Start: 2025-12-01 10:10:04 GMT [testing] Package: macsyfinder Source: macsyfinder (2.1.4-1) Version: 2.1.4-1+b2 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 (= 8.1.3-5) Description-md5: 0b9b635e7d46ea6cf9f81df42e76fb60 Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.1.4-1+b2_amd64.deb Size: 14537468 MD5sum: bae9b6f7a0b6098a47d01d491740a84b SHA256: c908281d201e271802f78742a02815a7e54fb39b775f947633235cc461a58609 [sid] Package: macsyfinder Source: macsyfinder (2.1.4-1) Version: 2.1.4-1+b3 Installed-Size: 37541 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 (>= 8.2), 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 (= 8.2.3-10) Description-md5: 0b9b635e7d46ea6cf9f81df42e76fb60 Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.1.4-1+b3_amd64.deb Size: 14490328 MD5sum: 7f8ad8fdb7a99806dd3ddf3c18ce1c12 SHA256: 1eda3ad64775b04667c7691b1d9dca57660b2b9ff4f30e61e32e57f57a0eee1f Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/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/forky-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+b3 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 1.6.1~202508211944~1.6.0-10-gffba2cce starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/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/forky-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+b3 0m0.0s INFO: Running on: Linux piu-slave-conova-01 6.1.0-41-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.158-1 (2025-11-09) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmptsg4gve9 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmptsg4gve9 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ forky 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/tmptsg4gve9/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', 'update'] 0m2.7s DUMP: Get:1 http://deb.debian.org/debian forky InRelease [148 kB] Get:2 http://deb.debian.org/debian forky/main amd64 Packages [9692 kB] Get:3 http://deb.debian.org/debian forky/main Translation-en [6455 kB] Fetched 16.3 MB in 1s (11.7 MB/s) Reading package lists... 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', 'update'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', '-yf', 'dist-upgrade'] 0m7.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following NEW packages will be installed: gcc-15-base The following packages will be upgraded: apt base-files base-passwd bash bsdutils diffutils gcc-14-base grep init-system-helpers libapt-pkg7.0 libaudit-common libaudit1 libblkid1 libcrypt1 libdb5.3t64 libdebconfclient0 libgcc-s1 libgmp10 libhogweed6t64 liblastlog2-2 liblz4-1 liblzma5 libmount1 libnettle8t64 libpcre2-8-0 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libssl3t64 libstdc++6 libsystemd0 libudev1 libuuid1 libzstd1 login login.defs mount openssl-provider-legacy passwd sysvinit-utils tzdata util-linux 45 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 18.1 MB of archives. After this operation, 342 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 base-files amd64 14 [72.9 kB] Get:2 http://deb.debian.org/debian forky/main amd64 bash amd64 5.3-1 [1556 kB] Get:3 http://deb.debian.org/debian forky/main amd64 diffutils amd64 1:3.12-1 [405 kB] Get:4 http://deb.debian.org/debian forky/main amd64 grep amd64 3.12-1 [443 kB] Get:5 http://deb.debian.org/debian forky/main amd64 libuuid1 amd64 2.41.2-4 [38.7 kB] Get:6 http://deb.debian.org/debian forky/main amd64 bsdutils amd64 1:2.41.2-4 [93.5 kB] Get:7 http://deb.debian.org/debian forky/main amd64 libblkid1 amd64 2.41.2-4 [174 kB] Get:8 http://deb.debian.org/debian forky/main amd64 libmount1 amd64 2.41.2-4 [211 kB] Get:9 http://deb.debian.org/debian forky/main amd64 libsmartcols1 amd64 2.41.2-4 [145 kB] Get:10 http://deb.debian.org/debian forky/main amd64 util-linux amd64 2.41.2-4 [1163 kB] Get:11 http://deb.debian.org/debian forky/main amd64 mount amd64 2.41.2-4 [163 kB] Get:12 http://deb.debian.org/debian forky/main amd64 libpcre2-8-0 amd64 10.46-1 [298 kB] Get:13 http://deb.debian.org/debian forky/main amd64 libselinux1 amd64 3.9-4 [85.8 kB] Get:14 http://deb.debian.org/debian forky/main amd64 libsystemd0 amd64 259~rc1-1 [469 kB] Get:15 http://deb.debian.org/debian forky/main amd64 gcc-15-base amd64 15.2.0-9 [53.7 kB] Get:16 http://deb.debian.org/debian forky/main amd64 libgcc-s1 amd64 15.2.0-9 [71.5 kB] Get:17 http://deb.debian.org/debian forky/main amd64 liblz4-1 amd64 1.10.0-6 [70.5 kB] Get:18 http://deb.debian.org/debian forky/main amd64 liblzma5 amd64 5.8.1-2 [310 kB] Get:19 http://deb.debian.org/debian forky/main amd64 openssl-provider-legacy amd64 3.5.4-1 [308 kB] Get:20 http://deb.debian.org/debian forky/main amd64 libzstd1 amd64 1.5.7+dfsg-2 [308 kB] Get:21 http://deb.debian.org/debian forky/main amd64 libssl3t64 amd64 3.5.4-1 [2446 kB] Get:22 http://deb.debian.org/debian forky/main amd64 libstdc++6 amd64 15.2.0-9 [736 kB] Get:23 http://deb.debian.org/debian forky/main amd64 libudev1 amd64 259~rc1-1 [157 kB] Get:24 http://deb.debian.org/debian forky/main amd64 libapt-pkg7.0 amd64 3.1.12 [1229 kB] Get:25 http://deb.debian.org/debian forky/main amd64 libdebconfclient0 amd64 0.282 [10.9 kB] Get:26 http://deb.debian.org/debian forky/main amd64 base-passwd amd64 3.6.8 [54.6 kB] Get:27 http://deb.debian.org/debian forky/main amd64 apt amd64 3.1.12 [1520 kB] Get:28 http://deb.debian.org/debian forky/main amd64 init-system-helpers all 1.69 [39.3 kB] Get:29 http://deb.debian.org/debian forky/main amd64 sysvinit-utils amd64 3.15-6 [35.0 kB] Get:30 http://deb.debian.org/debian forky/main amd64 libaudit-common all 1:4.1.2-1 [14.3 kB] Get:31 http://deb.debian.org/debian forky/main amd64 libaudit1 amd64 1:4.1.2-1 [60.4 kB] Get:32 http://deb.debian.org/debian forky/main amd64 login amd64 1:4.16.0-2+really2.41.2-4 [105 kB] Get:33 http://deb.debian.org/debian forky/main amd64 libcrypt1 amd64 1:4.5.1-1 [98.0 kB] Get:34 http://deb.debian.org/debian forky/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-10 [709 kB] Get:35 http://deb.debian.org/debian forky/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5 [574 kB] Get:36 http://deb.debian.org/debian forky/main amd64 libnettle8t64 amd64 3.10.2-1 [307 kB] Get:37 http://deb.debian.org/debian forky/main amd64 libhogweed6t64 amd64 3.10.2-1 [336 kB] Get:38 http://deb.debian.org/debian forky/main amd64 libsqlite3-0 amd64 3.46.1-8 [968 kB] Get:39 http://deb.debian.org/debian forky/main amd64 liblastlog2-2 amd64 2.41.2-4 [29.5 kB] Get:40 http://deb.debian.org/debian forky/main amd64 login.defs all 1:4.18.0-2 [211 kB] Get:41 http://deb.debian.org/debian forky/main amd64 libsemanage-common all 3.9-1 [7888 B] Get:42 http://deb.debian.org/debian forky/main amd64 libsepol2 amd64 3.9-2 [300 kB] Get:43 http://deb.debian.org/debian forky/main amd64 libsemanage2 amd64 3.9-1 [96.8 kB] Get:44 http://deb.debian.org/debian forky/main amd64 passwd amd64 1:4.18.0-2 [1286 kB] Get:45 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get:46 http://deb.debian.org/debian forky/main amd64 gcc-14-base amd64 14.3.0-10 [52.4 kB] Preconfiguring packages ... Fetched 18.1 MB in 0s (109 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 ... 4934 files and directories currently installed.) Preparing to unpack .../base-files_14_amd64.deb ... Unpacking base-files (14) over (13.8) ... Setting up base-files (14) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (Reading database ... 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(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 ... 4934 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.41.2-4_amd64.deb ... Unpacking bsdutils (1:2.41.2-4) over (1:2.41-5) ... Setting up bsdutils (1:2.41.2-4) ... (Reading database ... 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(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 ... 4931 files and directories currently installed.) Preparing to unpack .../util-linux_2.41.2-4_amd64.deb ... Unpacking util-linux (2.41.2-4) over (2.41-5) ... Setting up util-linux (2.41.2-4) ... (Reading database ... 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(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 ... 4904 files and directories currently installed.) Preparing to unpack .../gcc-15-base_15.2.0-9_amd64.deb ... Unpacking gcc-15-base:amd64 (15.2.0-9) ... Setting up gcc-15-base:amd64 (15.2.0-9) ... (Reading database ... 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(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 ... 4909 files and directories currently installed.) Preparing to unpack .../liblzma5_5.8.1-2_amd64.deb ... Unpacking liblzma5:amd64 (5.8.1-2) over (5.8.1-1) ... Setting up liblzma5:amd64 (5.8.1-2) ... (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 ... 4909 files and directories currently installed.) Preparing to unpack .../openssl-provider-legacy_3.5.4-1_amd64.deb ... Unpacking openssl-provider-legacy (3.5.4-1) over (3.5.1-1) ... Setting up openssl-provider-legacy (3.5.4-1) ... (Reading database ... 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(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 ... 4909 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.5.4-1_amd64.deb ... Unpacking libssl3t64:amd64 (3.5.4-1) over (3.5.1-1) ... Setting up libssl3t64:amd64 (3.5.4-1) ... (Reading database ... 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(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 ... 4909 files and directories currently installed.) Preparing to unpack .../libapt-pkg7.0_3.1.12_amd64.deb ... Unpacking libapt-pkg7.0:amd64 (3.1.12) over (3.0.3) ... Setting up libapt-pkg7.0:amd64 (3.1.12) ... (Reading database ... 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(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 ... 4910 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.1.2-1_amd64.deb ... Unpacking libaudit1:amd64 (1:4.1.2-1) over (1:4.0.2-2+b2) ... Setting up libaudit1:amd64 (1:4.1.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4909 files and directories currently installed.) Preparing to unpack .../login_1%3a4.16.0-2+really2.41.2-4_amd64.deb ... Unpacking login (1:4.16.0-2+really2.41.2-4) over (1:4.16.0-2+really2.41-5) ... Preparing to unpack .../libcrypt1_1%3a4.5.1-1_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.5.1-1) over (1:4.4.38-1) ... Setting up libcrypt1:amd64 (1:4.5.1-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4901 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-10_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-10) over (5.3.28+dfsg2-9) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-10) ... (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 ... 4901 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.3.0+dfsg-5_amd64.deb ... Unpacking libgmp10:amd64 (2:6.3.0+dfsg-5) over (2:6.3.0+dfsg-3) ... Setting up libgmp10:amd64 (2:6.3.0+dfsg-5) ... (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 ... 4901 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.10.2-1_amd64.deb ... Unpacking libnettle8t64:amd64 (3.10.2-1) over (3.10.1-1) ... Setting up libnettle8t64:amd64 (3.10.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4901 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.10.2-1_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.10.2-1) over (3.10.1-1) ... Setting up libhogweed6t64:amd64 (3.10.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4901 files and directories currently installed.) Preparing to unpack .../libsqlite3-0_3.46.1-8_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-8) over (3.46.1-7) ... Setting up libsqlite3-0:amd64 (3.46.1-8) ... (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 ... 4901 files and directories currently installed.) Preparing to unpack .../liblastlog2-2_2.41.2-4_amd64.deb ... Unpacking liblastlog2-2:amd64 (2.41.2-4) over (2.41-5) ... Setting up liblastlog2-2:amd64 (2.41.2-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4901 files and directories currently installed.) Preparing to unpack .../0-login.defs_1%3a4.18.0-2_all.deb ... Unpacking login.defs (1:4.18.0-2) over (1:4.17.4-2) ... Preparing to unpack .../1-libsemanage-common_3.9-1_all.deb ... Unpacking libsemanage-common (3.9-1) over (3.8.1-1) ... Preparing to unpack .../2-libsepol2_3.9-2_amd64.deb ... Unpacking libsepol2:amd64 (3.9-2) over (3.8.1-1) ... Preparing to unpack .../3-libsemanage2_3.9-1_amd64.deb ... Unpacking libsemanage2:amd64 (3.9-1) over (3.8.1-1) ... Preparing to unpack .../4-passwd_1%3a4.18.0-2_amd64.deb ... Unpacking passwd (1:4.18.0-2) over (1:4.17.4-2) ... Preparing to unpack .../5-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) over (2025b-4) ... Preparing to unpack .../6-gcc-14-base_14.3.0-10_amd64.deb ... Unpacking gcc-14-base:amd64 (14.3.0-10) over (14.2.0-19) ... Setting up gcc-14-base:amd64 (14.3.0-10) ... Setting up login.defs (1:4.18.0-2) ... Setting up libsemanage-common (3.9-1) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Dec 1 10:10:11 UTC 2025. Universal Time is now: Mon Dec 1 10:10:11 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libsepol2:amd64 (3.9-2) ... Setting up mount (2.41.2-4) ... Setting up libsemanage2:amd64 (3.9-1) ... Setting up login (1:4.16.0-2+really2.41.2-4) ... Setting up passwd (1:4.18.0-2) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for debianutils (5.23.2) ... 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', '-yf', 'dist-upgrade'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.5s DUMP: 4a8d07ee4aa39eabe04e574e55725bf4 - 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.5s INFO: Running scripts post_setup 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_setup_dummy_users'] 0m9.1s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_setup_dummy_users'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_setup_forbid_home'] 0m9.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_setup_forbid_home'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_setup_minimize'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_setup_minimize'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_setup_zz_backports'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_setup_zz_backports'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.2s DUMP: install ok installed apt apt 3.1.12 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.8 install ok installed bash bash 5.3-1 install ok installed bsdutils bsdutils 1:2.41.2-4 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.12-1 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.3.0-10 install ok installed gcc-15-base:amd64 gcc-15-base 15.2.0-9 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.1.12 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.2-1 install ok installed libblkid1:amd64 libblkid1 2.41.2-4 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 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.5.1-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.282 install ok installed libgcc-s1:amd64 libgcc-s1 15.2.0-9 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41.2-4 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-6 install ok installed liblzma5:amd64 liblzma5 5.8.1-2 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41.2-4 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.9-4 install ok installed libsemanage-common libsemanage-common 3.9-1 install ok installed libsemanage2:amd64 libsemanage2 3.9-1 install ok installed libsepol2:amd64 libsepol2 3.9-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.41.2-4 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-8 install ok installed libssl3t64:amd64 libssl3t64 3.5.4-1 install ok installed libstdc++6:amd64 libstdc++6 15.2.0-9 install ok installed libsystemd0:amd64 libsystemd0 259~rc1-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 259~rc1-1 install ok installed libuuid1:amd64 libuuid1 2.41.2-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-2 install ok installed login login 1:4.16.0-2+really2.41.2-4 install ok installed login.defs login.defs 1:4.18.0-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41.2-4 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.4-1 install ok installed passwd passwd 1:4.18.0-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.15-6 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-5 install ok installed util-linux util-linux 2.41.2-4 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.2s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m9.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m9.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m9.5s INFO: Running scripts is_testable 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/is_testable_uninstallable'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/is_testable_uninstallable'] 0m9.5s INFO: Running scripts pre_test 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_test_exceptions'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_test_exceptions'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_test_root_password'] 0m9.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_test_root_password'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m9.8s DUMP: Package: macsyfinder Source: macsyfinder (2.1.4-1) Version: 2.1.4-1+b2 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 (= 8.1.3-5) Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.1.4-1+b2_amd64.deb Size: 14537468 MD5sum: bae9b6f7a0b6098a47d01d491740a84b SHA256: c908281d201e271802f78742a02815a7e54fb39b775f947633235cc461a58609 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m9.8s INFO: apt-cache knows about the following packages: macsyfinder 0m9.8s INFO: Running scripts pre_install 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_database-server'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_database-server'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_exceptions'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_exceptions'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_extras'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_extras'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'policy'] 0m9.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian forky/main amd64 Packages release o=Debian,a=testing,n=forky,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'policy'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'policy', 'macsyfinder'] 0m9.9s DUMP: macsyfinder: Installed: (none) Candidate: 2.1.4-1+b2 Version table: 2.1.4-1+b2 500 500 http://deb.debian.org/debian forky/main amd64 Packages 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'policy', 'macsyfinder'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', '-y', 'install', 'macsyfinder'] 0m31.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: ca-certificates fonts-font-awesome fonts-lato hmmer isa-support libblas3 libdivsufsort3 libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgomp1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncursesw6 libnghttp2-14 libperl5.40 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libuv1t64 libyaml-0-2 media-types ncbi-blast+ ncbi-data ncbi-vdb-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-yaml python3.13 python3.13-minimal readline-common sphinx-rtd-theme-common sse4.2-support 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 isa-support libblas3 libdivsufsort3 libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgomp1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncursesw6 libnghttp2-14 libperl5.40 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libuv1t64 libyaml-0-2 macsyfinder media-types ncbi-blast+ ncbi-data ncbi-vdb-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-yaml python3.13 python3.13-minimal readline-common sphinx-rtd-theme-common sse4.2-support 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 101 MB of archives. After this operation, 445 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 fonts-lato all 2.015-1 [2780 kB] Get:2 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Get:3 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.9-1 [865 kB] Get:4 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.9-1 [2257 kB] Get:5 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get:6 http://deb.debian.org/debian forky/main amd64 media-types all 14.0.0 [30.8 kB] Get:7 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get:8 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get:9 http://deb.debian.org/debian forky/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:10 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get:11 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get:12 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.9-1 [1965 kB] Get:13 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.9-1 [764 kB] Get:14 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get:15 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get:16 http://deb.debian.org/debian forky/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-2 [139 kB] Get:17 http://deb.debian.org/debian forky/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get:18 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 15.2.0-9 [862 kB] Get:19 http://deb.debian.org/debian forky/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get:20 http://deb.debian.org/debian forky/main amd64 python3-numpy amd64 1:2.3.5+ds-2 [5096 kB] Get:21 http://deb.debian.org/debian forky/main amd64 isa-support amd64 27 [14.9 kB] Get:22 http://deb.debian.org/debian forky/main amd64 sse4.2-support amd64 27 [3692 B] Get:23 http://deb.debian.org/debian forky/main amd64 openssl amd64 3.5.4-1 [1496 kB] Get:24 http://deb.debian.org/debian forky/main amd64 ca-certificates all 20250419 [162 kB] Get:25 http://deb.debian.org/debian forky/main amd64 perl-modules-5.40 all 5.40.1-6 [3019 kB] Get:26 http://deb.debian.org/debian forky/main amd64 libgdbm6t64 amd64 1.26-1 [78.5 kB] Get:27 http://deb.debian.org/debian forky/main amd64 libgdbm-compat4t64 amd64 1.26-1 [52.8 kB] Get:28 http://deb.debian.org/debian forky/main amd64 libperl5.40 amd64 5.40.1-6 [4341 kB] Get:29 http://deb.debian.org/debian forky/main amd64 perl amd64 5.40.1-6 [267 kB] Get:30 http://deb.debian.org/debian forky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:31 http://deb.debian.org/debian forky/main amd64 libdivsufsort3 amd64 2.0.1-7 [45.8 kB] Get:32 http://deb.debian.org/debian forky/main amd64 hmmer amd64 3.4+dfsg-3 [1079 kB] Get:33 http://deb.debian.org/debian forky/main amd64 libgomp1 amd64 15.2.0-9 [140 kB] Get:34 http://deb.debian.org/debian forky/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get:35 http://deb.debian.org/debian forky/main amd64 libjs-sphinxdoc all 8.2.3-9 [27.7 kB] Get:36 http://deb.debian.org/debian forky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:37 http://deb.debian.org/debian forky/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get:38 http://deb.debian.org/debian forky/main amd64 libmbedcrypto16 amd64 3.6.5-0.1 [363 kB] Get:39 http://deb.debian.org/debian forky/main amd64 libmbedx509-7 amd64 3.6.5-0.1 [152 kB] Get:40 http://deb.debian.org/debian forky/main amd64 libmbedtls21 amd64 3.6.5-0.1 [246 kB] Get:41 http://deb.debian.org/debian forky/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get:42 http://deb.debian.org/debian forky/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get:43 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get:44 http://deb.debian.org/debian forky/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get:45 http://deb.debian.org/debian forky/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get:46 http://deb.debian.org/debian forky/main amd64 python3-certifi all 2025.11.12+ds-1 [10.0 kB] Get:47 http://deb.debian.org/debian forky/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get:48 http://deb.debian.org/debian forky/main amd64 python3-colorlog all 6.10.1-1 [27.9 kB] Get:49 http://deb.debian.org/debian forky/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:50 http://deb.debian.org/debian forky/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get:51 http://deb.debian.org/debian forky/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get:52 http://deb.debian.org/debian forky/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get:53 http://deb.debian.org/debian forky/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get:54 http://deb.debian.org/debian forky/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get:55 http://deb.debian.org/debian forky/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:56 http://deb.debian.org/debian forky/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get:57 http://deb.debian.org/debian forky/main amd64 python3-networkx all 3.4.2-2 [24.2 MB] Get:58 http://deb.debian.org/debian forky/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get:59 http://deb.debian.org/debian forky/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get:60 http://deb.debian.org/debian forky/main amd64 python3-pytz all 2025.2-4 [31.8 kB] Get:61 http://deb.debian.org/debian forky/main amd64 python3-pandas-lib amd64 2.3.3+dfsg-2 [4362 kB] Get:62 http://deb.debian.org/debian forky/main amd64 python3-pandas all 2.3.3+dfsg-2 [2935 kB] Get:63 http://deb.debian.org/debian forky/main amd64 python3-yaml amd64 6.0.2-2 [137 kB] Get:64 http://deb.debian.org/debian forky/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1023 kB] Get:65 http://deb.debian.org/debian forky/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get:66 http://deb.debian.org/debian forky/main amd64 ncbi-blast+ amd64 2.17.0+ds-6 [17.0 MB] Get:67 http://deb.debian.org/debian forky/main amd64 macsyfinder amd64 2.1.4-1+b2 [14.5 MB] Preconfiguring packages ... Fetched 101 MB in 1s (171 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 ... 4905 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 libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... 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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 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.9-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_amd64.deb ... Unpacking python3.13 (3.13.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5773 files and directories currently installed.) Preparing to unpack .../0-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package python3-numpy-dev:amd64. 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Selecting previously unselected package sse4.2-support. (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 ... 6845 files and directories currently installed.) Preparing to unpack .../00-sse4.2-support_27_amd64.deb ... Unpacking sse4.2-support (27) ... Selecting previously unselected package openssl. Preparing to unpack .../01-openssl_3.5.4-1_amd64.deb ... Unpacking openssl (3.5.4-1) ... Selecting previously unselected package ca-certificates. 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Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up libgomp1:amd64 (15.2.0-9) ... Setting up libblas3:amd64 (3.12.1-7) ... 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 python3-numpy-dev:amd64 (1:2.3.5+ds-2) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up libjs-sphinxdoc (8.2.3-9) ... Setting up libgfortran5:amd64 (15.2.0-9) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up perl-modules-5.40 (5.40.1-6) ... Setting up sse4.2-support (27) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up netbase (6.5) ... Setting up libmbedcrypto16:amd64 (3.6.5-0.1) ... Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1) ... Setting up libdivsufsort3:amd64 (2.0.1-7) ... Setting up openssl (3.5.4-1) ... Setting up readline-common (8.3-3) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up liblapack3:amd64 (3.12.1-7) ... 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 (5.40.1-6) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up perl (5.40.1-6) ... Setting up libmbedx509-7:amd64 (3.6.5-0.1) ... Setting up libmbedtls21:amd64 (3.6.5-0.1) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up hmmer (3.4+dfsg-3) ... Setting up libpython3.13-stdlib:amd64 (3.13.9-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3.13 (3.13.9-1) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Setting up python3 (3.13.7-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up ncbi-blast+ (2.17.0+ds-6) ... Setting up python3-packaging (25.0-1) ... Setting up python3-certifi (2025.11.12+ds-1) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up python3-numpy (1:2.3.5+ds-2) ... Setting up python3-dateutil (2.9.0-4) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-colorama (0.4.6-4) ... Setting up python3-colorlog (6.10.1-1) ... Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-2) ... Setting up python3-typeguard (4.4.4-1) ... Setting up python3-yaml (6.0.2-2) ... Setting up python3-pytz (2025.2-4) ... Setting up python3-inflect (7.5.0-1) ... Setting up python3-pandas (2.3.3+dfsg-2) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-networkx (3.4.2-2) ... Setting up macsyfinder (2.1.4-1+b2) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', '-y', 'install', 'macsyfinder'] 0m31.4s INFO: Running scripts post_install 0m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_install_exceptions'] 0m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_install_exceptions'] 0m31.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m32.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m32.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmptsg4gve9 to sid 0m32.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m32.2s INFO: Running scripts pre_distupgrade 0m32.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m32.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m32.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_distupgrade_exceptions'] 0m32.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_distupgrade_exceptions'] 0m32.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m32.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m32.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m32.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m32.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m32.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m32.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', 'update'] 0m34.7s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [176 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.2 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7454 kB] Fetched 17.9 MB in 2s (9797 kB/s) Reading package lists... 0m34.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', 'update'] 0m34.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', '-yf', 'dist-upgrade'] 0m39.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-more-itertools python3-pkg-resources python3-typeguard python3-typing-extensions Use 'sudo apt autoremove' to remove them. The following packages will be upgraded: libcap2 libjs-sphinxdoc libncursesw6 libperl5.40 libsystemd0 libtinfo6 libudev1 macsyfinder ncurses-base ncurses-bin perl perl-base perl-modules-5.40 python3-networkx sqv 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 50.5 MB of archives. After this operation, 13.3 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.5+20251123-1 [445 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libperl5.40 amd64 5.40.1-7 [4317 kB] Get:3 http://deb.debian.org/debian sid/main amd64 perl amd64 5.40.1-7 [267 kB] Get:4 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.40.1-7 [1679 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl-modules-5.40 all 5.40.1-7 [3012 kB] Get:6 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.5+20251123-1 [277 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.75-10+b2 [28.7 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 259~rc2-1 [470 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5+20251123-1 [136 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.5+20251123-1 [353 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 259~rc2-1 [157 kB] Get:12 http://deb.debian.org/debian sid/main amd64 sqv amd64 1.3.0-3+b1 [650 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libjs-sphinxdoc all 8.2.3-10 [27.7 kB] Get:14 http://deb.debian.org/debian sid/main amd64 python3-networkx all 3.4.2-3 [24.2 MB] Get:15 http://deb.debian.org/debian sid/main amd64 macsyfinder amd64 2.1.4-1+b3 [14.5 MB] Fetched 50.5 MB in 0s (183 MB/s) (Reading database ... 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(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 ... 15932 files and directories currently installed.) Preparing to unpack .../libjs-sphinxdoc_8.2.3-10_all.deb ... Unpacking libjs-sphinxdoc (8.2.3-10) over (8.2.3-9) ... Preparing to unpack .../python3-networkx_3.4.2-3_all.deb ... Unpacking python3-networkx (3.4.2-3) over (3.4.2-2) ... Preparing to unpack .../macsyfinder_2.1.4-1+b3_amd64.deb ... Unpacking macsyfinder (2.1.4-1+b3) over (2.1.4-1+b2) ... Setting up python3-networkx (3.4.2-3) ... Setting up libncursesw6:amd64 (6.5+20251123-1) ... Setting up libjs-sphinxdoc (8.2.3-10) ... Setting up perl-modules-5.40 (5.40.1-7) ... Setting up macsyfinder (2.1.4-1+b3) ... Setting up libperl5.40:amd64 (5.40.1-7) ... Setting up perl (5.40.1-7) ... Processing triggers for libc-bin (2.41-12) ... 0m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', '-yf', 'dist-upgrade'] 0m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m40.2s DUMP: 74b51794d1aea675d281e6377fa4b2f2 - 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m40.6s DUMP: Package: macsyfinder Source: macsyfinder (2.1.4-1) Version: 2.1.4-1+b3 Installed-Size: 37541 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 (>= 8.2), 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 (= 8.2.3-10) Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.1.4-1+b3_amd64.deb Size: 14490328 MD5sum: 7f8ad8fdb7a99806dd3ddf3c18ce1c12 SHA256: 1eda3ad64775b04667c7691b1d9dca57660b2b9ff4f30e61e32e57f57a0eee1f 0m40.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m40.6s INFO: apt-cache knows about the following packages: macsyfinder 0m40.6s INFO: Running scripts pre_install 0m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_database-server'] 0m40.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_database-server'] 0m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_exceptions'] 0m40.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_exceptions'] 0m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_extras'] 0m40.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_extras'] 0m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_foreign_architecture'] 0m40.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_foreign_architecture'] 0m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m40.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'policy'] 0m40.7s 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: 0m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'policy'] 0m40.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'policy', 'macsyfinder'] 0m40.7s DUMP: macsyfinder: Installed: 2.1.4-1+b3 Candidate: 2.1.4-1+b3 Version table: *** 2.1.4-1+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'policy', 'macsyfinder'] 0m40.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', '-y', 'install', 'macsyfinder'] 0m41.2s DUMP: Reading package lists... Building dependency tree... Reading state information... macsyfinder is already the newest version (2.1.4-1+b3). Solving dependencies... The following packages were automatically installed and are no longer required: python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-more-itertools python3-pkg-resources python3-typeguard python3-typing-extensions Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', '-y', 'install', 'macsyfinder'] 0m41.2s INFO: Running scripts post_install 0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_install_exceptions'] 0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_install_exceptions'] 0m41.2s INFO: Running scripts post_distupgrade 0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_distupgrade_exceptions'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_distupgrade_exceptions'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_distupgrade_zz_backports'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_distupgrade_zz_backports'] 0m41.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m42.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m42.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m42.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m42.9s INFO: Running scripts pre_install 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_database-server'] 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_database-server'] 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_exceptions'] 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_exceptions'] 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_extras'] 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_extras'] 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'policy'] 0m42.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'policy'] 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'policy', 'macsyfinder'] 0m43.0s DUMP: macsyfinder: Installed: 2.1.4-1+b3 Candidate: 2.1.4-1+b3 Version table: *** 2.1.4-1+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-cache', 'policy', 'macsyfinder'] 0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', '-y', 'install', 'macsyfinder=2.1.4-1+b3'] 0m43.5s DUMP: Reading package lists... Building dependency tree... Reading state information... macsyfinder is already the newest version (2.1.4-1+b3). Solving dependencies... The following packages were automatically installed and are no longer required: python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-more-itertools python3-pkg-resources python3-typeguard python3-typing-extensions Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', '-y', 'install', 'macsyfinder=2.1.4-1+b3'] 0m43.5s INFO: Running scripts post_install 0m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_install_exceptions'] 0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_install_exceptions'] 0m43.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m44.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m45.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', '-ac', '--ignore-obsolete'] 0m46.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', '-ac', '--ignore-obsolete'] 0m46.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m46.8s DUMP: 0.15.9~deb12u1 0m46.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m46.8s INFO: Running adequate version 0.15.9~deb12u1 now. 0m46.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'macsyfinder'] 0m46.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'macsyfinder'] 0m46.9s INFO: Running scripts pre_remove 0m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_remove_exceptions'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/pre_remove_exceptions'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m48.1s DUMP: install ok installed apt apt 3.1.12 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.8 install ok installed bash bash 5.3-1 install ok installed bsdutils bsdutils 1:2.41.2-4 install ok installed ca-certificates ca-certificates 20250419 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.12-1 install ok installed dpkg dpkg 1.22.21 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 14.3.0-10 install ok installed gcc-15-base:amd64 gcc-15-base 15.2.0-9 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.13-1 install ok installed hmmer hmmer 3.4+dfsg-3 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69 install ok installed isa-support:amd64 isa-support 27 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.1.12 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.2-1 install ok installed libblas3:amd64 libblas3 3.12.1-7 install ok installed libblkid1:amd64 libblkid1 2.41.2-4 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 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b2 install ok installed libcrypt1:amd64 libcrypt1 1:4.5.1-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.282 install ok installed libdivsufsort3:amd64 libdivsufsort3 2.0.1-7 install ok installed libexpat1:amd64 libexpat1 2.7.3-1 install ok installed libffi8:amd64 libffi8 3.5.2-2 install ok installed libgcc-s1:amd64 libgcc-s1 15.2.0-9 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.26-1 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.26-1 install ok installed libgfortran5:amd64 libgfortran5 15.2.0-9 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5 install ok installed libgomp1:amd64 libgomp1 15.2.0-9 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1 install ok installed libjs-jquery libjs-jquery 3.7.1+dfsg+~3.5.33-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 8.2.3-10 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed liblapack3:amd64 liblapack3 3.12.1-7 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41.2-4 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b2 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-6 install ok installed liblzma5:amd64 liblzma5 5.8.1-2 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.5-0.1 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.5-0.1 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.5-0.1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41.2-4 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.2.1+dfsg-2 install ok installed libncursesw6:amd64 libncursesw6 6.5+20251123-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1.1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1 install ok installed libperl5.40:amd64 libperl5.40 5.40.1-7 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.7-1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.9-1 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.9-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.3-3 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.9-4 install ok installed libsemanage-common libsemanage-common 3.9-1 install ok installed libsemanage2:amd64 libsemanage2 3.9-1 install ok installed libsepol2:amd64 libsepol2 3.9-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.41.2-4 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-8 install ok installed libssl3t64:amd64 libssl3t64 3.5.4-1 install ok installed libstdc++6:amd64 libstdc++6 15.2.0-9 install ok installed libsystemd0:amd64 libsystemd0 259~rc2-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20251123-1 install ok installed libudev1:amd64 libudev1 259~rc2-1 install ok installed libuuid1:amd64 libuuid1 2.41.2-4 install ok installed libuv1t64:amd64 libuv1t64 1.51.0-2 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 1.5.7+dfsg-2 install ok installed login login 1:4.16.0-2+really2.41.2-4 install ok installed login.defs login.defs 1:4.18.0-2 install ok installed macsyfinder macsyfinder 2.1.4-1+b3 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed media-types media-types 14.0.0 install ok installed mount mount 2.41.2-4 install ok installed ncbi-blast+ ncbi-blast+ 2.17.0+ds-6 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-6 install ok installed ncbi-vdb-data ncbi-vdb-data 3.2.1+dfsg-2 install ok installed ncurses-base ncurses-base 6.5+20251123-1 install ok installed ncurses-bin ncurses-bin 6.5+20251123-1 install ok installed netbase netbase 6.5 install ok installed openssl openssl 3.5.4-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.4-1 install ok installed passwd passwd 1:4.18.0-2 install ok installed perl perl 5.40.1-7 install ok installed perl-base perl-base 5.40.1-7 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.1-7 install ok installed python3 python3 3.13.7-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-certifi python3-certifi 2025.11.12+ds-1 install ok installed python3-colorama python3-colorama 0.4.6-4 install ok installed python3-colorlog python3-colorlog 6.10.1-1 install ok installed python3-dateutil python3-dateutil 2.9.0-4 install ok installed python3-inflect python3-inflect 7.5.0-1 install ok installed python3-jaraco.context python3-jaraco.context 6.0.1-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-minimal python3-minimal 3.13.7-1 install ok installed python3-more-itertools python3-more-itertools 10.8.0-1 install ok installed python3-networkx python3-networkx 3.4.2-3 install ok installed python3-numpy python3-numpy 1:2.3.5+ds-2 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.3.5+ds-2 install ok installed python3-packaging python3-packaging 25.0-1 install ok installed python3-pandas python3-pandas 2.3.3+dfsg-2 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.3.3+dfsg-2 install ok installed python3-pkg-resources python3-pkg-resources 78.1.1-0.1 install ok installed python3-pytz python3-pytz 2025.2-4 install ok installed python3-typeguard python3-typeguard 4.4.4-1 install ok installed python3-typing-extensions python3-typing-extensions 4.15.0-1 install ok installed python3-yaml python3-yaml 6.0.2-2 install ok installed python3.13 python3.13 3.13.9-1 install ok installed python3.13-minimal python3.13-minimal 3.13.9-1 install ok installed readline-common readline-common 8.3-3 install ok installed sed sed 4.9-2 install ok installed sphinx-rtd-theme-common sphinx-rtd-theme-common 3.0.2+dfsg-3 install ok installed sqv sqv 1.3.0-3+b1 install ok installed sse4.2-support sse4.2-support 27 install ok installed sysvinit-utils sysvinit-utils 3.15-6 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-5 install ok installed util-linux util-linux 2.41.2-4 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', 'remove', '--allow-remove-essential', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'isa-support:amd64', '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', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libuv1t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'ncbi-vdb-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-yaml', 'python3.13', 'python3.13-minimal', 'readline-common', 'sphinx-rtd-theme-common', 'sse4.2-support', 'macsyfinder'] 0m51.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following packages will be REMOVED: ca-certificates fonts-font-awesome fonts-lato hmmer isa-support libblas3 libdivsufsort3 libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgomp1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncursesw6 libnghttp2-14 libperl5.40 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libuv1t64 libyaml-0-2 macsyfinder media-types ncbi-blast+ ncbi-data ncbi-vdb-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-yaml python3.13 python3.13-minimal readline-common sphinx-rtd-theme-common sse4.2-support 0 upgraded, 0 newly installed, 67 to remove and 0 not upgraded. After this operation, 445 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 ... 15931 files and directories currently installed.) Removing macsyfinder (2.1.4-1+b3) ... Removing python3-certifi (2025.11.12+ds-1) ... Removing ca-certificates (20250419) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing sphinx-rtd-theme-common (3.0.2+dfsg-3) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing fonts-lato (2.015-1) ... Removing hmmer (3.4+dfsg-3) ... Removing ncbi-blast+ (2.17.0+ds-6) ... Removing sse4.2-support (27) ... Removing isa-support:amd64 (27) ... Removing python3-pandas (2.3.3+dfsg-2) ... Removing python3-pandas-lib:amd64 (2.3.3+dfsg-2) ... Removing python3-numpy (1:2.3.5+ds-2) ... Removing liblapack3:amd64 (3.12.1-7) ... Removing libblas3:amd64 (3.12.1-7) ... Removing libdivsufsort3:amd64 (2.0.1-7) ... Removing python3-yaml (6.0.2-2) ... Removing python3-pkg-resources (78.1.1-0.1) ... Removing python3-inflect (7.5.0-1) ... Removing python3-typeguard (4.4.4-1) ... Removing python3-pytz (2025.2-4) ... Removing python3-jaraco.context (6.0.1-1) ... Removing perl (5.40.1-7) ... Removing libperl5.40:amd64 (5.40.1-7) ... Removing libgdbm-compat4t64:amd64 (1.26-1) ... Removing libgdbm6t64:amd64 (1.26-1) ... Removing libgfortran5:amd64 (15.2.0-9) ... Removing libgomp1:amd64 (15.2.0-9) ... Removing libjs-jquery (3.7.1+dfsg+~3.5.33-1) ... Removing libjs-sphinxdoc (8.2.3-10) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing liblmdb0:amd64 (0.9.31-1+b2) ... Removing libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Removing libmbedtls21:amd64 (3.6.5-0.1) ... Removing libmbedx509-7:amd64 (3.6.5-0.1) ... Removing libmbedcrypto16:amd64 (3.6.5-0.1) ... Removing libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Removing libuv1t64:amd64 (1.51.0-2) ... Removing libyaml-0-2:amd64 (0.2.5-2) ... Removing ncbi-data (6.1.20170106+dfsg2-6) ... Removing ncbi-vdb-data (3.2.1+dfsg-2) ... Removing openssl (3.5.4-1) ... Removing perl-modules-5.40 (5.40.1-7) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-colorama (0.4.6-4) ... Removing python3-colorlog (6.10.1-1) ... Removing python3-dateutil (2.9.0-4) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-more-itertools (10.8.0-1) ... Removing python3-networkx (3.4.2-3) ... Removing python3-numpy-dev:amd64 (1:2.3.5+ds-2) ... Removing python3-packaging (25.0-1) ... Removing python3-typing-extensions (4.15.0-1) ... Removing python3 (3.13.7-1) ... Removing python3.13 (3.13.9-1) ... Removing python3-minimal (3.13.7-1) ... Removing python3.13-minimal (3.13.9-1) ... Removing libexpat1:amd64 (2.7.3-1) ... Removing libpython3-stdlib:amd64 (3.13.7-1) ... Removing libpython3.13-stdlib:amd64 (3.13.9-1) ... find: '/usr/lib/python3': No such file or directory Removing libffi8:amd64 (3.5.2-2) ... Removing libncursesw6:amd64 (6.5+20251123-1) ... Removing libpython3.13-minimal:amd64 (3.13.9-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.3-3) ... 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 media-types (14.0.0) ... Removing netbase (6.5) ... Removing readline-common (8.3-3) ... Processing triggers for libc-bin (2.41-12) ... 0m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', 'remove', '--allow-remove-essential', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'isa-support:amd64', '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', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libuv1t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'ncbi-vdb-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-yaml', 'python3.13', 'python3.13-minimal', 'readline-common', 'sphinx-rtd-theme-common', 'sse4.2-support', 'macsyfinder'] 0m51.5s INFO: Running scripts post_remove 0m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_remove_exceptions'] 0m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_remove_exceptions'] 0m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg', '--purge', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'isa-support:amd64', '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', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libuv1t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'ncbi-vdb-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-yaml', 'python3.13', 'python3.13-minimal', 'readline-common', 'sphinx-rtd-theme-common', 'sse4.2-support'] 0m51.7s DUMP: (Reading database ... 4924 files and directories currently installed.) Purging configuration files for ca-certificates (20250419) ... 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 isa-support 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 (3.7.1+dfsg+~3.5.33-1) ... 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 libncbi-vdb3 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 (3.13.9-1) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.3-3) ... 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 (14.0.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-6) ... Purging configuration files for ncbi-vdb-data (3.2.1+dfsg-2) ... Purging configuration files for netbase (6.5) ... Purging configuration files for openssl (3.5.4-1) ... Purging configuration files for perl (5.40.1-7) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed Purging configuration files for python3 (3.13.7-1) ... 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 Purging configuration files for python3-numpy (1:2.3.5+ds-2) ... dpkg: warning: ignoring request to remove python3-numpy-dev which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-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-yaml which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.9-1) ... Purging configuration files for readline-common (8.3-3) ... dpkg: warning: ignoring request to remove sphinx-rtd-theme-common which isn't installed Purging configuration files for sse4.2-support (27) ... 0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg', '--purge', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'isa-support:amd64', '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', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libuv1t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'ncbi-vdb-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-yaml', 'python3.13', 'python3.13-minimal', 'readline-common', 'sphinx-rtd-theme-common', 'sse4.2-support'] 0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg', '--purge', 'macsyfinder'] 0m51.7s DUMP: (Reading database ... 4907 files and directories currently installed.) Purging configuration files for macsyfinder (2.1.4-1+b3) ... 0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg', '--purge', 'macsyfinder'] 0m51.7s INFO: Running scripts post_purge 0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_purge_exceptions'] 0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_purge_exceptions'] 0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg', '--purge', '--pending'] 0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg', '--purge', '--pending'] 0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg', '--remove', '--pending'] 0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg', '--remove', '--pending'] 0m51.7s INFO: Running scripts post_test 0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_test_exceptions'] 0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'tmp/scripts/post_test_exceptions'] 0m51.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m52.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m52.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg-divert', '--list'] 0m52.0s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged 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 /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 0m52.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'dpkg-divert', '--list'] 0m52.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', 'clean'] 0m52.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptsg4gve9', 'apt-get', 'clean'] 0m52.0s DEBUG: Recording chroot state 0m53.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/shm'] 0m53.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/shm'] 0m53.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/console'] 0m53.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/console'] 0m53.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/ptmx'] 0m53.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/ptmx'] 0m53.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/pts'] 0m53.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/dev/pts'] 0m53.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/proc'] 0m53.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmptsg4gve9/proc'] 0m53.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m53.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmptsg4gve9'] 0m53.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmptsg4gve9 0m53.2s INFO: PASS: Upgrading between Debian distributions. 0m53.2s INFO: PASS: All tests. 0m53.2s INFO: piuparts run ends. ret=0 End: 2025-12-01 10:10:57 GMT