Start: 2025-02-12 04:05:38 GMT [testing] Package: macsyfinder Version: 2.1.4-1 Installed-Size: 37593 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-certifi, python3-colorama, python3-colorlog, python3-networkx, python3-packaging, python3-pandas, python3-yaml, python3:any, libjs-jquery (>= 3.6.0), libjs-sphinxdoc (>= 7.4), sphinx-rtd-theme-common (>= 2.0.0+dfsg), hmmer, ncbi-blast+, libjs-underscore Description: detection of macromolecular systems in protein datasets Homepage: https://github.com/gem-pasteur/macsyfinder Built-Using: sphinx (= 7.4.7-3) Description-md5: 0b9b635e7d46ea6cf9f81df42e76fb60 Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.1.4-1_amd64.deb Size: 14541036 MD5sum: 8ca6e392bc129ad572e312caf23ed1e4 SHA256: 478d72d28b8b836e0dd9b9e8b957842fd08ae5ed145834ffd5bf6889c5e7a868 [sid] Package: macsyfinder Source: macsyfinder (2.1.4-1) Version: 2.1.4-1+b1 Installed-Size: 37591 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-certifi, python3-colorama, python3-colorlog, python3-networkx, python3-packaging, python3-pandas, python3-yaml, python3:any, libjs-jquery (>= 3.6.0), libjs-sphinxdoc (>= 8.1), sphinx-rtd-theme-common (>= 3.0.2+dfsg), hmmer, ncbi-blast+, libjs-underscore Description: detection of macromolecular systems in protein datasets Homepage: https://github.com/gem-pasteur/macsyfinder Built-Using: sphinx (= 8.1.3-4) Description-md5: 0b9b635e7d46ea6cf9f81df42e76fb60 Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.1.4-1+b1_amd64.deb Size: 14537052 MD5sum: a6ad2116fdedd14828a0650da0943574 SHA256: 7f080c1503a14120106286a8028b534e8ab4e98585b026dcb0153bf9776095a0 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 macsyfinder=2.1.4-1+b1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt macsyfinder=2.1.4-1+b1 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/tmpjdin93o4 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpjdin93o4 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', '--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/tmpjdin93o4', '--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/tmpjdin93o4/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/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/tmpjdin93o4/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/tmpjdin93o4/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpjdin93o4/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', 'update'] 0m2.3s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [175 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9431 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6316 kB] Fetched 15.9 MB in 1s (14.1 MB/s) Reading package lists... 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', 'update'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', '-yf', 'dist-upgrade'] 0m4.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: bsdutils dpkg gcc-14-base libblkid1 libgcc-s1 libmount1 libsmartcols1 libstdc++6 libtinfo6 libuuid1 login mount ncurses-base ncurses-bin sqv util-linux 16 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6162 kB of archives. After this operation, 46.1 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.40.4-3 [106 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 dpkg amd64 1.22.15 [1537 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 ncurses-bin amd64 6.5+20250125-2 [438 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libuuid1 amd64 2.40.4-3 [36.3 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.40.4-3 [169 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libmount1 amd64 2.40.4-3 [200 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libsmartcols1 amd64 2.40.4-3 [140 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 util-linux amd64 2.40.4-3 [1214 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 mount amd64 2.40.4-3 [155 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 ncurses-base all 6.5+20250125-2 [273 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 login amd64 1:4.16.0-2+really2.40.4-3 [88.5 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 gcc-14-base amd64 14.2.0-16 [48.9 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libstdc++6 amd64 14.2.0-16 [713 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libgcc-s1 amd64 14.2.0-16 [72.8 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libtinfo6 amd64 6.5+20250125-2 [348 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 sqv amd64 1.2.1-6 [623 kB] Fetched 6162 kB in 0s (86.9 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5024 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 ... (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 ... 5024 files and directories currently installed.) Preparing to unpack .../dpkg_1.22.15_amd64.deb ... Unpacking dpkg (1.22.15) over (1.22.14) ... Setting up dpkg (1.22.15) ... (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 ... 5024 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.5+20250125-2_amd64.deb ... Unpacking ncurses-bin (6.5+20250125-2) over (6.5-2+b1) ... Setting up ncurses-bin (6.5+20250125-2) ... (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 ... 5023 files and directories currently installed.) Preparing to unpack .../libuuid1_2.40.4-3_amd64.deb ... Unpacking libuuid1:amd64 (2.40.4-3) over (2.40.4-2) ... Setting up libuuid1:amd64 (2.40.4-3) ... (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 ... 5023 files and directories currently installed.) Preparing to unpack .../libblkid1_2.40.4-3_amd64.deb ... Unpacking libblkid1:amd64 (2.40.4-3) over (2.40.4-2) ... Setting up libblkid1:amd64 (2.40.4-3) ... (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 ... 5023 files and directories currently installed.) Preparing to unpack .../libmount1_2.40.4-3_amd64.deb ... Unpacking libmount1:amd64 (2.40.4-3) over (2.40.4-2) ... Setting up libmount1:amd64 (2.40.4-3) ... (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 ... 5023 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40.4-3_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40.4-3) over (2.40.4-2) ... Setting up libsmartcols1:amd64 (2.40.4-3) ... (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 ... 5023 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.4-3_amd64.deb ... Unpacking util-linux (2.40.4-3) over (2.40.4-2) ... Setting up util-linux (2.40.4-3) ... (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 ... 5023 files and directories currently installed.) Preparing to unpack .../mount_2.40.4-3_amd64.deb ... Unpacking mount (2.40.4-3) over (2.40.4-2) ... Preparing to unpack .../ncurses-base_6.5+20250125-2_all.deb ... Unpacking ncurses-base (6.5+20250125-2) over (6.5-2) ... Setting up ncurses-base (6.5+20250125-2) ... (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 ... 5023 files and directories currently installed.) Preparing to unpack .../login_1%3a4.16.0-2+really2.40.4-3_amd64.deb ... Unpacking login (1:4.16.0-2+really2.40.4-3) over (1:4.16.0-2+really2.40.4-2) ... Preparing to unpack .../gcc-14-base_14.2.0-16_amd64.deb ... Unpacking gcc-14-base:amd64 (14.2.0-16) over (14.2.0-12) ... Setting up gcc-14-base:amd64 (14.2.0-16) ... (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 ... 5023 files and directories currently installed.) Preparing to unpack .../libstdc++6_14.2.0-16_amd64.deb ... Unpacking libstdc++6:amd64 (14.2.0-16) over (14.2.0-12) ... Setting up libstdc++6:amd64 (14.2.0-16) ... (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 ... 5023 files and directories currently installed.) Preparing to unpack .../libgcc-s1_14.2.0-16_amd64.deb ... Unpacking libgcc-s1:amd64 (14.2.0-16) over (14.2.0-12) ... Setting up libgcc-s1:amd64 (14.2.0-16) ... (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 ... 5023 files and directories currently installed.) Preparing to unpack .../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 ... (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 ... 5022 files and directories currently installed.) Preparing to unpack .../archives/sqv_1.2.1-6_amd64.deb ... Unpacking sqv (1.2.1-6) over (1.2.1-5) ... Setting up sqv (1.2.1-6) ... Setting up mount (2.40.4-3) ... Setting up login (1:4.16.0-2+really2.40.4-3) ... Processing triggers for libc-bin (2.40-6) ... 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', '-yf', 'dist-upgrade'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.8s DUMP: 64969b0e2242ea8d60062d268c1e1f3a - 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.8s INFO: Running scripts post_setup 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_setup_dummy_users'] 0m5.3s 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 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_setup_dummy_users'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_setup_forbid_home'] 0m5.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_setup_forbid_home'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.4s 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' 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_setup_minimize'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_setup_minimize'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_setup_zz_backports'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_setup_zz_backports'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.4s 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 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 libext2fs2t64:amd64 libext2fs2t64 1.47.2-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-16 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-3 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.4-3 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-2 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 2.40.4-3 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 mount mount 2.40.4-3 install ok installed ncurses-base ncurses-base 6.5+20250125-2 install ok installed ncurses-bin ncurses-bin 6.5+20250125-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.0-2 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 1.2.1-6 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 2.40.4-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m5.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m5.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m5.8s INFO: Running scripts is_testable 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/is_testable_uninstallable'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/is_testable_uninstallable'] 0m5.8s INFO: Running scripts pre_test 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_test_exceptions'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_test_exceptions'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_test_root_password'] 0m5.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_test_root_password'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m6.0s DUMP: Package: macsyfinder Version: 2.1.4-1 Installed-Size: 37593 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-certifi, python3-colorama, python3-colorlog, python3-networkx, python3-packaging, python3-pandas, python3-yaml, python3:any, libjs-jquery (>= 3.6.0), libjs-sphinxdoc (>= 7.4), sphinx-rtd-theme-common (>= 2.0.0+dfsg), hmmer, ncbi-blast+, libjs-underscore Description-en: detection of macromolecular systems in protein datasets MacSyFinder is a program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems with MacSyFinder to reflect these conserved features, and to allow their efficient detection . This package presents the Open Source Java API to biological databases and a series of mostly sequence-based algorithms. Description-md5: 0b9b635e7d46ea6cf9f81df42e76fb60 Homepage: https://github.com/gem-pasteur/macsyfinder Built-Using: sphinx (= 7.4.7-3) Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.1.4-1_amd64.deb Size: 14541036 MD5sum: 8ca6e392bc129ad572e312caf23ed1e4 SHA256: 478d72d28b8b836e0dd9b9e8b957842fd08ae5ed145834ffd5bf6889c5e7a868 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m6.0s INFO: apt-cache knows about the following packages: macsyfinder 0m6.0s INFO: Running scripts pre_install 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_database-server'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_database-server'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_exceptions'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_exceptions'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_extras'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_extras'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'policy'] 0m6.1s 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: 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'policy'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'policy', 'macsyfinder'] 0m6.2s DUMP: macsyfinder: Installed: (none) Candidate: 2.1.4-1 Version table: 2.1.4-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'policy', 'macsyfinder'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', '-y', 'install', 'macsyfinder'] 0m28.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates fonts-font-awesome fonts-lato hmmer libblas3 libdivsufsort3 libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgomp1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncursesw6 libnghttp2-14 libperl5.40 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsqlite3-0 libuv1t64 libyaml-0-2 media-types ncbi-blast+ ncbi-data netbase openssl perl perl-modules-5.40 python3 python3-autocommand python3-certifi python3-colorama python3-colorlog python3-dateutil python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pkg-resources python3-pytz python3-typeguard python3-typing-extensions python3-tz python3-yaml python3.13 python3.13-minimal readline-common sphinx-rtd-theme-common Suggested packages: hmmer-doc gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv gcc gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc python3-statsmodels python3-setuptools python3.13-venv python3.13-doc binutils binfmt-support readline-doc Recommended packages: javascript-common libgpm2 python3-gdal python3-matplotlib python3-pydot python3-pygraphviz python3-scipy python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables python3-jinja2 python3-numba The following NEW packages will be installed: ca-certificates fonts-font-awesome fonts-lato hmmer libblas3 libdivsufsort3 libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgomp1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncursesw6 libnghttp2-14 libperl5.40 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsqlite3-0 libuv1t64 libyaml-0-2 macsyfinder media-types ncbi-blast+ ncbi-data netbase openssl perl perl-modules-5.40 python3 python3-autocommand python3-certifi python3-colorama python3-colorlog python3-dateutil python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pkg-resources python3-pytz python3-typeguard python3-typing-extensions python3-tz python3-yaml python3.13 python3.13-minimal readline-common sphinx-rtd-theme-common 0 upgraded, 64 newly installed, 0 to remove and 0 not upgraded. Need to get 89.6 MB of archives. After this operation, 441 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 fonts-lato all 2.015-1 [2780 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5+20250125-2 [135 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get:16 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.0-2 [1422 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.0-8 [3015 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.0-8 [267 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-16 [137 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.12.14+ds-1 [9624 B] Get:42 http://deb.debian.org/debian trixie/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 python3-colorlog all 6.9.0-1 [27.5 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:50 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get:53 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [4736 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 python3-pytz all 2025.1-3 [150 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2025.1-3 [4004 B] Get:58 http://deb.debian.org/debian trixie/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-8 [7295 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 python3-pandas all 2.2.3+dfsg-8 [3097 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6+b1 [15.2 MB] Get:64 http://deb.debian.org/debian trixie/main amd64 macsyfinder amd64 2.1.4-1 [14.5 MB] Preconfiguring packages ... Fetched 89.6 MB in 1s (133 MB/s) Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5026 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_amd64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:amd64 (3.13.2-1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../07-libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../08-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... 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Unpacking python3-packaging (24.2-1) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../38-python3-dateutil_2.9.0-3_all.deb ... Unpacking python3-dateutil (2.9.0-3) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../39-python3-numpy_1%3a1.26.4+ds-13_amd64.deb ... Unpacking python3-numpy (1:1.26.4+ds-13) ... Selecting previously unselected package python3-pytz. Preparing to unpack .../40-python3-pytz_2025.1-3_all.deb ... Unpacking python3-pytz (2025.1-3) ... Selecting previously unselected package python3-tz. Preparing to unpack .../41-python3-tz_2025.1-3_all.deb ... Unpacking python3-tz (2025.1-3) ... Selecting previously unselected package python3-pandas-lib:amd64. Preparing to unpack .../42-python3-pandas-lib_2.2.3+dfsg-8_amd64.deb ... Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../43-python3-pandas_2.2.3+dfsg-8_all.deb ... Unpacking python3-pandas (2.2.3+dfsg-8) ... Selecting previously unselected package python3-yaml. Preparing to unpack .../44-python3-yaml_6.0.2-1+b1_amd64.deb ... Unpacking python3-yaml (6.0.2-1+b1) ... Selecting previously unselected package sphinx-rtd-theme-common. Preparing to unpack .../45-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../46-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../47-ncbi-blast+_2.16.0+ds-6+b1_amd64.deb ... Unpacking ncbi-blast+ (2.16.0+ds-6+b1) ... Selecting previously unselected package macsyfinder. Preparing to unpack .../48-macsyfinder_2.1.4-1_amd64.deb ... Unpacking macsyfinder (2.1.4-1) ... Setting up media-types (10.1.0) ... Setting up liblmdb0:amd64 (0.9.31-1+b2) ... Setting up ncbi-data (6.1.20170106+dfsg2-5) ... Setting up fonts-lato (2.015-1) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up libyaml-0-2:amd64 (0.2.5-2) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libuv1t64:amd64 (1.50.0-2) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libgomp1:amd64 (14.2.0-16) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libncursesw6:amd64 (6.5+20250125-2) ... Setting up libgfortran5:amd64 (14.2.0-16) ... Setting up libffi8:amd64 (3.4.6-1) ... Setting up perl-modules-5.40 (5.40.0-8) ... Setting up netbase (6.4) ... Setting up libmbedcrypto16:amd64 (3.6.2-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libdivsufsort3:amd64 (2.0.1-6+b1) ... Setting up openssl (3.4.0-2) ... Setting up readline-common (8.2-6) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libperl5.40:amd64 (5.40.0-8) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up perl (5.40.0-8) ... Setting up libmbedx509-7:amd64 (3.6.2-3) ... Setting up libjs-sphinxdoc (8.1.3-4) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up hmmer (3.4+dfsg-2) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up python3.13 (3.13.2-1) ... Setting up python3 (3.13.1-2) ... Setting up python3-autocommand (2.2.2-3) ... Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-certifi (2024.12.14+ds-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:1.26.4+ds-13) ... Setting up python3-dateutil (2.9.0-3) ... 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-colorama (0.4.6-4) ... Setting up python3-colorlog (6.9.0-1) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-yaml (6.0.2-1+b1) ... Setting up python3-pytz (2025.1-3) ... Setting up python3-tz (2025.1-3) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pandas (2.2.3+dfsg-8) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-networkx (3.2.1-5) ... Setting up macsyfinder (2.1.4-1) ... Processing triggers for libc-bin (2.40-6) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', '-y', 'install', 'macsyfinder'] 0m28.0s INFO: Running scripts post_install 0m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_install_exceptions'] 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_install_exceptions'] 0m28.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m28.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m28.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpjdin93o4 to sid 0m28.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m28.8s INFO: Running scripts pre_distupgrade 0m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_distupgrade_exceptions'] 0m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_distupgrade_exceptions'] 0m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', 'update'] 0m31.6s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7366 kB] Fetched 17.6 MB in 2s (9366 kB/s) Reading package lists... 0m31.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', 'update'] 0m31.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', '-yf', 'dist-upgrade'] 0m38.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: python3-numpy-dev The following packages will be upgraded: apt libapt-pkg6.0t64 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libselinux1 libsepol2 libssl3t64 macsyfinder media-types openssl openssl-provider-legacy python3-numpy sqv sysvinit-utils tzdata 18 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 30.9 MB of archives. After this operation, 7571 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.4.1-1 [302 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.4.1-1 [2304 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.28 [1119 kB] Get:4 http://deb.debian.org/debian sid/main amd64 sqv amd64 1.2.1-6+b1 [623 kB] Get:5 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.28 [1440 kB] Get:6 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.14-1 [33.3 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.7.0-3 [248 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.7.0-3 [69.7 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.45-1 [298 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.8-2 [84.5 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.7.0-3 [48.9 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.7.0-3 [177 kB] Get:13 http://deb.debian.org/debian sid/main amd64 tzdata all 2025a-2 [259 kB] Get:14 http://deb.debian.org/debian sid/main amd64 media-types all 11.0.0 [27.6 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.8-1 [296 kB] Get:16 http://deb.debian.org/debian sid/main amd64 macsyfinder amd64 2.1.4-1+b1 [14.5 MB] Get:17 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get:18 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:2.2.2+ds-2 [7507 kB] Get:19 http://deb.debian.org/debian sid/main amd64 python3-numpy-dev amd64 1:2.2.2+ds-2 [138 kB] Preconfiguring packages ... Fetched 30.9 MB in 0s (190 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 ... 16057 files and directories currently installed.) Preparing to unpack .../openssl-provider-legacy_3.4.1-1_amd64.deb ... Unpacking openssl-provider-legacy (3.4.1-1) over (3.4.0-2) ... Setting up openssl-provider-legacy (3.4.1-1) ... (Reading database ... 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Unpacking macsyfinder (2.1.4-1+b1) over (2.1.4-1) ... Preparing to unpack .../4-openssl_3.4.1-1_amd64.deb ... Unpacking openssl (3.4.1-1) over (3.4.0-2) ... Preparing to unpack .../5-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 .../6-python3-numpy-dev_1%3a2.2.2+ds-2_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.2.2+ds-2) ... Setting up media-types (11.0.0) ... Installing new version of config file /etc/mime.types ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Feb 12 04:06:14 UTC 2025. Universal Time is now: Wed Feb 12 04:06:14 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up python3-numpy-dev:amd64 (1:2.2.2+ds-2) ... Setting up libsepol2:amd64 (3.8-1) ... Setting up python3-numpy (1:2.2.2+ds-2) ... Setting up macsyfinder (2.1.4-1+b1) ... Setting up openssl (3.4.1-1) ... Processing triggers for libc-bin (2.40-6) ... 0m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', '-yf', 'dist-upgrade'] 0m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m39.2s DUMP: cf5c5d672adc6c7abda4efc9e4a100c2 - 0m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m39.5s DUMP: Package: macsyfinder Source: macsyfinder (2.1.4-1) Version: 2.1.4-1+b1 Installed-Size: 37591 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-certifi, python3-colorama, python3-colorlog, python3-networkx, python3-packaging, python3-pandas, python3-yaml, python3:any, libjs-jquery (>= 3.6.0), libjs-sphinxdoc (>= 8.1), sphinx-rtd-theme-common (>= 3.0.2+dfsg), hmmer, ncbi-blast+, libjs-underscore Description-en: detection of macromolecular systems in protein datasets MacSyFinder is a program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems with MacSyFinder to reflect these conserved features, and to allow their efficient detection . This package presents the Open Source Java API to biological databases and a series of mostly sequence-based algorithms. Description-md5: 0b9b635e7d46ea6cf9f81df42e76fb60 Homepage: https://github.com/gem-pasteur/macsyfinder Built-Using: sphinx (= 8.1.3-4) Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.1.4-1+b1_amd64.deb Size: 14537052 MD5sum: a6ad2116fdedd14828a0650da0943574 SHA256: 7f080c1503a14120106286a8028b534e8ab4e98585b026dcb0153bf9776095a0 0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m39.5s INFO: apt-cache knows about the following packages: macsyfinder 0m39.5s INFO: Running scripts pre_install 0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_database-server'] 0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_database-server'] 0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_exceptions'] 0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_exceptions'] 0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_extras'] 0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_extras'] 0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_foreign_architecture'] 0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_foreign_architecture'] 0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'policy'] 0m39.6s 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: 0m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'policy'] 0m39.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'policy', 'macsyfinder'] 0m39.6s DUMP: macsyfinder: Installed: 2.1.4-1+b1 Candidate: 2.1.4-1+b1 Version table: *** 2.1.4-1+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'policy', 'macsyfinder'] 0m39.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', '-y', 'install', 'macsyfinder'] 0m40.1s DUMP: Reading package lists... Building dependency tree... Reading state information... macsyfinder is already the newest version (2.1.4-1+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', '-y', 'install', 'macsyfinder'] 0m40.1s INFO: Running scripts post_install 0m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_install_exceptions'] 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_install_exceptions'] 0m40.2s INFO: Running scripts post_distupgrade 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_distupgrade_exceptions'] 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_distupgrade_exceptions'] 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_distupgrade_zz_backports'] 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_distupgrade_zz_backports'] 0m40.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m41.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m41.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m42.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m42.1s INFO: Running scripts pre_install 0m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_database-server'] 0m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_database-server'] 0m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_exceptions'] 0m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_exceptions'] 0m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_extras'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_extras'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'policy'] 0m42.3s 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: 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'policy'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'policy', 'macsyfinder'] 0m42.3s DUMP: macsyfinder: Installed: 2.1.4-1+b1 Candidate: 2.1.4-1+b1 Version table: *** 2.1.4-1+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-cache', 'policy', 'macsyfinder'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', '-y', 'install', 'macsyfinder=2.1.4-1+b1'] 0m42.9s DUMP: Reading package lists... Building dependency tree... Reading state information... macsyfinder is already the newest version (2.1.4-1+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', '-y', 'install', 'macsyfinder=2.1.4-1+b1'] 0m42.9s INFO: Running scripts post_install 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_install_exceptions'] 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_install_exceptions'] 0m43.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m43.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m44.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', '-ac', '--ignore-obsolete'] 0m46.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', '-ac', '--ignore-obsolete'] 0m46.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m46.6s DUMP: 0.15.6 0m46.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m46.6s INFO: Running adequate version 0.15.6 now. 0m46.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'macsyfinder'] 0m46.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'macsyfinder'] 0m46.8s INFO: Running scripts pre_remove 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m47.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m47.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_remove_exceptions'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/pre_remove_exceptions'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m48.0s DUMP: install ok installed apt apt 2.9.28 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 ca-certificates ca-certificates 20241223 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.89 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-2 install ok installed dpkg dpkg 1.22.15 install ok installed e2fsprogs e2fsprogs 1.47.2-1 install ok installed findutils findutils 4.10.0-3 install ok installed fonts-font-awesome fonts-font-awesome 5.0.10+really4.7.0~dfsg-4.1 install ok installed fonts-lato fonts-lato 2.015-1 install ok installed 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 hmmer hmmer 3.4+dfsg-2 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 2.9.28 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 libdivsufsort3:amd64 libdivsufsort3 2.0.1-6+b1 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-16 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 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 libgomp1:amd64 libgomp1 14.2.0-16 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 8.1.3-4 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed liblapack3:amd64 liblapack3 3.12.1-2 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b2 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 libmbedcrypto16:amd64 libmbedcrypto16 3.6.2-3 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.2-3 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.2-3 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 libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-8 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 3.8-2 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 3.8-1 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 3.4.1-1 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 libuv1t64:amd64 libuv1t64 1.50.0-2 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-2 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 macsyfinder macsyfinder 2.1.4-1+b1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed media-types media-types 11.0.0 install ok installed mount mount 2.40.4-3 install ok installed ncbi-blast+ ncbi-blast+ 2.16.0+ds-6+b1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-5 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 openssl 3.4.1-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.1-1 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl perl 5.40.0-8 install ok installed perl-base perl-base 5.40.0-8 install ok installed perl-modules-5.40 perl-modules-5.40 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-certifi python3-certifi 2024.12.14+ds-1 install ok installed python3-colorama python3-colorama 0.4.6-4 install ok installed python3-colorlog python3-colorlog 6.9.0-1 install ok installed python3-dateutil python3-dateutil 2.9.0-3 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-minimal python3-minimal 3.13.1-2 install ok installed python3-more-itertools python3-more-itertools 10.6.0-1 install ok installed python3-networkx python3-networkx 3.2.1-5 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-packaging python3-packaging 24.2-1 install ok installed python3-pandas python3-pandas 2.2.3+dfsg-8 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.2.3+dfsg-8 install ok installed python3-pkg-resources python3-pkg-resources 75.6.0-1 install ok installed python3-pytz python3-pytz 2025.1-3 install ok installed python3-typeguard python3-typeguard 4.4.1-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3-tz python3-tz 2025.1-3 install ok installed python3-yaml python3-yaml 6.0.2-1+b1 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 sphinx-rtd-theme-common sphinx-rtd-theme-common 3.0.2+dfsg-2 install ok installed sqv sqv 1.2.1-6+b1 install ok installed sysvinit-utils sysvinit-utils 3.14-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025a-2 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.4-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', 'remove', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'libblas3:amd64', 'libdivsufsort3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libuv1t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'python3', 'python3-autocommand', 'python3-certifi', 'python3-colorama', 'python3-colorlog', 'python3-dateutil', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-pytz', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-yaml', 'python3.13', 'python3.13-minimal', 'readline-common', 'sphinx-rtd-theme-common', 'macsyfinder'] 0m51.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates fonts-font-awesome fonts-lato hmmer libblas3 libdivsufsort3 libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgomp1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncursesw6 libnghttp2-14 libperl5.40 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsqlite3-0 libuv1t64 libyaml-0-2 macsyfinder media-types ncbi-blast+ ncbi-data netbase openssl perl perl-modules-5.40 python3 python3-autocommand python3-certifi python3-colorama python3-colorlog python3-dateutil python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-networkx python3-numpy python3-numpy-dev python3-packaging python3-pandas python3-pandas-lib python3-pkg-resources python3-pytz python3-typeguard python3-typing-extensions python3-tz python3-yaml python3.13 python3.13-minimal readline-common sphinx-rtd-theme-common 0 upgraded, 0 newly installed, 65 to remove and 0 not upgraded. After this operation, 449 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 ... 16119 files and directories currently installed.) Removing macsyfinder (2.1.4-1+b1) ... Removing python3-certifi (2024.12.14+ds-1) ... Removing ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing sphinx-rtd-theme-common (3.0.2+dfsg-2) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing fonts-lato (2.015-1) ... Removing hmmer (3.4+dfsg-2) ... Removing python3-pandas (2.2.3+dfsg-8) ... Removing python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... Removing python3-numpy (1:2.2.2+ds-2) ... Removing liblapack3:amd64 (3.12.1-2) ... Removing libblas3:amd64 (3.12.1-2) ... Removing libdivsufsort3:amd64 (2.0.1-6+b1) ... Removing python3-yaml (6.0.2-1+b1) ... Removing python3-networkx (3.2.1-5) ... Removing python3-pkg-resources (75.6.0-1) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.1-1) ... Removing ncbi-blast+ (2.16.0+ds-6+b1) ... Removing python3-tz (2025.1-3) ... Removing python3-pytz (2025.1-3) ... Removing perl (5.40.0-8) ... Removing libperl5.40:amd64 (5.40.0-8) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgfortran5:amd64 (14.2.0-16) ... Removing libgomp1:amd64 (14.2.0-16) ... Removing libjs-sphinxdoc (8.1.3-4) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing liblmdb0:amd64 (0.9.31-1+b2) ... Removing libmbedtls21:amd64 (3.6.2-3) ... Removing libmbedx509-7:amd64 (3.6.2-3) ... Removing libmbedcrypto16:amd64 (3.6.2-3) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libuv1t64:amd64 (1.50.0-2) ... Removing libyaml-0-2:amd64 (0.2.5-2) ... Removing ncbi-data (6.1.20170106+dfsg2-5) ... Removing openssl (3.4.1-1) ... Removing perl-modules-5.40 (5.40.0-8) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-colorama (0.4.6-4) ... Removing python3-colorlog (6.9.0-1) ... Removing python3-dateutil (2.9.0-3) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-more-itertools (10.6.0-1) ... Removing python3-numpy-dev:amd64 (1:2.2.2+ds-2) ... Removing python3-packaging (24.2-1) ... Removing python3-typing-extensions (4.12.2-2) ... 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 (11.0.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.40-6) ... 0m51.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', 'remove', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'libblas3:amd64', 'libdivsufsort3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libuv1t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'python3', 'python3-autocommand', 'python3-certifi', 'python3-colorama', 'python3-colorlog', 'python3-dateutil', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-pytz', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-yaml', 'python3.13', 'python3.13-minimal', 'readline-common', 'sphinx-rtd-theme-common', 'macsyfinder'] 0m51.3s INFO: Running scripts post_remove 0m51.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_remove_exceptions'] 0m51.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_remove_exceptions'] 0m51.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg', '--purge', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'libblas3:amd64', 'libdivsufsort3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libuv1t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'python3', 'python3-autocommand', 'python3-certifi', 'python3-colorama', 'python3-colorlog', 'python3-dateutil', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-pytz', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-yaml', 'python3.13', 'python3.13-minimal', 'readline-common', 'sphinx-rtd-theme-common'] 0m51.5s DUMP: (Reading database ... 5044 files and directories currently installed.) Purging configuration files for ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... dpkg: warning: ignoring request to remove fonts-lato which isn't installed dpkg: warning: ignoring request to remove hmmer which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libdivsufsort3 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 libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto16 which isn't installed dpkg: warning: ignoring request to remove libmbedtls21 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-7 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.13-minimal:amd64 (3.13.2-1) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libuv1t64 which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed Purging configuration files for media-types (11.0.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-5) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.4.1-1) ... Purging configuration files for perl (5.40.0-8) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed 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-certifi which isn't installed dpkg: warning: ignoring request to remove python3-colorama which isn't installed dpkg: warning: ignoring request to remove python3-colorlog which isn't installed dpkg: warning: ignoring request to remove python3-dateutil 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-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-networkx 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-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pandas which isn't installed dpkg: warning: ignoring request to remove python3-pandas-lib which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pytz which isn't installed dpkg: warning: ignoring request to remove python3-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-yaml 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) ... dpkg: warning: ignoring request to remove sphinx-rtd-theme-common which isn't installed 0m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg', '--purge', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'libblas3:amd64', 'libdivsufsort3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libuv1t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'python3', 'python3-autocommand', 'python3-certifi', 'python3-colorama', 'python3-colorlog', 'python3-dateutil', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-pytz', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-yaml', 'python3.13', 'python3.13-minimal', 'readline-common', 'sphinx-rtd-theme-common'] 0m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg', '--purge', 'macsyfinder'] 0m51.5s DUMP: (Reading database ... 5028 files and directories currently installed.) Purging configuration files for macsyfinder (2.1.4-1+b1) ... 0m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg', '--purge', 'macsyfinder'] 0m51.5s INFO: Running scripts post_purge 0m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_purge_exceptions'] 0m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_purge_exceptions'] 0m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg', '--purge', '--pending'] 0m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg', '--purge', '--pending'] 0m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg', '--remove', '--pending'] 0m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg', '--remove', '--pending'] 0m51.5s INFO: Running scripts post_test 0m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_test_exceptions'] 0m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'tmp/scripts/post_test_exceptions'] 0m51.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m51.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg-divert', '--list'] 0m51.8s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'dpkg-divert', '--list'] 0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', 'clean'] 0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjdin93o4', 'apt-get', 'clean'] 0m51.8s DEBUG: Recording chroot state 0m52.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/shm'] 0m52.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/shm'] 0m52.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/console'] 0m52.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/console'] 0m52.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/ptmx'] 0m52.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/ptmx'] 0m52.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/pts'] 0m52.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/dev/pts'] 0m52.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/proc'] 0m52.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpjdin93o4/proc'] 0m52.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m52.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpjdin93o4'] 0m52.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpjdin93o4 0m53.0s INFO: PASS: Upgrading between Debian distributions. 0m53.0s INFO: PASS: All tests. 0m53.0s INFO: piuparts run ends. ret=0 End: 2025-02-12 04:06:31 GMT