmount1 amd64 2.40.4-2 [199 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libsmartcols1 amd64 2.40.4-2 [140 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 util-linux amd64 2.40.4-2 [1213 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 mount amd64 2.40.4-2 [155 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libselinux1 amd64 3.7-3.1 [76.8 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.26 [1433 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libpam0g amd64 1.7.0-2 [69.8 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libpam-modules-bin amd64 1.7.0-2 [48.8 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libpam-modules amd64 1.7.0-2 [177 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libpam-runtime all 1.7.0-2 [248 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 login amd64 1:4.16.0-2+really2.40.4-2 [88.4 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libsemanage-common all 3.7-2.1 [7208 B] Get:19 http://deb.debian.org/debian trixie/main amd64 libsemanage2 amd64 3.7-2.1 [91.2 kB] Preconfiguring packages ... Fetched 6974 kB in 0s (74.0 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 ... 5029 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.4-2_amd64.deb ... Unpacking bsdutils (1:2.40.4-2) over (1:2.40.4-1) ... Setting up bsdutils (1:2.40.4-2) ... (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 ... 5029 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.10.0-3_amd64.deb ... Unpacking liblz4-1:amd64 (1.10.0-3) over (1.9.4-4) ... Setting up liblz4-1:amd64 (1.10.0-3) ... (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 ... 5029 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.26_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.26) over (2.9.23) ... Setting up libapt-pkg6.0t64:amd64 (2.9.26) ... (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 ... 5029 files and directories currently installed.) Preparing to unpack .../dpkg_1.22.14_amd64.deb ... Unpacking dpkg (1.22.14) over (1.22.11) ... Setting up dpkg (1.22.14) ... (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 ... 5028 files and directories currently installed.) Preparing to unpack .../libuuid1_2.40.4-2_amd64.deb ... Unpacking libuuid1:amd64 (2.40.4-2) over (2.40.4-1) ... Setting up libuuid1:amd64 (2.40.4-2) ... (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 ... 5028 files and directories currently installed.) Preparing to unpack .../libblkid1_2.40.4-2_amd64.deb ... Unpacking libblkid1:amd64 (2.40.4-2) over (2.40.4-1) ... Setting up libblkid1:amd64 (2.40.4-2) ... (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 ... 5028 files and directories currently installed.) Preparing to unpack .../libmount1_2.40.4-2_amd64.deb ... Unpacking libmount1:amd64 (2.40.4-2) over (2.40.4-1) ... Setting up libmount1:amd64 (2.40.4-2) ... (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 ... 5028 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40.4-2_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40.4-2) over (2.40.4-1) ... Setting up libsmartcols1:amd64 (2.40.4-2) ... (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 ... 5028 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.4-2_amd64.deb ... Unpacking util-linux (2.40.4-2) over (2.40.4-1) ... Setting up util-linux (2.40.4-2) ... (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 ... 5028 files and directories currently installed.) Preparing to unpack .../mount_2.40.4-2_amd64.deb ... Unpacking mount (2.40.4-2) over (2.40.4-1) ... Preparing to unpack .../libselinux1_3.7-3.1_amd64.deb ... Unpacking libselinux1:amd64 (3.7-3.1) over (3.7-3+b1) ... Setting up libselinux1:amd64 (3.7-3.1) ... (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 ... 5027 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.26_amd64.deb ... Unpacking apt (2.9.26) over (2.9.23) ... Setting up apt (2.9.26) ... (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 ... 5027 files and directories currently installed.) Preparing to unpack .../libpam0g_1.7.0-2_amd64.deb ... Unpacking libpam0g:amd64 (1.7.0-2) over (1.5.3-7+b1) ... Setting up libpam0g:amd64 (1.7.0-2) ... (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 .../libpam-modules-bin_1.7.0-2_amd64.deb ... Unpacking libpam-modules-bin (1.7.0-2) over (1.5.3-7+b1) ... Setting up libpam-modules-bin (1.7.0-2) ... (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 ... 5017 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.7.0-2_amd64.deb ... Unpacking libpam-modules:amd64 (1.7.0-2) over (1.5.3-7+b1) ... Setting up libpam-modules:amd64 (1.7.0-2) ... Installing new version of config file /etc/security/access.conf ... Installing new version of config file /etc/security/namespace.init ... Installing new version of config file /etc/security/pwhistory.conf ... (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 ... 4965 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.7.0-2_all.deb ... Unpacking libpam-runtime (1.7.0-2) over (1.5.3-7) ... Setting up libpam-runtime (1.7.0-2) ... (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 .../login_1%3a4.16.0-2+really2.40.4-2_amd64.deb ... Unpacking login (1:4.16.0-2+really2.40.4-2) over (1:4.16.0-2+really2.40.4-1) ... Preparing to unpack .../libsemanage-common_3.7-2.1_all.deb ... Unpacking libsemanage-common (3.7-2.1) over (3.7-2) ... Preparing to unpack .../libsemanage2_3.7-2.1_amd64.deb ... Unpacking libsemanage2:amd64 (3.7-2.1) over (3.7-2+b1) ... Setting up libsemanage-common (3.7-2.1) ... Setting up mount (2.40.4-2) ... Setting up libsemanage2:amd64 (3.7-2.1) ... Setting up login (1:4.16.0-2+really2.40.4-2) ... Processing triggers for libc-bin (2.40-6) ... 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', '-yf', 'dist-upgrade'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.3s DUMP: 3e49d7583483f29ad4fb946dfd7db203 - 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.3s INFO: Running scripts post_setup 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_setup_dummy_users'] 0m8.2s 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 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_setup_dummy_users'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_setup_forbid_home'] 0m8.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_setup_forbid_home'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.2s 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' 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_setup_minimize'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_setup_minimize'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_setup_zz_backports'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_setup_zz_backports'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.3s DUMP: install ok installed apt apt 2.9.26 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 1:2.40.4-2 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-11 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 1.22.14 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 14.2.0-12 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 2.9.26 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 2.40.4-2 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 2.40-6 install ok installed libc6:amd64 libc6 2.40-6 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 14.2.0-12 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 2.40.4-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-2 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-2 install ok installed libpam-runtime libpam-runtime 1.7.0-2 install ok installed libpam0g:amd64 libpam0g 1.7.0-2 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 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-2 install ok installed libss2:amd64 libss2 1.47.2-1 install ok installed libssl3t64:amd64 libssl3t64 3.4.0-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-12 install ok installed libsystemd0:amd64 libsystemd0 257.2-3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257.2-3 install ok installed libuuid1:amd64 libuuid1 2.40.4-2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed login login 1:4.16.0-2+really2.40.4-2 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.4-2 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.0-2 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl-base perl-base 5.40.0-8 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.2.1-5 install ok installed sysvinit-utils sysvinit-utils 3.13-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2024b-6 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.4-2 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m8.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m8.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m8.5s INFO: Running scripts is_testable 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/is_testable_uninstallable'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/is_testable_uninstallable'] 0m8.5s INFO: Running scripts pre_test 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_test_exceptions'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_test_exceptions'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_test_root_password'] 0m8.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_test_root_password'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'show', '--no-all-versions', 'python3-pdbfixer'] 0m8.8s DUMP: Package: python3-pdbfixer Source: python-pdbfixer Version: 1.9-6 Installed-Size: 2411 Maintainer: Debian Python Team Architecture: all Depends: python3-pkg-resources, python3-legacy-cgi, python3-numpy, python3-openmm, python3:any Description-en: Fix problems in Protein Data Bank files (Python 3) PDBFixer is an application for fixing problems in Protein Data Bank files in preparation for simulating them. It can automatically fix the following problems: . - Add missing heavy atoms. - Add missing hydrogen atoms. - Build missing loops. - Convert non-standard residues to their standard equivalents. - Select a single position for atoms with multiple alternate positions listed. - Delete unwanted chains from the model. - Delete unwanted heterogens. - Build a water box for explicit solvent simulations. Description-md5: de2ea7573d40aeeb33dde41eadef7ef0 Homepage: https://github.com/openmm/pdbfixer Section: python Priority: optional Filename: pool/main/p/python-pdbfixer/python3-pdbfixer_1.9-6_all.deb Size: 434416 MD5sum: 8a5922ca53974f8063935c22c8afd9d8 SHA256: 090674a5f9ee8c5a1d770fa67153b5b30ace4900220185b65b1af2561edb75a2 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'show', '--no-all-versions', 'python3-pdbfixer'] 0m8.8s INFO: apt-cache knows about the following packages: python3-pdbfixer 0m8.8s INFO: Running scripts pre_install 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_database-server'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_database-server'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_exceptions'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_exceptions'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_extras'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_extras'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'policy'] 0m9.0s 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: 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'policy'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'policy', 'python3-pdbfixer'] 0m9.0s DUMP: python3-pdbfixer: Installed: (none) Candidate: 1.9-6 Version table: 1.9-6 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'policy', 'python3-pdbfixer'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', '-y', 'install', 'python3-pdbfixer'] 0m18.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libblas3 libexpat1 libffi8 libgfortran5 liblapack3 libncursesw6 libopenmm-dev libopenmm8.1 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsqlite3-0 media-types netbase python3 python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-legacy-cgi python3-minimal python3-more-itertools python3-numpy python3-openmm python3-pkg-resources python3-typeguard python3-typing-extensions python3.13 python3.13-minimal readline-common Suggested packages: python3-doc python3-tk python3-venv gcc gfortran python-numpy-doc python3-dev python3-pytest python3-setuptools python3.13-venv python3.13-doc binutils binfmt-support readline-doc Recommended packages: libgpm2 ca-certificates The following NEW packages will be installed: libblas3 libexpat1 libffi8 libgfortran5 liblapack3 libncursesw6 libopenmm-dev libopenmm8.1 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsqlite3-0 media-types netbase python3 python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-legacy-cgi python3-minimal python3-more-itertools python3-numpy python3-openmm python3-pdbfixer python3-pkg-resources python3-typeguard python3-typing-extensions python3.13 python3.13-minimal readline-common 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 24.6 MB of archives. After this operation, 172 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.1-3+b1 [859 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.1-3+b1 [2203 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.1-3+b1 [1973 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.1-3+b1 [740 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get:15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-12 [836 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-2 [1059 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libopenmm-dev amd64 8.1.2+dfsg-2 [345 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:27 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 python3-legacy-cgi all 2.6.1-2 [16.1 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [4736 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 python3-openmm amd64 8.1.2+dfsg-2 [6798 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 python3-pdbfixer all 1.9-6 [434 kB] Fetched 24.6 MB in 0s (121 MB/s) Selecting previously unselected package libpython3.13-minimal: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 ... 5029 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.1-3+b1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.1-3+b1) ... 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_3.13.1-3+b1_amd64.deb ... Unpacking python3.13-minimal (3.13.1-3+b1) ... Setting up libpython3.13-minimal:amd64 (3.13.1-3+b1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.1-3+b1) ... 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 ... 5365 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_3.4.6-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.6-1) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../04-libncursesw6_6.5-2+b1_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2+b1) ... 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_3.13.1-3+b1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.1-3+b1) ... Selecting previously unselected package python3.13. Preparing to unpack .../09-python3.13_3.13.1-3+b1_amd64.deb ... Unpacking python3.13 (3.13.1-3+b1) ... 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 ... 5878 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.1-2_amd64.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../01-libblas3_3.12.0-4_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-4) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../02-libgfortran5_14.2.0-12_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-12) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../03-liblapack3_3.12.0-4_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-4) ... Selecting previously unselected package libopenmm8.1. Preparing to unpack .../04-libopenmm8.1_8.1.2+dfsg-2_amd64.deb ... Unpacking libopenmm8.1 (8.1.2+dfsg-2) ... Selecting previously unselected package libopenmm-dev. Preparing to unpack .../05-libopenmm-dev_8.1.2+dfsg-2_amd64.deb ... Unpacking libopenmm-dev (8.1.2+dfsg-2) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../06-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../07-python3-more-itertools_10.6.0-1_all.deb ... Unpacking python3-more-itertools (10.6.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../08-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../09-python3-typeguard_4.4.1-1_all.deb ... Unpacking python3-typeguard (4.4.1-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../10-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../11-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../12-python3-jaraco.functools_4.1.0-1_all.deb ... Unpacking python3-jaraco.functools (4.1.0-1) ... Selecting previously unselected package python3-legacy-cgi. Preparing to unpack .../13-python3-legacy-cgi_2.6.1-2_all.deb ... Unpacking python3-legacy-cgi (2.6.1-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../14-python3-numpy_1%3a1.26.4+ds-13_amd64.deb ... Unpacking python3-numpy (1:1.26.4+ds-13) ... Selecting previously unselected package python3-openmm. Preparing to unpack .../15-python3-openmm_8.1.2+dfsg-2_amd64.deb ... Unpacking python3-openmm (8.1.2+dfsg-2) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../16-python3-pkg-resources_75.6.0-1_all.deb ... Unpacking python3-pkg-resources (75.6.0-1) ... Selecting previously unselected package python3-pdbfixer. Preparing to unpack .../17-python3-pdbfixer_1.9-6_all.deb ... Unpacking python3-pdbfixer (1.9-6) ... Setting up media-types (10.1.0) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libblas3:amd64 (3.12.0-4) ... 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 libncursesw6:amd64 (6.5-2+b1) ... Setting up libgfortran5:amd64 (14.2.0-12) ... Setting up libffi8:amd64 (3.4.6-1) ... Setting up netbase (6.4) ... Setting up libopenmm8.1 (8.1.2+dfsg-2) ... Setting up readline-common (8.2-6) ... Setting up liblapack3:amd64 (3.12.0-4) ... 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 libopenmm-dev (8.1.2+dfsg-2) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-3+b1) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up python3.13 (3.13.1-3+b1) ... Setting up python3 (3.13.1-2) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:1.26.4+ds-13) ... Setting up python3-legacy-cgi (2.6.1-2) ... Setting up python3-openmm (8.1.2+dfsg-2) ... /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' """ Tokenizer method for the mmCIF syntax file - /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' pattern = re.compile('bias_(.*)_(.*)\.npy') /usr/lib/python3/dist-packages/openmm/openmm.py:1556: SyntaxWarning: invalid escape sequence '\S' match = re.search("<([^?]\S*)", inputString) Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-pdbfixer (1.9-6) ... Processing triggers for libc-bin (2.40-6) ... 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', '-y', 'install', 'python3-pdbfixer'] 0m18.5s INFO: Running scripts post_install 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_install_exceptions'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_install_exceptions'] 0m18.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m19.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m19.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpb_q2w9ig to sid 0m19.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m19.1s INFO: Running scripts pre_distupgrade 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_distupgrade_exceptions'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_distupgrade_exceptions'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', 'update'] 0m22.0s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7346 kB] Fetched 17.6 MB in 2s (8514 kB/s) Reading package lists... 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', 'update'] 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', '-yf', 'dist-upgrade'] 0m32.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-more-itertools python3-pkg-resources python3-typeguard python3-typing-extensions Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: python3-numpy-dev The following packages will be upgraded: apt bsdutils dash dpkg gcc-14-base libapt-pkg6.0t64 libblas3 libblkid1 libgcc-s1 libgfortran5 liblapack3 libmount1 libncursesw6 libopenmm-dev libopenmm8.1 libpython3.13-minimal libpython3.13-stdlib libselinux1 libsmartcols1 libstdc++6 libtinfo6 libuuid1 libxxhash0 login mawk mount ncurses-base ncurses-bin python3-numpy python3-openmm python3-pdbfixer python3.13 python3.13-minimal tzdata util-linux 35 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 34.3 MB of archives. After this operation, 7657 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.4-3 [106 kB] Get:2 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-12 [98.5 kB] Get:3 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-16 [48.9 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-16 [72.8 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-16 [713 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.3-2 [27.1 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.27 [1120 kB] Get:9 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.15 [1537 kB] Get:10 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.5+20250125-2 [438 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.4-3 [36.3 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.4-3 [169 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.4-3 [200 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.4-3 [140 kB] Get:15 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.4-3 [1214 kB] Get:16 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.4-3 [155 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.7-4 [77.1 kB] Get:18 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.27 [1440 kB] Get:19 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.5+20250125-2 [273 kB] Get:20 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.4-3 [88.5 kB] Get:21 http://deb.debian.org/debian sid/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get:23 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get:25 http://deb.debian.org/debian sid/main amd64 tzdata all 2025a-1 [259 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5+20250125-2 [135 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.5+20250125-2 [348 kB] Get:28 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20250131-1 [141 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:30 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libopenmm-dev amd64 8.1.2+dfsg-3 [345 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-3 [1058 kB] Get:33 http://deb.debian.org/debian sid/main amd64 python3-openmm amd64 8.1.2+dfsg-3 [6782 kB] Get:34 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:2.2.2+ds-2 [7507 kB] Get:35 http://deb.debian.org/debian sid/main amd64 python3-numpy-dev amd64 1:2.2.2+ds-2 [138 kB] Get:36 http://deb.debian.org/debian sid/main amd64 python3-pdbfixer all 1.9-7 [435 kB] Preconfiguring packages ... Fetched 34.3 MB in 0s (183 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 ... 7675 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.4-3_amd64.deb ... Unpacking bsdutils (1:2.40.4-3) over (1:2.40.4-2) ... Setting up bsdutils (1:2.40.4-3) ... (Reading database ... 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Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) over (3.13.1-3+b1) ... Preparing to unpack .../3-python3.13-minimal_3.13.2-1_amd64.deb ... Unpacking python3.13-minimal (3.13.2-1) over (3.13.1-3+b1) ... Preparing to unpack .../4-libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) over (3.13.1-3+b1) ... Preparing to unpack .../5-tzdata_2025a-1_all.deb ... Unpacking tzdata (2025a-1) over (2024b-6) ... Preparing to unpack .../6-libncursesw6_6.5+20250125-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.5+20250125-2) over (6.5-2+b1) ... Preparing to unpack .../7-libtinfo6_6.5+20250125-2_amd64.deb ... Unpacking libtinfo6:amd64 (6.5+20250125-2) over (6.5-2+b1) ... Setting up libtinfo6:amd64 (6.5+20250125-2) ... (Reading database ... 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Preparing to unpack .../3-libopenmm-dev_8.1.2+dfsg-3_amd64.deb ... Unpacking libopenmm-dev (8.1.2+dfsg-3) over (8.1.2+dfsg-2) ... Preparing to unpack .../4-libopenmm8.1_8.1.2+dfsg-3_amd64.deb ... Unpacking libopenmm8.1 (8.1.2+dfsg-3) over (8.1.2+dfsg-2) ... Preparing to unpack .../5-python3-openmm_8.1.2+dfsg-3_amd64.deb ... Unpacking python3-openmm (8.1.2+dfsg-3) over (8.1.2+dfsg-2) ... Preparing to unpack .../6-python3-numpy_1%3a2.2.2+ds-2_amd64.deb ... Unpacking python3-numpy (1:2.2.2+ds-2) over (1:1.26.4+ds-13) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../7-python3-numpy-dev_1%3a2.2.2+ds-2_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.2.2+ds-2) ... Preparing to unpack .../8-python3-pdbfixer_1.9-7_all.deb ... Unpacking python3-pdbfixer (1.9-7) over (1.9-6) ... Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Feb 5 09:09:29 UTC 2025. Universal Time is now: Wed Feb 5 09:09:29 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:amd64 (3.13.2-1) ... Setting up libblas3:amd64 (3.12.1-2) ... Setting up python3-numpy-dev:amd64 (1:2.2.2+ds-2) ... Setting up libncursesw6:amd64 (6.5+20250125-2) ... Setting up libgfortran5:amd64 (14.2.0-16) ... Setting up mount (2.40.4-3) ... Setting up python3.13-minimal (3.13.2-1) ... Setting up mawk (1.3.4.20250131-1) ... Setting up libopenmm8.1 (8.1.2+dfsg-3) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up login (1:4.16.0-2+really2.40.4-3) ... Setting up liblapack3:amd64 (3.12.1-2) ... Setting up python3.13 (3.13.2-1) ... Setting up libopenmm-dev (8.1.2+dfsg-3) ... Setting up python3-numpy (1:2.2.2+ds-2) ... Setting up python3-openmm (8.1.2+dfsg-3) ... /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' """ Tokenizer method for the mmCIF syntax file - /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' pattern = re.compile('bias_(.*)_(.*)\.npy') /usr/lib/python3/dist-packages/openmm/openmm.py:1556: SyntaxWarning: invalid escape sequence '\S' match = re.search("<([^?]\S*)", inputString) Setting up python3-pdbfixer (1.9-7) ... Processing triggers for debianutils (5.21) ... Processing triggers for libc-bin (2.40-6) ... 0m32.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', '-yf', 'dist-upgrade'] 0m32.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m33.7s DUMP: 3e307044ab4e9ac679c0c4835b166cb7 - 0m33.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m33.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'show', '--no-all-versions', 'python3-pdbfixer'] 0m34.0s DUMP: Package: python3-pdbfixer Source: python-pdbfixer Version: 1.9-7 Installed-Size: 2411 Maintainer: Debian Python Team Architecture: all Depends: python3-legacy-cgi, python3-numpy, python3-openmm, python3:any Description-en: Fix problems in Protein Data Bank files (Python 3) PDBFixer is an application for fixing problems in Protein Data Bank files in preparation for simulating them. It can automatically fix the following problems: . - Add missing heavy atoms. - Add missing hydrogen atoms. - Build missing loops. - Convert non-standard residues to their standard equivalents. - Select a single position for atoms with multiple alternate positions listed. - Delete unwanted chains from the model. - Delete unwanted heterogens. - Build a water box for explicit solvent simulations. Description-md5: de2ea7573d40aeeb33dde41eadef7ef0 Homepage: https://github.com/openmm/pdbfixer Section: python Priority: optional Filename: pool/main/p/python-pdbfixer/python3-pdbfixer_1.9-7_all.deb Size: 435260 MD5sum: ab31bbdda8207c89271ce414c5746e4f SHA256: 97d7b555accd80b97cc857b46bc1474f9af7997c41d00c8db60818b007917882 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'show', '--no-all-versions', 'python3-pdbfixer'] 0m34.0s INFO: apt-cache knows about the following packages: python3-pdbfixer 0m34.0s INFO: Running scripts pre_install 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_database-server'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_database-server'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_exceptions'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_exceptions'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_extras'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_extras'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_foreign_architecture'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_foreign_architecture'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'policy'] 0m34.1s 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: 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'policy'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'policy', 'python3-pdbfixer'] 0m34.2s DUMP: python3-pdbfixer: Installed: 1.9-7 Candidate: 1.9-7 Version table: *** 1.9-7 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'policy', 'python3-pdbfixer'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', '-y', 'install', 'python3-pdbfixer'] 0m34.8s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-pdbfixer is already the newest version (1.9-7). The following packages were automatically installed and are no longer required: python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-more-itertools python3-pkg-resources python3-typeguard python3-typing-extensions Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', '-y', 'install', 'python3-pdbfixer'] 0m34.8s INFO: Running scripts post_install 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_install_exceptions'] 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_install_exceptions'] 0m34.8s INFO: Running scripts post_distupgrade 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_distupgrade_exceptions'] 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_distupgrade_exceptions'] 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_distupgrade_zz_backports'] 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_distupgrade_zz_backports'] 0m34.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m35.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m35.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m35.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m35.8s INFO: Running scripts pre_install 0m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_database-server'] 0m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_database-server'] 0m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_exceptions'] 0m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_exceptions'] 0m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_extras'] 0m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_extras'] 0m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_foreign_architecture'] 0m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_foreign_architecture'] 0m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'policy'] 0m35.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m35.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'policy'] 0m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'policy', 'python3-pdbfixer'] 0m36.0s DUMP: python3-pdbfixer: Installed: 1.9-7 Candidate: 1.9-7 Version table: *** 1.9-7 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-cache', 'policy', 'python3-pdbfixer'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', '-y', 'install', 'python3-pdbfixer=1.9-7'] 0m36.4s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-pdbfixer is already the newest version (1.9-7). The following packages were automatically installed and are no longer required: python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-more-itertools python3-pkg-resources python3-typeguard python3-typing-extensions Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m36.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', '-y', 'install', 'python3-pdbfixer=1.9-7'] 0m36.4s INFO: Running scripts post_install 0m36.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_install_exceptions'] 0m36.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_install_exceptions'] 0m36.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m36.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m37.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', '-ac', '--ignore-obsolete'] 0m38.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', '-ac', '--ignore-obsolete'] 0m38.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m38.4s DUMP: 0.15.6 0m38.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m38.4s INFO: Running adequate version 0.15.6 now. 0m38.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'python3-pdbfixer'] 0m38.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'python3-pdbfixer'] 0m38.5s INFO: Running scripts pre_remove 0m38.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m38.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m38.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m38.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m38.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_remove_exceptions'] 0m39.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/pre_remove_exceptions'] 0m39.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m39.3s DUMP: install ok installed apt apt 2.9.27 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 2.9.27 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 libblas3:amd64 libblas3 3.12.1-2 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 2.40-6 install ok installed libc6:amd64 libc6 2.40-6 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 libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-16 install ok installed libgfortran5:amd64 libgfortran5 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 liblapack3:amd64 liblapack3 3.12.1-2 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 libncursesw6:amd64 libncursesw6 6.5+20250125-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libopenmm-dev libopenmm-dev 8.1.2+dfsg-3 install ok installed libopenmm8.1 libopenmm8.1 8.1.2+dfsg-3 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-2 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-2 install ok installed libpam-runtime libpam-runtime 1.7.0-2 install ok installed libpam0g:amd64 libpam0g 1.7.0-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-5 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 libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-4 install ok installed libsemanage-common libsemanage-common 3.7-2.1 install ok installed libsemanage2:amd64 libsemanage2 3.7-2.1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-3 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 3.4.0-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-16 install ok installed libsystemd0:amd64 libsystemd0 257.2-3 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250125-2 install ok installed libudev1:amd64 libudev1 257.2-3 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 1:4.16.0-7 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 10.1.0 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 netbase netbase 6.4 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.0-2 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl-base perl-base 5.40.0-8 install ok installed python3 python3 3.13.1-2 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-legacy-cgi python3-legacy-cgi 2.6.1-2 install ok installed python3-minimal python3-minimal 3.13.1-2 install ok installed python3-more-itertools python3-more-itertools 10.6.0-1 install ok installed python3-numpy python3-numpy 1:2.2.2+ds-2 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.2+ds-2 install ok installed python3-openmm python3-openmm 8.1.2+dfsg-3 install ok installed python3-pdbfixer python3-pdbfixer 1.9-7 install ok installed python3-pkg-resources python3-pkg-resources 75.6.0-1 install ok installed python3-typeguard python3-typeguard 4.4.1-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3.13 python3.13 3.13.2-1 install ok installed python3.13-minimal python3.13-minimal 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 sqv sqv 1.2.1-5 install ok installed sysvinit-utils sysvinit-utils 3.13-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025a-1 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 0m39.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m39.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', 'remove', 'libblas3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libopenmm-dev', 'libopenmm8.1', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'python3', 'python3-autocommand', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-legacy-cgi', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-openmm', 'python3-pkg-resources', 'python3-typeguard', 'python3-typing-extensions', 'python3.13', 'python3.13-minimal', 'readline-common', 'python3-pdbfixer'] 0m41.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libblas3 libexpat1 libffi8 libgfortran5 liblapack3 libncursesw6 libopenmm-dev libopenmm8.1 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsqlite3-0 media-types netbase python3 python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-legacy-cgi python3-minimal python3-more-itertools python3-numpy python3-numpy-dev python3-openmm python3-pdbfixer python3-pkg-resources python3-typeguard python3-typing-extensions python3.13 python3.13-minimal readline-common 0 upgraded, 0 newly installed, 33 to remove and 0 not upgraded. After this operation, 180 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 ... 7728 files and directories currently installed.) Removing python3-pdbfixer (1.9-7) ... Removing python3-openmm (8.1.2+dfsg-3) ... Removing python3-numpy (1:2.2.2+ds-2) ... Removing liblapack3:amd64 (3.12.1-2) ... Removing libblas3:amd64 (3.12.1-2) ... Removing python3-pkg-resources (75.6.0-1) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.1-1) ... Removing python3-typing-extensions (4.12.2-2) ... Removing libgfortran5:amd64 (14.2.0-16) ... Removing libopenmm-dev (8.1.2+dfsg-3) ... Removing libopenmm8.1 (8.1.2+dfsg-3) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-legacy-cgi (2.6.1-2) ... Removing python3-more-itertools (10.6.0-1) ... Removing python3-numpy-dev:amd64 (1:2.2.2+ds-2) ... 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 (3.4.6-1) ... Removing libncursesw6:amd64 (6.5+20250125-2) ... 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 (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.40-6) ... 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', 'remove', 'libblas3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libopenmm-dev', 'libopenmm8.1', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'python3', 'python3-autocommand', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-legacy-cgi', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-openmm', 'python3-pkg-resources', 'python3-typeguard', 'python3-typing-extensions', 'python3.13', 'python3.13-minimal', 'readline-common', 'python3-pdbfixer'] 0m41.5s INFO: Running scripts post_remove 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_remove_exceptions'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_remove_exceptions'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg', '--purge', 'libblas3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libopenmm-dev', 'libopenmm8.1', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'python3', 'python3-autocommand', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-legacy-cgi', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-openmm', 'python3-pkg-resources', 'python3-typeguard', 'python3-typing-extensions', 'python3.13', 'python3.13-minimal', 'readline-common'] 0m41.6s DUMP: dpkg: warning: ignoring request to remove libblas3 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 libgfortran5 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libopenmm-dev which isn't installed dpkg: warning: ignoring request to remove libopenmm8.1 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed (Reading database ... 5033 files and directories currently 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 Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for python3 (3.13.1-2) ... dpkg: warning: ignoring request to remove python3-autocommand which isn't installed dpkg: warning: ignoring request to remove python3-inflect which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.context which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.functools which isn't installed dpkg: warning: ignoring request to remove python3-legacy-cgi which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-numpy-dev which isn't installed dpkg: warning: ignoring request to remove python3-openmm which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.2-1) ... Purging configuration files for readline-common (8.2-6) ... 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg', '--purge', 'libblas3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libopenmm-dev', 'libopenmm8.1', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'python3', 'python3-autocommand', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-legacy-cgi', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-openmm', 'python3-pkg-resources', 'python3-typeguard', 'python3-typing-extensions', 'python3.13', 'python3.13-minimal', 'readline-common'] 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg', '--purge', 'python3-pdbfixer'] 0m41.6s DUMP: dpkg: warning: ignoring request to remove python3-pdbfixer which isn't installed 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg', '--purge', 'python3-pdbfixer'] 0m41.6s INFO: Running scripts post_purge 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_purge_exceptions'] 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_purge_exceptions'] 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg', '--purge', '--pending'] 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg', '--purge', '--pending'] 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg', '--remove', '--pending'] 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg', '--remove', '--pending'] 0m41.6s INFO: Running scripts post_test 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_test_exceptions'] 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'tmp/scripts/post_test_exceptions'] 0m41.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m41.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m41.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg-divert', '--list'] 0m41.9s 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 0m41.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'dpkg-divert', '--list'] 0m41.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', 'clean'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig', 'apt-get', 'clean'] 0m42.0s DEBUG: Recording chroot state 0m42.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/shm'] 0m42.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/shm'] 0m42.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/console'] 0m42.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/console'] 0m42.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/ptmx'] 0m42.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/ptmx'] 0m42.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/pts'] 0m42.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/dev/pts'] 0m42.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/proc'] 0m42.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig/proc'] 0m42.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m42.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpb_q2w9ig'] 0m42.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpb_q2w9ig 0m42.9s INFO: PASS: Upgrading between Debian distributions. 0m42.9s INFO: PASS: All tests. 0m42.9s INFO: piuparts run ends. ret=0 End: 2025-02-05 09:09:44 GMT