Start: 2025-09-18 03:47:57 GMT Package: augur Version: 24.4.0-3 Installed-Size: 1058 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-bcbio-gff, python3-biopython, python3-cvxopt, python3-importlib-resources | python3-supported-min (>= 3.11), python3-isodate, python3-jsonschema, python3-networkx, python3-numpy, python3-packaging, python3-pandas, python3-pyfastx, python3-scipy, python3-treetime (>= 0.9.4), python3-xopen (>= 1.7.0-1~), python3:any, python3-boto3, python3-dendropy, python3-matplotlib, python3-schedule, python3-seaborn, python3-zstandard, seqmagick, python3-ipdb, mafft, raxml, fasttree, vcftools Recommends: iqtree Description: pipeline components for real-time virus analysis Homepage: https://github.com/nextstrain/augur Description-md5: e2aaa44840d7b632d0e95700bc100196 Section: science Priority: optional Filename: pool/main/a/augur/augur_24.4.0-3_all.deb Size: 261712 MD5sum: 5f0e121db7f92a14fd48ff94d6dc1ffc SHA256: 85a8d958ce86d25eb11d388c5d4b52df7a7b233ef0731e4b71484331bed813d4 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-log-alternatives --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 forky --no-upgrade-test --apt augur=24.4.0-3 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-log-alternatives --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 forky --no-upgrade-test --apt augur=24.4.0-3 0m0.0s INFO: Running on: Linux piu-slave-conova-01 6.1.0-39-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.148-1 (2025-08-26) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpmml3a1xm 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpmml3a1xm 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', '--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/tmpmml3a1xm', '--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/tmpmml3a1xm/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/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/tmpmml3a1xm/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/tmpmml3a1xm/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/6', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/6', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/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-log-alternatives to /srv/piuparts.debian.org/tmp/tmpmml3a1xm/tmp/scripts/ 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpmml3a1xm/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-get', 'update'] 0m2.5s DUMP: Get:1 http://deb.debian.org/debian forky InRelease [147 kB] Get:2 http://deb.debian.org/debian forky/main amd64 Packages [9799 kB] Get:3 http://deb.debian.org/debian forky/main Translation-en [6535 kB] Fetched 16.5 MB in 1s (13.2 MB/s) Reading package lists... 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-get', 'update'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-get', '-yf', 'dist-upgrade'] 0m6.4s 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 bash bsdutils gcc-14-base init-system-helpers libapt-pkg7.0 libaudit-common libaudit1 libblkid1 libgcc-s1 libgmp10 liblastlog2-2 liblzma5 libmount1 libpcre2-8-0 libsmartcols1 libsqlite3-0 libssl3t64 libstdc++6 libsystemd0 libudev1 libuuid1 libzstd1 login login.defs mount openssl-provider-legacy passwd tzdata util-linux 31 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 15.3 MB of archives. After this operation, 1642 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 bsdutils amd64 1:2.41.1-3 [117 kB] Get:4 http://deb.debian.org/debian forky/main amd64 liblastlog2-2 amd64 2.41.1-3 [29.3 kB] Get:5 http://deb.debian.org/debian forky/main amd64 libuuid1 amd64 2.41.1-3 [38.9 kB] Get:6 http://deb.debian.org/debian forky/main amd64 libblkid1 amd64 2.41.1-3 [188 kB] Get:7 http://deb.debian.org/debian forky/main amd64 libmount1 amd64 2.41.1-3 [229 kB] Get:8 http://deb.debian.org/debian forky/main amd64 libsmartcols1 amd64 2.41.1-3 [157 kB] Get:9 http://deb.debian.org/debian forky/main amd64 util-linux amd64 2.41.1-3 [1306 kB] Get:10 http://deb.debian.org/debian forky/main amd64 mount amd64 2.41.1-3 [172 kB] Get:11 http://deb.debian.org/debian forky/main amd64 libsqlite3-0 amd64 3.46.1-8 [968 kB] Get:12 http://deb.debian.org/debian forky/main amd64 gcc-15-base amd64 15.2.0-4 [52.8 kB] Get:13 http://deb.debian.org/debian forky/main amd64 libgcc-s1 amd64 15.2.0-4 [71.7 kB] Get:14 http://deb.debian.org/debian forky/main amd64 liblzma5 amd64 5.8.1-1.1 [316 kB] Get:15 http://deb.debian.org/debian forky/main amd64 openssl-provider-legacy amd64 3.5.2-1 [307 kB] Get:16 http://deb.debian.org/debian forky/main amd64 libzstd1 amd64 1.5.7+dfsg-1.1 [320 kB] Get:17 http://deb.debian.org/debian forky/main amd64 libssl3t64 amd64 3.5.2-1 [2438 kB] Get:18 http://deb.debian.org/debian forky/main amd64 libstdc++6 amd64 15.2.0-4 [738 kB] Get:19 http://deb.debian.org/debian forky/main amd64 libsystemd0 amd64 258~rc4-1 [465 kB] Get:20 http://deb.debian.org/debian forky/main amd64 libudev1 amd64 258~rc4-1 [156 kB] Get:21 http://deb.debian.org/debian forky/main amd64 libapt-pkg7.0 amd64 3.1.5 [1182 kB] Get:22 http://deb.debian.org/debian forky/main amd64 apt amd64 3.1.5 [1479 kB] Get:23 http://deb.debian.org/debian forky/main amd64 init-system-helpers all 1.69 [39.3 kB] Get:24 http://deb.debian.org/debian forky/main amd64 libaudit-common all 1:4.1.1-1 [14.0 kB] Get:25 http://deb.debian.org/debian forky/main amd64 libaudit1 amd64 1:4.1.1-1 [61.6 kB] Get:26 http://deb.debian.org/debian forky/main amd64 login amd64 1:4.16.0-2+really2.41.1-3 [119 kB] Get:27 http://deb.debian.org/debian forky/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5 [574 kB] Get:28 http://deb.debian.org/debian forky/main amd64 libpcre2-8-0 amd64 10.46-1 [298 kB] Get:29 http://deb.debian.org/debian forky/main amd64 login.defs all 1:4.18.0-1 [211 kB] Get:30 http://deb.debian.org/debian forky/main amd64 passwd amd64 1:4.18.0-1 [1284 kB] Get:31 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get:32 http://deb.debian.org/debian forky/main amd64 gcc-14-base amd64 14.3.0-8 [52.1 kB] Preconfiguring packages ... Fetched 15.3 MB in 0s (127 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 .../libblkid1_2.41.1-3_amd64.deb ... Unpacking libblkid1:amd64 (2.41.1-3) over (2.41-5) ... Setting up libblkid1:amd64 (2.41.1-3) ... (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 .../libsmartcols1_2.41.1-3_amd64.deb ... Unpacking libsmartcols1:amd64 (2.41.1-3) over (2.41-5) ... Setting up libsmartcols1:amd64 (2.41.1-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4934 files and directories currently installed.) Preparing to unpack .../util-linux_2.41.1-3_amd64.deb ... Unpacking util-linux (2.41.1-3) over (2.41-5) ... Setting up util-linux (2.41.1-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4935 files and directories currently installed.) Preparing to unpack .../mount_2.41.1-3_amd64.deb ... Unpacking mount (2.41.1-3) over (2.41-5) ... 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) ... Selecting previously unselected package gcc-15-base:amd64. (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 ... 4940 files and directories currently installed.) Preparing to unpack .../libgcc-s1_15.2.0-4_amd64.deb ... Unpacking libgcc-s1:amd64 (15.2.0-4) over (14.2.0-19) ... Setting up libgcc-s1:amd64 (15.2.0-4) ... (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 ... 4940 files and directories currently installed.) Preparing to unpack .../liblzma5_5.8.1-1.1_amd64.deb ... Unpacking liblzma5:amd64 (5.8.1-1.1) over (5.8.1-1) ... Setting up liblzma5:amd64 (5.8.1-1.1) ... (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 ... 4940 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.5.2-1_amd64.deb ... Unpacking libssl3t64:amd64 (3.5.2-1) over (3.5.1-1) ... Setting up libssl3t64:amd64 (3.5.2-1) ... (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 ... 4940 files and directories currently installed.) Preparing to unpack .../libstdc++6_15.2.0-4_amd64.deb ... Unpacking libstdc++6:amd64 (15.2.0-4) over (14.2.0-19) ... Setting up libstdc++6:amd64 (15.2.0-4) ... (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 ... 4940 files and directories currently installed.) Preparing to unpack .../libsystemd0_258~rc4-1_amd64.deb ... Unpacking libsystemd0:amd64 (258~rc4-1) over (257.7-1) ... Setting up libsystemd0:amd64 (258~rc4-1) ... (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 ... 4940 files and directories currently installed.) Preparing to unpack .../libudev1_258~rc4-1_amd64.deb ... Unpacking libudev1:amd64 (258~rc4-1) over (257.7-1) ... Setting up libudev1:amd64 (258~rc4-1) ... (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 ... 4940 files and directories currently installed.) Preparing to unpack .../libapt-pkg7.0_3.1.5_amd64.deb ... Unpacking libapt-pkg7.0:amd64 (3.1.5) over (3.0.3) ... Setting up libapt-pkg7.0:amd64 (3.1.5) ... (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 ... 4940 files and directories currently installed.) Preparing to unpack .../archives/apt_3.1.5_amd64.deb ... Unpacking apt (3.1.5) over (3.0.3) ... Setting up apt (3.1.5) ... (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 ... 4938 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.69_all.deb ... Unpacking init-system-helpers (1.69) over (1.68) ... Setting up init-system-helpers (1.69) ... (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 ... 4939 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a4.1.1-1_all.deb ... Unpacking libaudit-common (1:4.1.1-1) over (1:4.0.2-2) ... Setting up libaudit-common (1:4.1.1-1) ... (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 ... 4939 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.1.1-1_amd64.deb ... Unpacking libaudit1:amd64 (1:4.1.1-1) over (1:4.0.2-2+b2) ... Setting up libaudit1:amd64 (1:4.1.1-1) ... (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 ... 4938 files and directories currently installed.) Preparing to unpack .../login_1%3a4.16.0-2+really2.41.1-3_amd64.deb ... Unpacking login (1:4.16.0-2+really2.41.1-3) over (1:4.16.0-2+really2.41-5) ... 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 ... 4941 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.46-1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.46-1) over (10.45-1) ... Setting up libpcre2-8-0:amd64 (10.46-1) ... (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 ... 4941 files and directories currently installed.) Preparing to unpack .../login.defs_1%3a4.18.0-1_all.deb ... Unpacking login.defs (1:4.18.0-1) over (1:4.17.4-2) ... Preparing to unpack .../passwd_1%3a4.18.0-1_amd64.deb ... Unpacking passwd (1:4.18.0-1) over (1:4.17.4-2) ... Preparing to unpack .../tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) over (2025b-4) ... Preparing to unpack .../gcc-14-base_14.3.0-8_amd64.deb ... Unpacking gcc-14-base:amd64 (14.3.0-8) over (14.2.0-19) ... Setting up gcc-14-base:amd64 (14.3.0-8) ... Setting up login.defs (1:4.18.0-1) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Sep 18 03:48:03 UTC 2025. Universal Time is now: Thu Sep 18 03:48:03 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up passwd (1:4.18.0-1) ... Setting up mount (2.41.1-3) ... Setting up login (1:4.16.0-2+really2.41.1-3) ... Processing triggers for debianutils (5.23.2) ... Processing triggers for libc-bin (2.41-12) ... 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-get', '-yf', 'dist-upgrade'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.3s DUMP: d135347dcb90b98cd15e34ce5efbfe38 - 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.3s INFO: Running scripts post_setup 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_setup_dummy_users'] 0m8.0s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_setup_dummy_users'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_setup_forbid_home'] 0m8.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_setup_forbid_home'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_setup_minimize'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_setup_minimize'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_setup_zz_backports'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_setup_zz_backports'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-get', 'clean'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-get', 'clean'] 0m8.1s DEBUG: Recording chroot state 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.5s DUMP: install ok installed apt apt 3.1.5 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.3-1 install ok installed bsdutils bsdutils 1:2.41.1-3 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 1:3.10-4 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 14.3.0-8 install ok installed gcc-15-base:amd64 gcc-15-base 15.2.0-4 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.1.5 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.1.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.1-1 install ok installed libblkid1:amd64 libblkid1 2.41.1-3 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 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 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libgcc-s1:amd64 libgcc-s1 15.2.0-4 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41.1-3 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1.1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41.1-3 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 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 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41.1-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-8 install ok installed libssl3t64:amd64 libssl3t64 3.5.2-1 install ok installed libstdc++6:amd64 libstdc++6 15.2.0-4 install ok installed libsystemd0:amd64 libsystemd0 258~rc4-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 258~rc4-1 install ok installed libuuid1:amd64 libuuid1 2.41.1-3 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1.1 install ok installed login login 1:4.16.0-2+really2.41.1-3 install ok installed login.defs login.defs 1:4.18.0-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41.1-3 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 3.5.2-1 install ok installed passwd passwd 1:4.18.0-1 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 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-5 install ok installed util-linux util-linux 2.41.1-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg-divert', '--list'] 0m8.5s 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 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg-divert', '--list'] 0m8.5s INFO: Running scripts is_testable 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/is_testable_uninstallable'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/is_testable_uninstallable'] 0m8.5s INFO: apt-cache does not know about any of the requested packages 0m8.5s INFO: Running scripts pre_test 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_test_exceptions'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_test_exceptions'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_test_root_password'] 0m8.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_test_root_password'] 0m8.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm'] 0m8.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm'] 0m9.1s DEBUG: No broken symlinks as far as we can find. 0m9.1s INFO: Running scripts pre_install 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_install_database-server'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_install_database-server'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_install_exceptions'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_install_exceptions'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_install_extras'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_install_extras'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_install_log_alternatives'] 0m9.1s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_install_log_alternatives'] 0m9.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm'] 0m9.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm'] 0m9.8s DEBUG: No broken symlinks as far as we can find. 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-cache', 'policy'] 0m10.4s 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: 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-cache', 'policy'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-cache', 'policy', 'augur'] 0m10.4s DUMP: augur: Installed: (none) Candidate: 24.4.0-3 Version table: 24.4.0-3 500 500 http://deb.debian.org/debian forky/main amd64 Packages 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-cache', 'policy', 'augur'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-get', '-y', 'install', 'augur=24.4.0-3'] 1m54.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: blt ca-certificates fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libabsl20240722 libamd3 libaom3 libatomic1 libavif16 libblas3 libbrotli1 libcairo2 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdav1d7 libdeflate0 libdsdp-5.8t64 libexpat1 libffi8 libfftw3-double3 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgav1-1 libgcrypt20 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglpk40 libgomp1 libgpg-error0 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo liblapack3 liblcms2-2 liblerc4 libltdl7 libncursesw6 libopenjp2-7 libperl5.40 libpixman-1-0 libpng16-16t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 librav1e0.7 libreadline8t64 libsharpyuv0 libsuitesparseconfig7 libsvtav1enc2 libtcl8.6 libtiff6 libtk8.6 libumfpack6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2-16 libxrender1 libxslt1.1 libxss1 libyuv0 libzopfli1 mafft media-types netbase openssl perl perl-modules-5.40 pigz python-matplotlib-data python3 python3-asttokens python3-attr python3-autocommand python3-bcbio-gff python3-biopython python3-boto3 python3-botocore python3-brotli python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-contourpy python3-cvxopt python3-cycler python3-dateutil python3-decorator python3-dendropy python3-executing python3-fonttools python3-freetype python3-fs python3-idna python3-inflect python3-ipdb python3-ipython python3-isodate python3-jaraco.context python3-jaraco.functools python3-jaraco.text python3-jedi python3-jmespath python3-jsonschema python3-jsonschema-specifications python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-matplotlib-inline python3-minimal python3-more-itertools python3-mpmath python3-networkx python3-numpy python3-numpy-dev python3-packaging python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pyfaidx python3-pyfastx python3-pygments python3-pygtrie python3-pyparsing python3-pytz python3-referencing python3-reportlab python3-requests python3-rlpycairo python3-rpds-py python3-s3transfer python3-schedule python3-scipy python3-seaborn python3-setuptools python3-six python3-stack-data python3-sympy python3-tk python3-traitlets python3-treetime python3-typeguard python3-typeshed python3-typing-extensions python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wcwidth python3-xopen python3-zipp python3-zopfli python3-zstandard python3.13 python3.13-minimal python3.13-tk raxml readline-common seqmagick sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core Suggested packages: blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre libfftw3-bin libfftw3-dev rng-tools gdbm-l10n low-memory-monitor libiodbc2-dev default-libmysqlclient-dev gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html liblcms2-utils sensible-utils tcl8.6 tk8.6 perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss muscle3 phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 python3-igraph samtools t-coffee wise python-charset-normalizer-doc python-cvxopt-doc python-cycler-doc python-ipython-doc python-jsonschema-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 gir1.2-gtk-4.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc python3-statsmodels python-pexpect-doc python-pil-doc python-pygments-doc ttf-bitstream-vera python-pygtrie-doc python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc python-setuptools-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python-traitlets-doc python-zstandard-doc python3.13-venv python3.13-doc binutils binfmt-support readline-doc sgml-base-doc debhelper Recommended packages: iqtree libglib2.0-data shared-mime-info xdg-user-dirs libgpg-error-l10n libgpm2 ncbi-blast+ libwww-perl lynx ruby python-biopython-doc python3-fqdn python3-isoduration python3-json-pointer python3-rfc3339-validator python3-rfc3986-validator python3-rfc3987 python3-uritemplate python3-webcolors python3-bs4 python3-cssselect python3-html5lib python3-gdal python3-pydot python3-pygraphviz python3-yaml python3-tz python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-tables python3-jinja2 python3-numba python3-olefile fonts-dejavu-extra g++ | c++-compiler python3-pooch isympy-common python3-isal tabix The following NEW packages will be installed: augur blt ca-certificates fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libabsl20240722 libamd3 libaom3 libatomic1 libavif16 libblas3 libbrotli1 libcairo2 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdav1d7 libdeflate0 libdsdp-5.8t64 libexpat1 libffi8 libfftw3-double3 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgav1-1 libgcrypt20 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglpk40 libgomp1 libgpg-error0 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo liblapack3 liblcms2-2 liblerc4 libltdl7 libncursesw6 libopenjp2-7 libperl5.40 libpixman-1-0 libpng16-16t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 librav1e0.7 libreadline8t64 libsharpyuv0 libsuitesparseconfig7 libsvtav1enc2 libtcl8.6 libtiff6 libtk8.6 libumfpack6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2-16 libxrender1 libxslt1.1 libxss1 libyuv0 libzopfli1 mafft media-types netbase openssl perl perl-modules-5.40 pigz python-matplotlib-data python3 python3-asttokens python3-attr python3-autocommand python3-bcbio-gff python3-biopython python3-boto3 python3-botocore python3-brotli python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-contourpy python3-cvxopt python3-cycler python3-dateutil python3-decorator python3-dendropy python3-executing python3-fonttools python3-freetype python3-fs python3-idna python3-inflect python3-ipdb python3-ipython python3-isodate python3-jaraco.context python3-jaraco.functools python3-jaraco.text python3-jedi python3-jmespath python3-jsonschema python3-jsonschema-specifications python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-matplotlib-inline python3-minimal python3-more-itertools python3-mpmath python3-networkx python3-numpy python3-numpy-dev python3-packaging python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pyfaidx python3-pyfastx python3-pygments python3-pygtrie python3-pyparsing python3-pytz python3-referencing python3-reportlab python3-requests python3-rlpycairo python3-rpds-py python3-s3transfer python3-schedule python3-scipy python3-seaborn python3-setuptools python3-six python3-stack-data python3-sympy python3-tk python3-traitlets python3-treetime python3-typeguard python3-typeshed python3-typing-extensions python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wcwidth python3-xopen python3-zipp python3-zopfli python3-zstandard python3.13 python3.13-minimal python3.13-tk raxml readline-common seqmagick sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 202 newly installed, 0 to remove and 0 not upgraded. Need to get 169 MB of archives. After this operation, 784 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get:2 http://deb.debian.org/debian forky/main amd64 pigz amd64 2.8-1 [62.7 kB] Get:3 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get:4 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 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 13.0.0 [29.3 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 3.13.7-1 [1960 kB] Get:13 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.7-1 [761 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 1:2.2.4+ds-1.2 [142 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 15.2.0-4 [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 1:2.2.4+ds-1.2 [5224 kB] Get:21 http://deb.debian.org/debian forky/main amd64 openssl amd64 3.5.2-1 [1493 kB] Get:22 http://deb.debian.org/debian forky/main amd64 ca-certificates all 20250419 [162 kB] Get:23 http://deb.debian.org/debian forky/main amd64 perl-modules-5.40 all 5.40.1-6 [3019 kB] Get:24 http://deb.debian.org/debian forky/main amd64 libgdbm6t64 amd64 1.26-1 [78.5 kB] Get:25 http://deb.debian.org/debian forky/main amd64 libgdbm-compat4t64 amd64 1.26-1 [52.8 kB] Get:26 http://deb.debian.org/debian forky/main amd64 libperl5.40 amd64 5.40.1-6 [4341 kB] Get:27 http://deb.debian.org/debian forky/main amd64 perl amd64 5.40.1-6 [267 kB] Get:28 http://deb.debian.org/debian forky/main amd64 python3-charset-normalizer amd64 3.4.3-1 [131 kB] Get:29 http://deb.debian.org/debian forky/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1041 kB] Get:30 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:31 http://deb.debian.org/debian forky/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get:32 http://deb.debian.org/debian forky/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:33 http://deb.debian.org/debian forky/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:34 http://deb.debian.org/debian forky/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:35 http://deb.debian.org/debian forky/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get:36 http://deb.debian.org/debian forky/main amd64 x11-common all 1:7.7+25 [217 kB] Get:37 http://deb.debian.org/debian forky/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:38 http://deb.debian.org/debian forky/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get:39 http://deb.debian.org/debian forky/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:40 http://deb.debian.org/debian forky/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get:41 http://deb.debian.org/debian forky/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get:42 http://deb.debian.org/debian forky/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:43 http://deb.debian.org/debian forky/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:44 http://deb.debian.org/debian forky/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:45 http://deb.debian.org/debian forky/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:46 http://deb.debian.org/debian forky/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:47 http://deb.debian.org/debian forky/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get:48 http://deb.debian.org/debian forky/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get:49 http://deb.debian.org/debian forky/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:50 http://deb.debian.org/debian forky/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get:51 http://deb.debian.org/debian forky/main amd64 libtk8.6 amd64 8.6.17-1 [794 kB] Get:52 http://deb.debian.org/debian forky/main amd64 python3.13-tk amd64 3.13.7-1 [108 kB] Get:53 http://deb.debian.org/debian forky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get:54 http://deb.debian.org/debian forky/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get:55 http://deb.debian.org/debian forky/main amd64 python3-tk amd64 3.13.5-1 [9604 B] Get:56 http://deb.debian.org/debian forky/main amd64 python3-pil.imagetk amd64 11.3.0-1 [81.1 kB] Get:57 http://deb.debian.org/debian forky/main amd64 libaom3 amd64 3.12.1-1 [1871 kB] Get:58 http://deb.debian.org/debian forky/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get:59 http://deb.debian.org/debian forky/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get:60 http://deb.debian.org/debian forky/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get:61 http://deb.debian.org/debian forky/main amd64 librav1e0.7 amd64 0.7.1-9+b2 [946 kB] Get:62 http://deb.debian.org/debian forky/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get:63 http://deb.debian.org/debian forky/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get:64 http://deb.debian.org/debian forky/main amd64 libyuv0 amd64 0.0.1916.20250814-1 [172 kB] Get:65 http://deb.debian.org/debian forky/main amd64 libavif16 amd64 1.3.0-1 [135 kB] Get:66 http://deb.debian.org/debian forky/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get:67 http://deb.debian.org/debian forky/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:68 http://deb.debian.org/debian forky/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get:69 http://deb.debian.org/debian forky/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:70 http://deb.debian.org/debian forky/main amd64 libatomic1 amd64 15.2.0-4 [9508 B] Get:71 http://deb.debian.org/debian forky/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get:72 http://deb.debian.org/debian forky/main amd64 libgraphite2-3 amd64 1.3.14-3 [75.1 kB] Get:73 http://deb.debian.org/debian forky/main amd64 libharfbuzz0b amd64 11.4.5-1 [505 kB] Get:74 http://deb.debian.org/debian forky/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get:75 http://deb.debian.org/debian forky/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:76 http://deb.debian.org/debian forky/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:77 http://deb.debian.org/debian forky/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:78 http://deb.debian.org/debian forky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:79 http://deb.debian.org/debian forky/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:80 http://deb.debian.org/debian forky/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get:81 http://deb.debian.org/debian forky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get:82 http://deb.debian.org/debian forky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get:83 http://deb.debian.org/debian forky/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get:84 http://deb.debian.org/debian forky/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:85 http://deb.debian.org/debian forky/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:86 http://deb.debian.org/debian forky/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:87 http://deb.debian.org/debian forky/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get:88 http://deb.debian.org/debian forky/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get:89 http://deb.debian.org/debian forky/main amd64 python3-freetype all 2.5.1-2 [89.4 kB] Get:90 http://deb.debian.org/debian forky/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:91 http://deb.debian.org/debian forky/main amd64 python3-reportlab all 4.4.3-1 [1168 kB] Get:92 http://deb.debian.org/debian forky/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get:93 http://deb.debian.org/debian forky/main amd64 xml-core all 0.19 [20.1 kB] Get:94 http://deb.debian.org/debian forky/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:95 http://deb.debian.org/debian forky/main amd64 python3-biopython amd64 1.85+dfsg-5 [1674 kB] Get:96 http://deb.debian.org/debian forky/main amd64 python3-six all 1.17.0-1 [16.5 kB] Get:97 http://deb.debian.org/debian forky/main amd64 python3-bcbio-gff all 0.7.1-2 [33.7 kB] Get:98 http://deb.debian.org/debian forky/main amd64 libgomp1 amd64 15.2.0-4 [140 kB] Get:99 http://deb.debian.org/debian forky/main amd64 libsuitesparseconfig7 amd64 1:7.11.0+dfsg-2 [33.4 kB] Get:100 http://deb.debian.org/debian forky/main amd64 libamd3 amd64 1:7.11.0+dfsg-2 [51.0 kB] Get:101 http://deb.debian.org/debian forky/main amd64 libcamd3 amd64 1:7.11.0+dfsg-2 [47.8 kB] Get:102 http://deb.debian.org/debian forky/main amd64 libccolamd3 amd64 1:7.11.0+dfsg-2 [49.7 kB] Get:103 http://deb.debian.org/debian forky/main amd64 libcolamd3 amd64 1:7.11.0+dfsg-2 [42.4 kB] Get:104 http://deb.debian.org/debian forky/main amd64 libcholmod5 amd64 1:7.11.0+dfsg-2 [703 kB] Get:105 http://deb.debian.org/debian forky/main amd64 libdsdp-5.8t64 amd64 5.8-11 [183 kB] Get:106 http://deb.debian.org/debian forky/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get:107 http://deb.debian.org/debian forky/main amd64 libltdl7 amd64 2.5.4-5 [416 kB] Get:108 http://deb.debian.org/debian forky/main amd64 libglpk40 amd64 5.0-2 [398 kB] Get:109 http://deb.debian.org/debian forky/main amd64 libgslcblas0 amd64 2.8+dfsg-5.1 [137 kB] Get:110 http://deb.debian.org/debian forky/main amd64 libgsl28 amd64 2.8+dfsg-5.1 [1068 kB] Get:111 http://deb.debian.org/debian forky/main amd64 libumfpack6 amd64 1:7.11.0+dfsg-2 [309 kB] Get:112 http://deb.debian.org/debian forky/main amd64 python3-cvxopt amd64 1.3.0+dfsg-1+b9 [265 kB] Get:113 http://deb.debian.org/debian forky/main amd64 python3-isodate all 0.7.2-1 [19.5 kB] Get:114 http://deb.debian.org/debian forky/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get:115 http://deb.debian.org/debian forky/main amd64 python3-rpds-py amd64 0.21.0-2+b1 [257 kB] Get:116 http://deb.debian.org/debian forky/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get:117 http://deb.debian.org/debian forky/main amd64 python3-referencing all 0.36.2-1 [23.7 kB] Get:118 http://deb.debian.org/debian forky/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get:119 http://deb.debian.org/debian forky/main amd64 python3-jsonschema all 4.19.2-6 [71.4 kB] Get:120 http://deb.debian.org/debian forky/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:121 http://deb.debian.org/debian forky/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get:122 http://deb.debian.org/debian forky/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get:123 http://deb.debian.org/debian forky/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get:124 http://deb.debian.org/debian forky/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:125 http://deb.debian.org/debian forky/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get:126 http://deb.debian.org/debian forky/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get:127 http://deb.debian.org/debian forky/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get:128 http://deb.debian.org/debian forky/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get:129 http://deb.debian.org/debian forky/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get:130 http://deb.debian.org/debian forky/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get:131 http://deb.debian.org/debian forky/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get:132 http://deb.debian.org/debian forky/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get:133 http://deb.debian.org/debian forky/main amd64 python3-pytz all 2025.2-3 [152 kB] Get:134 http://deb.debian.org/debian forky/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-9 [4595 kB] Get:135 http://deb.debian.org/debian forky/main amd64 python3-pandas all 2.2.3+dfsg-9 [3097 kB] Get:136 http://deb.debian.org/debian forky/main amd64 python3-pyfaidx all 0.8.1.3-2 [29.1 kB] Get:137 http://deb.debian.org/debian forky/main amd64 python3-pyfastx amd64 2.2.0-1+b1 [58.1 kB] Get:138 http://deb.debian.org/debian forky/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get:139 http://deb.debian.org/debian forky/main amd64 python3-scipy amd64 1.15.3-1.1 [17.0 MB] Get:140 http://deb.debian.org/debian forky/main amd64 fonts-lyx all 2.4.4-1 [190 kB] Get:141 http://deb.debian.org/debian forky/main amd64 python-matplotlib-data all 3.10.1+dfsg1-5 [2737 kB] Get:142 http://deb.debian.org/debian forky/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:143 http://deb.debian.org/debian forky/main amd64 python3-contourpy amd64 1.3.1-2 [215 kB] Get:144 http://deb.debian.org/debian forky/main amd64 python3-cycler all 0.12.1-2 [9616 B] Get:145 http://deb.debian.org/debian forky/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get:146 http://deb.debian.org/debian forky/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get:147 http://deb.debian.org/debian forky/main amd64 python3-fs all 2.4.16-8 [95.2 kB] Get:148 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get:149 http://deb.debian.org/debian forky/main amd64 libgpg-error0 amd64 1.55-2 [88.1 kB] Get:150 http://deb.debian.org/debian forky/main amd64 libgcrypt20 amd64 1.11.2-2 [865 kB] Get:151 http://deb.debian.org/debian forky/main amd64 libxslt1.1 amd64 1.1.43-0.2 [155 kB] Get:152 http://deb.debian.org/debian forky/main amd64 python3-lxml amd64 6.0.1-1 [1434 kB] Get:153 http://deb.debian.org/debian forky/main amd64 python3-lz4 amd64 4.4.4+dfsg-1 [25.4 kB] Get:154 http://deb.debian.org/debian forky/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:155 http://deb.debian.org/debian forky/main amd64 python3-sympy all 1.14.0-2 [4228 kB] Get:156 http://deb.debian.org/debian forky/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get:157 http://deb.debian.org/debian forky/main amd64 python3-unicodedata2 amd64 16.0.0+ds-1 [324 kB] Get:158 http://deb.debian.org/debian forky/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get:159 http://deb.debian.org/debian forky/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get:160 http://deb.debian.org/debian forky/main amd64 unicode-data all 16.0.0-1 [9197 kB] Get:161 http://deb.debian.org/debian forky/main amd64 python3-fonttools amd64 4.57.0-2 [1457 kB] Get:162 http://deb.debian.org/debian forky/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get:163 http://deb.debian.org/debian forky/main amd64 libqhull-r8.0 amd64 2020.2-7 [248 kB] Get:164 http://deb.debian.org/debian forky/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-5 [23.8 MB] Get:165 http://deb.debian.org/debian forky/main amd64 python3-treetime all 0.11.4-1 [938 kB] Get:166 http://deb.debian.org/debian forky/main amd64 python3-xopen all 1.7.0-3 [16.8 kB] Get:167 http://deb.debian.org/debian forky/main amd64 python3-jmespath all 1.0.1-1 [21.1 kB] Get:168 http://deb.debian.org/debian forky/main amd64 python3-urllib3 all 2.5.0-1 [116 kB] Get:169 http://deb.debian.org/debian forky/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get:170 http://deb.debian.org/debian forky/main amd64 python3-idna all 3.10-1 [42.0 kB] Get:171 http://deb.debian.org/debian forky/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get:172 http://deb.debian.org/debian forky/main amd64 python3-requests all 2.32.5+dfsg-1 [72.4 kB] Get:173 http://deb.debian.org/debian forky/main amd64 python3-botocore all 1.37.9+repack-1 [7311 kB] Get:174 http://deb.debian.org/debian forky/main amd64 python3-s3transfer all 0.11.4-1 [57.7 kB] Get:175 http://deb.debian.org/debian forky/main amd64 python3-boto3 all 1.37.9-1 [339 kB] Get:176 http://deb.debian.org/debian forky/main amd64 python3-dendropy all 4.6.1-2 [277 kB] Get:177 http://deb.debian.org/debian forky/main amd64 python3-schedule all 1.2.2-1 [14.9 kB] Get:178 http://deb.debian.org/debian forky/main amd64 python3-seaborn all 0.13.2-5 [215 kB] Get:179 http://deb.debian.org/debian forky/main amd64 python3-zstandard amd64 0.24.0-1 [351 kB] Get:180 http://deb.debian.org/debian forky/main amd64 python3-pygtrie all 2.2-3 [17.1 kB] Get:181 http://deb.debian.org/debian forky/main amd64 seqmagick all 0.8.6-3 [40.1 kB] Get:182 http://deb.debian.org/debian forky/main amd64 python3-parso all 0.8.4-1 [67.8 kB] Get:183 http://deb.debian.org/debian forky/main amd64 python3-typeshed all 0.0~git20241223.ea91db2-4 [1531 kB] Get:184 http://deb.debian.org/debian forky/main amd64 python3-jedi all 0.19.1+ds1-1 [691 kB] Get:185 http://deb.debian.org/debian forky/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get:186 http://deb.debian.org/debian forky/main amd64 python3-matplotlib-inline all 0.1.7-1 [9032 B] Get:187 http://deb.debian.org/debian forky/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB] Get:188 http://deb.debian.org/debian forky/main amd64 python3-prompt-toolkit all 3.0.52-1 [280 kB] Get:189 http://deb.debian.org/debian forky/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get:190 http://deb.debian.org/debian forky/main amd64 python3-asttokens all 3.0.0-2 [20.2 kB] Get:191 http://deb.debian.org/debian forky/main amd64 python3-executing all 2.2.0-0.3 [24.6 kB] Get:192 http://deb.debian.org/debian forky/main amd64 python3-pure-eval all 0.2.3-1 [11.2 kB] Get:193 http://deb.debian.org/debian forky/main amd64 python3-stack-data all 0.6.3-1 [21.6 kB] Get:194 http://deb.debian.org/debian forky/main amd64 python3-ptyprocess all 0.7.0-6 [14.5 kB] Get:195 http://deb.debian.org/debian forky/main amd64 python3-pexpect all 4.9-3 [55.6 kB] Get:196 http://deb.debian.org/debian forky/main amd64 python3-ipython all 8.35.0-2 [576 kB] Get:197 http://deb.debian.org/debian forky/main amd64 python3-ipdb all 0.13.13-3 [17.5 kB] Get:198 http://deb.debian.org/debian forky/main amd64 mafft amd64 7.525-1 [1186 kB] Get:199 http://deb.debian.org/debian forky/main amd64 raxml amd64 8.2.13+dfsg-2+b1 [1514 kB] Get:200 http://deb.debian.org/debian forky/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get:201 http://deb.debian.org/debian forky/main amd64 vcftools amd64 0.1.17-1 [468 kB] Get:202 http://deb.debian.org/debian forky/main amd64 augur all 24.4.0-3 [262 kB] Preconfiguring packages ... Fetched 169 MB in 1s (165 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4946 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package pigz. Preparing to unpack .../archives/pigz_2.8-1_amd64.deb ... Unpacking pigz (2.8-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. 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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_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up media-types (13.0.0) ... Setting up libgraphite2-3:amd64 (1.3.14-3) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up libaom3:amd64 (3.12.1-1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up libgdbm6t64:amd64 (1.26-1) ... Setting up libgpg-error0:amd64 (1.55-2) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5.1) ... Setting up libgdbm-compat4t64:amd64 (1.26-1) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up fonts-lyx (2.4.4-1) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up x11-common (1:7.7+25) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libdeflate0:amd64 (1.23-2) ... Setting up libgcrypt20:amd64 (1.11.2-2) ... Setting up libqhull-r8.0:amd64 (2020.2-7) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libgomp1:amd64 (15.2.0-4) ... Setting up libabsl20240722:amd64 (20240722.0-4) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up unicode-data (16.0.0-1) ... Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... 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 libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libzopfli1 (1.0.3-3) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libsvtav1enc2:amd64 (2.3.0+dfsg-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (4.4.0-3) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.50-1) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1.2) ... Setting up libatomic1:amd64 (15.2.0-4) ... Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgav1-1:amd64 (0.19.0-3+b1) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up libltdl7:amd64 (2.5.4-5) ... Setting up libfftw3-double3:amd64 (3.3.10-2+b1) ... Setting up libgfortran5:amd64 (15.2.0-4) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up libdav1d7:amd64 (1.5.1-1) ... Setting up perl-modules-5.40 (5.40.1-6) ... Setting up pigz (2.8-1) ... Setting up libtiff6:amd64 (4.7.0-5) ... Setting up librav1e0.7:amd64 (0.7.1-9+b2) ... Setting up libxslt1.1:amd64 (1.1.43-0.2) ... Setting up libsuitesparseconfig7:amd64 (1:7.11.0+dfsg-2) ... Setting up libopenjp2-7:amd64 (2.5.3-2.1) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up fasttree (2.1.11-2) ... Setting up netbase (6.5) ... Setting up sgml-base (1.31+nmu1) ... Setting up libgsl28:amd64 (2.8+dfsg-5.1) ... Setting up python-matplotlib-data (3.10.1+dfsg1-5) ... Setting up openssl (3.5.2-1) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up libyuv0:amd64 (0.0.1916.20250814-1) ... Setting up readline-common (8.3-3) ... Setting up raxml (8.2.13+dfsg-2+b1) ... Setting up libavif16:amd64 (1.3.0-1) ... 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 libamd3:amd64 (1:7.11.0+dfsg-2) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up libcolamd3:amd64 (1:7.11.0+dfsg-2) ... Setting up fontconfig-config (2.15.0-2.4) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libcamd3:amd64 (1:7.11.0+dfsg-2) ... 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 libglib2.0-0t64:amd64 (2.84.4-3) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libglpk40:amd64 (5.0-2) ... Setting up libccolamd3:amd64 (1:7.11.0+dfsg-2) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (11.4.5-1) ... Setting up libdsdp-5.8t64 (5.8-11) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2.4) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up vcftools (0.1.17-1) ... Setting up libcholmod5:amd64 (1:7.11.0+dfsg-2) ... Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up python3.13 (3.13.7-1) ... Setting up mafft (7.525-1) ... Setting up libtk8.6:amd64 (8.6.17-1) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-freetype (2.5.1-2) ... Setting up xfonts-utils (1:7.7+7) ... Setting up python3-autocommand (2.2.2-3) ... Setting up libcairo2:amd64 (1.18.4-1+b1) ... Setting up python3.13-tk (3.13.7-1) ... Setting up python3-platformdirs (4.4.0-1) ... Setting up python3-zopfli (0.2.3.post1-1+b1) ... Setting up python3-fs (2.4.16-8) ... Setting up python3-six (1.17.0-1) ... Setting up python3-isodate (0.7.2-1) ... Setting up python3-decorator (5.2.1-2) ... Setting up python3-pygtrie (2.2-3) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-xopen (1.7.0-3) ... Setting up python3-zstandard (0.24.0-1) ... Setting up python3-packaging (25.0-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-wcwidth (0.2.13+dfsg1-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up python3-typeshed (0.0~git20241223.ea91db2-4) ... Setting up python3-jmespath (1.0.1-1) ... Setting up python3-brotli (1.1.0-2+b7) ... Setting up libraqm0:amd64 (0.10.3-1) ... Setting up python3-cycler (0.12.1-2) ... Setting up python3-kiwisolver (1.4.7-3+b1) ... Setting up python3-idna (3.10-1) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up python3-numpy (1:2.2.4+ds-1.2) ... Setting up python3-urllib3 (2.5.0-1) ... Setting up python3-rpds-py (0.21.0-2+b1) ... Setting up libumfpack6:amd64 (1:7.11.0+dfsg-2) ... Setting up python3-lxml:amd64 (6.0.1-1) ... Setting up python3-traitlets (5.14.3+really5.14.3-1) ... Setting up python3-dateutil (2.9.0-4) ... Setting up python3-contourpy (1.3.1-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-dendropy (4.6.1-2) ... Setting up python3-ptyprocess (0.7.0-6) ... Setting up python3-prompt-toolkit (3.0.52-1) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up python3-schedule (1.2.2-1) ... Setting up python3-pyfaidx (0.8.1.3-2) ... Setting up python3-sympy (1.14.0-2) ... Setting up python3-attr (25.3.0-1) ... Setting up python3-pure-eval (0.2.3-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... Setting up python3-scipy (1.15.3-1.1) ... Setting up python3-cairo (1.27.0-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-parso (0.8.4-1) ... Setting up python3-cvxopt (1.3.0+dfsg-1+b9) ... Setting up python3-lz4 (4.4.4+dfsg-1) ... Setting up python3-asttokens (3.0.0-2) ... Setting up python3-charset-normalizer (3.4.3-1) ... Setting up python3-unicodedata2 (16.0.0+ds-1) ... Setting up blt (2.5.3+dfsg-8) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-9) ... Setting up python3-typeguard (4.4.4-1) ... Setting up python3-pyfastx (2.2.0-1+b1) ... Setting up python3-tk:amd64 (3.13.5-1) ... Setting up python3-pytz (2025.2-3) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-matplotlib-inline (0.1.7-1) ... Setting up python3-pil:amd64 (11.3.0-1) ... Setting up python3-inflect (7.5.0-1) ... Setting up python3-pandas (2.2.3+dfsg-9) ... Setting up python3-pil.imagetk:amd64 (11.3.0-1) ... Setting up python3-executing (2.2.0-0.3) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pexpect (4.9-3) ... Setting up python3-requests (2.32.5+dfsg-1) ... Setting up python3-reportlab (4.4.3-1) ... Setting up python3-stack-data (0.6.3-1) ... Setting up python3-referencing (0.36.2-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up python3-jedi (0.19.1+ds1-1) ... Setting up python3-networkx (3.2.1-5) ... Setting up python3-ipython (8.35.0-2) ... Setting up python3-botocore (1.37.9+repack-1) ... Setting up python3-ipdb (0.13.13-3) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up python3-s3transfer (0.11.4-1) ... Setting up python3-jsonschema (4.19.2-6) ... Setting up python3-boto3 (1.37.9-1) ... Setting up python3-fonttools (4.57.0-2) ... Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... Setting up python3-matplotlib (3.10.1+dfsg1-5) ... Setting up python3-seaborn (0.13.2-5) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-5) ... Setting up python3-treetime (0.11.4-1) ... Setting up seqmagick (0.8.6-3) ... Setting up python3-bcbio-gff (0.7.1-2) ... Setting up augur (24.4.0-3) ... 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. 1m54.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-get', '-y', 'install', 'augur=24.4.0-3'] 1m54.0s INFO: Running scripts post_install 1m54.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_install_exceptions'] 1m54.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_install_exceptions'] 1m54.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_install_log_alternatives'] 1m54.0s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=python3: piuparts=augur=24.4.0-3: /usr/bin/update-alternatives --auto /usr/bin/python3 LOG-ALTERNATIVES: dpkg=libblas3: piuparts=augur=24.4.0-3: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 LOG-ALTERNATIVES: dpkg=liblapack3: piuparts=augur=24.4.0-3: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 LOG-ALTERNATIVES: dpkg=perl: piuparts=augur=24.4.0-3: /usr/bin/update-alternatives --remove rename /usr/bin/prename 1m54.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_install_log_alternatives'] 1m54.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'systemd-tmpfiles', '--cat-config'] 1m54.0s DUMP: chroot: failed to run command 'systemd-tmpfiles': No such file or directory 1m54.0s DEBUG: Command failed (status=127), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'systemd-tmpfiles', '--cat-config'] 1m54.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm'] 1m56.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm'] 1m59.4s ERROR: WARN: Broken symlinks: /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-Italic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-Italic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-BoldItalic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-BoldItalic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-Bold.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-Bold.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerif-Italic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerif-BoldItalic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-Oblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-Oblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-BoldOblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-BoldOblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-Bold.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-Bold.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-Oblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-ExtraLight.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-ExtraLight.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-BoldOblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuMathTeXGyre.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuMathTeXGyre.ttf (python3-reportlab) /usr/share/doc/python3-networkx/html/_static/sphinx_highlight.js -> ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js (python3-networkx) /usr/share/doc/python3-networkx/html/_static/searchtools.js -> ../../../../javascript/sphinxdoc/1.0/searchtools.js (python3-networkx) /usr/share/doc/python3-networkx/html/_static/language_data.js -> ../../../../javascript/sphinxdoc/1.0/language_data.js (python3-networkx) /usr/share/doc/python3-networkx/html/_static/doctools.js -> ../../../../javascript/sphinxdoc/1.0/doctools.js (python3-networkx) 2m1.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', '-ac', '--ignore-obsolete'] 2m16.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', '-ac', '--ignore-obsolete'] 2m16.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m16.3s DUMP: 0.15.9~deb12u1 2m16.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m16.3s INFO: Running adequate version 0.15.9~deb12u1 now. 2m16.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'augur'] 2m16.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'augur'] 2m16.5s INFO: Running scripts pre_remove 2m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m25.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_remove_exceptions'] 2m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/pre_remove_exceptions'] 2m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m26.2s DUMP: install ok installed apt apt 3.1.5 install ok installed augur augur 24.4.0-3 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.3-1 install ok installed blt blt 2.5.3+dfsg-8 install ok installed bsdutils bsdutils 1:2.41.1-3 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 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed fasttree fasttree 2.1.11-2 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig-config fontconfig-config 2.15.0-2.4 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-lyx fonts-lyx 2.4.4-1 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.3.0-8 install ok installed gcc-15-base:amd64 gcc-15-base 15.2.0-4 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69 install ok installed libabsl20240722:amd64 libabsl20240722 20240722.0-4 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libamd3:amd64 libamd3 1:7.11.0+dfsg-2 install ok installed libaom3:amd64 libaom3 3.12.1-1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.1.5 install ok installed libatomic1:amd64 libatomic1 15.2.0-4 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.1.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.1-1 install ok installed libavif16:amd64 libavif16 1.3.0-1 install ok installed libblas3:amd64 libblas3 3.12.1-7 install ok installed libblkid1:amd64 libblkid1 2.41.1-3 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b7 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 libcairo2:amd64 libcairo2 1.18.4-1+b1 install ok installed libcamd3:amd64 libcamd3 1:7.11.0+dfsg-2 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 libccolamd3:amd64 libccolamd3 1:7.11.0+dfsg-2 install ok installed libcholmod5:amd64 libcholmod5 1:7.11.0+dfsg-2 install ok installed libcolamd3:amd64 libcolamd3 1:7.11.0+dfsg-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdav1d7:amd64 libdav1d7 1.5.1-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libdeflate0:amd64 libdeflate0 1.23-2 install ok installed libdsdp-5.8t64 libdsdp-5.8t64 5.8-11 install ok installed libexpat1:amd64 libexpat1 2.7.1-2 install ok installed libffi8:amd64 libffi8 3.5.2-2 install ok installed libfftw3-double3:amd64 libfftw3-double3 3.3.10-2+b1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-2.4 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1+b2 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1 install ok installed libgav1-1:amd64 libgav1-1 0.19.0-3+b1 install ok installed libgcc-s1:amd64 libgcc-s1 15.2.0-4 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.2-2 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 15.2.0-4 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.84.4-3 install ok installed libglpk40:amd64 libglpk40 5.0-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5 install ok installed libgomp1:amd64 libgomp1 15.2.0-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.55-2 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-3 install ok installed libgsl28:amd64 libgsl28 2.8+dfsg-5.1 install ok installed libgslcblas0:amd64 libgslcblas0 2.8+dfsg-5.1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 11.4.5-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed libimagequant0:amd64 libimagequant0 4.4.0-3 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-4 install ok installed liblapack3:amd64 liblapack3 3.12.1-7 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41.1-3 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed libltdl7:amd64 libltdl7 2.5.4-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1.1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41.1-3 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.3-2.1 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 libperl5.40:amd64 libperl5.40 5.40.1-6 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.50-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.7-1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.7-1 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.7-1 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-7 install ok installed libraqm0:amd64 libraqm0 0.10.3-1 install ok installed librav1e0.7:amd64 librav1e0.7 0.7.1-9+b2 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 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.5.0-0.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41.1-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-8 install ok installed libssl3t64:amd64 libssl3t64 3.5.2-1 install ok installed libstdc++6:amd64 libstdc++6 15.2.0-4 install ok installed libsuitesparseconfig7:amd64 libsuitesparseconfig7 1:7.11.0+dfsg-2 install ok installed libsvtav1enc2:amd64 libsvtav1enc2 2.3.0+dfsg-1 install ok installed libsystemd0:amd64 libsystemd0 258~rc4-1 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.17+dfsg-1 install ok installed libtiff6:amd64 libtiff6 4.7.0-5 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libtk8.6:amd64 libtk8.6 8.6.17-1 install ok installed libudev1:amd64 libudev1 258~rc4-1 install ok installed libumfpack6:amd64 libumfpack6 1:7.11.0+dfsg-2 install ok installed libuuid1:amd64 libuuid1 2.41.1-3 install ok installed libwebp7:amd64 libwebp7 1.5.0-0.1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.5.0-0.1 install ok installed libwebpmux3:amd64 libwebpmux3 1.5.0-0.1 install ok installed libx11-6:amd64 libx11-6 2:1.8.12-1 install ok installed libx11-data libx11-data 2:1.8.12-1 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3 install ok installed libxft2:amd64 libxft2 2.3.6-1+b4 install ok installed libxml2-16:amd64 libxml2-16 2.14.5+dfsg-0.2 install ok installed libxrender1:amd64 libxrender1 1:0.9.12-1 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.43-0.2 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b3 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libyuv0:amd64 libyuv0 0.0.1916.20250814-1 install ok installed libzopfli1 libzopfli1 1.0.3-3 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1.1 install ok installed login login 1:4.16.0-2+really2.41.1-3 install ok installed login.defs login.defs 1:4.18.0-1 install ok installed mafft mafft 7.525-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed media-types media-types 13.0.0 install ok installed mount mount 2.41.1-3 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 netbase netbase 6.5 install ok installed openssl openssl 3.5.2-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.2-1 install ok installed passwd passwd 1:4.18.0-1 install ok installed perl perl 5.40.1-6 install ok installed perl-base perl-base 5.40.1-6 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.1-6 install ok installed pigz pigz 2.8-1 install ok installed python-matplotlib-data python-matplotlib-data 3.10.1+dfsg1-5 install ok installed python3 python3 3.13.7-1 install ok installed python3-asttokens python3-asttokens 3.0.0-2 install ok installed python3-attr python3-attr 25.3.0-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-bcbio-gff python3-bcbio-gff 0.7.1-2 install ok installed python3-biopython python3-biopython 1.85+dfsg-5 install ok installed python3-boto3 python3-boto3 1.37.9-1 install ok installed python3-botocore python3-botocore 1.37.9+repack-1 install ok installed python3-brotli python3-brotli 1.1.0-2+b7 install ok installed python3-cairo python3-cairo 1.27.0-2 install ok installed python3-certifi python3-certifi 2025.1.31+ds-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-2 install ok installed python3-charset-normalizer python3-charset-normalizer 3.4.3-1 install ok installed python3-contourpy python3-contourpy 1.3.1-2 install ok installed python3-cvxopt python3-cvxopt 1.3.0+dfsg-1+b9 install ok installed python3-cycler python3-cycler 0.12.1-2 install ok installed python3-dateutil python3-dateutil 2.9.0-4 install ok installed python3-decorator python3-decorator 5.2.1-2 install ok installed python3-dendropy python3-dendropy 4.6.1-2 install ok installed python3-executing python3-executing 2.2.0-0.3 install ok installed python3-fonttools python3-fonttools 4.57.0-2 install ok installed python3-freetype python3-freetype 2.5.1-2 install ok installed python3-fs python3-fs 2.4.16-8 install ok installed python3-idna python3-idna 3.10-1 install ok installed python3-inflect python3-inflect 7.5.0-1 install ok installed python3-ipdb python3-ipdb 0.13.13-3 install ok installed python3-ipython python3-ipython 8.35.0-2 install ok installed python3-isodate python3-isodate 0.7.2-1 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-jaraco.text python3-jaraco.text 4.0.0-1 install ok installed python3-jedi python3-jedi 0.19.1+ds1-1 install ok installed python3-jmespath python3-jmespath 1.0.1-1 install ok installed python3-jsonschema python3-jsonschema 4.19.2-6 install ok installed python3-jsonschema-specifications python3-jsonschema-specifications 2023.12.1-2 install ok installed python3-kiwisolver python3-kiwisolver 1.4.7-3+b1 install ok installed python3-lxml:amd64 python3-lxml 6.0.1-1 install ok installed python3-lz4 python3-lz4 4.4.4+dfsg-1 install ok installed python3-matplotlib python3-matplotlib 3.10.1+dfsg1-5 install ok installed python3-matplotlib-inline python3-matplotlib-inline 0.1.7-1 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-mpmath python3-mpmath 1.3.0-1 install ok installed python3-networkx python3-networkx 3.2.1-5 install ok installed python3-numpy python3-numpy 1:2.2.4+ds-1.2 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.4+ds-1.2 install ok installed python3-packaging python3-packaging 25.0-1 install ok installed python3-pandas python3-pandas 2.2.3+dfsg-9 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.2.3+dfsg-9 install ok installed python3-parso python3-parso 0.8.4-1 install ok installed python3-pexpect python3-pexpect 4.9-3 install ok installed python3-pil:amd64 python3-pil 11.3.0-1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 11.3.0-1 install ok installed python3-pkg-resources python3-pkg-resources 78.1.1-0.1 install ok installed python3-platformdirs python3-platformdirs 4.4.0-1 install ok installed python3-prompt-toolkit python3-prompt-toolkit 3.0.52-1 install ok installed python3-ptyprocess python3-ptyprocess 0.7.0-6 install ok installed python3-pure-eval python3-pure-eval 0.2.3-1 install ok installed python3-pyfaidx python3-pyfaidx 0.8.1.3-2 install ok installed python3-pyfastx python3-pyfastx 2.2.0-1+b1 install ok installed python3-pygments python3-pygments 2.18.0+dfsg-2 install ok installed python3-pygtrie python3-pygtrie 2.2-3 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-pytz python3-pytz 2025.2-3 install ok installed python3-referencing python3-referencing 0.36.2-1 install ok installed python3-reportlab python3-reportlab 4.4.3-1 install ok installed python3-requests python3-requests 2.32.5+dfsg-1 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-rpds-py python3-rpds-py 0.21.0-2+b1 install ok installed python3-s3transfer python3-s3transfer 0.11.4-1 install ok installed python3-schedule python3-schedule 1.2.2-1 install ok installed python3-scipy python3-scipy 1.15.3-1.1 install ok installed python3-seaborn python3-seaborn 0.13.2-5 install ok installed python3-setuptools python3-setuptools 78.1.1-0.1 install ok installed python3-six python3-six 1.17.0-1 install ok installed python3-stack-data python3-stack-data 0.6.3-1 install ok installed python3-sympy python3-sympy 1.14.0-2 install ok installed python3-tk:amd64 python3-tk 3.13.5-1 install ok installed python3-traitlets python3-traitlets 5.14.3+really5.14.3-1 install ok installed python3-treetime python3-treetime 0.11.4-1 install ok installed python3-typeguard python3-typeguard 4.4.4-1 install ok installed python3-typeshed python3-typeshed 0.0~git20241223.ea91db2-4 install ok installed python3-typing-extensions python3-typing-extensions 4.15.0-1 install ok installed python3-ufolib2 python3-ufolib2 0.17.1+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 16.0.0+ds-1 install ok installed python3-urllib3 python3-urllib3 2.5.0-1 install ok installed python3-wcwidth python3-wcwidth 0.2.13+dfsg1-1 install ok installed python3-xopen python3-xopen 1.7.0-3 install ok installed python3-zipp python3-zipp 3.23.0-1 install ok installed python3-zopfli python3-zopfli 0.2.3.post1-1+b1 install ok installed python3-zstandard python3-zstandard 0.24.0-1 install ok installed python3.13 python3.13 3.13.7-1 install ok installed python3.13-minimal python3.13-minimal 3.13.7-1 install ok installed python3.13-tk python3.13-tk 3.13.7-1 install ok installed raxml raxml 8.2.13+dfsg-2+b1 install ok installed readline-common readline-common 8.3-3 install ok installed sed sed 4.9-2 install ok installed seqmagick seqmagick 0.8.6-3 install ok installed sgml-base sgml-base 1.31+nmu1 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-8 install ok installed tzdata tzdata 2025b-5 install ok installed unicode-data unicode-data 16.0.0-1 install ok installed util-linux util-linux 2.41.1-3 install ok installed vcftools vcftools 0.1.17-1 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+25 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+7 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 2m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-get', 'remove', '--allow-remove-essential', 'blt', 'ca-certificates', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libabsl20240722:amd64', 'libamd3:amd64', 'libaom3:amd64', 'libatomic1:amd64', 'libavif16:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcamd3:amd64', 'libccolamd3:amd64', 'libcholmod5:amd64', 'libcolamd3:amd64', 'libdav1d7:amd64', 'libdeflate0:amd64', 'libdsdp-5.8t64', 'libexpat1:amd64', 'libffi8:amd64', 'libfftw3-double3:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgav1-1:amd64', 'libgcrypt20:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libltdl7:amd64', 'libncursesw6:amd64', 'libopenjp2-7:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'librav1e0.7:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsuitesparseconfig7:amd64', 'libsvtav1enc2:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libumfpack6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2-16:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libyuv0:amd64', 'libzopfli1', 'mafft', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'pigz', 'python-matplotlib-data', 'python3', 'python3-asttokens', 'python3-attr', 'python3-autocommand', 'python3-bcbio-gff', 'python3-biopython', 'python3-boto3', 'python3-botocore', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cvxopt', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-executing', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-idna', 'python3-inflect', 'python3-ipdb', 'python3-ipython', 'python3-isodate', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jaraco.text', 'python3-jedi', 'python3-jmespath', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-matplotlib-inline', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-parso', 'python3-pexpect', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-prompt-toolkit', 'python3-ptyprocess', 'python3-pure-eval', 'python3-pyfaidx', 'python3-pyfastx', 'python3-pygments', 'python3-pygtrie', 'python3-pyparsing', 'python3-pytz', 'python3-referencing', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-rpds-py', 'python3-s3transfer', 'python3-schedule', 'python3-scipy', 'python3-seaborn', 'python3-setuptools', 'python3-six', 'python3-stack-data', 'python3-sympy', 'python3-tk:amd64', 'python3-traitlets', 'python3-treetime', 'python3-typeguard', 'python3-typeshed', 'python3-typing-extensions', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wcwidth', 'python3-xopen', 'python3-zipp', 'python3-zopfli', 'python3-zstandard', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'raxml', 'readline-common', 'seqmagick', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'vcftools', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'augur'] 3m19.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: augur blt ca-certificates fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libabsl20240722 libamd3 libaom3 libatomic1 libavif16 libblas3 libbrotli1 libcairo2 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdav1d7 libdeflate0 libdsdp-5.8t64 libexpat1 libffi8 libfftw3-double3 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgav1-1 libgcrypt20 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglpk40 libgomp1 libgpg-error0 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo liblapack3 liblcms2-2 liblerc4 libltdl7 libncursesw6 libopenjp2-7 libperl5.40 libpixman-1-0 libpng16-16t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 librav1e0.7 libreadline8t64 libsharpyuv0 libsuitesparseconfig7 libsvtav1enc2 libtcl8.6 libtiff6 libtk8.6 libumfpack6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2-16 libxrender1 libxslt1.1 libxss1 libyuv0 libzopfli1 mafft media-types netbase openssl perl perl-modules-5.40 pigz python-matplotlib-data python3 python3-asttokens python3-attr python3-autocommand python3-bcbio-gff python3-biopython python3-boto3 python3-botocore python3-brotli python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-contourpy python3-cvxopt python3-cycler python3-dateutil python3-decorator python3-dendropy python3-executing python3-fonttools python3-freetype python3-fs python3-idna python3-inflect python3-ipdb python3-ipython python3-isodate python3-jaraco.context python3-jaraco.functools python3-jaraco.text python3-jedi python3-jmespath python3-jsonschema python3-jsonschema-specifications python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-matplotlib-inline python3-minimal python3-more-itertools python3-mpmath python3-networkx python3-numpy python3-numpy-dev python3-packaging python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pyfaidx python3-pyfastx python3-pygments python3-pygtrie python3-pyparsing python3-pytz python3-referencing python3-reportlab python3-requests python3-rlpycairo python3-rpds-py python3-s3transfer python3-schedule python3-scipy python3-seaborn python3-setuptools python3-six python3-stack-data python3-sympy python3-tk python3-traitlets python3-treetime python3-typeguard python3-typeshed python3-typing-extensions python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wcwidth python3-xopen python3-zipp python3-zopfli python3-zstandard python3.13 python3.13-minimal python3.13-tk raxml readline-common seqmagick sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 202 to remove and 0 not upgraded. After this operation, 784 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 ... 40163 files and directories currently installed.) Removing augur (24.4.0-3) ... Removing seqmagick (0.8.6-3) ... Removing python3-treetime (0.11.4-1) ... Removing python3-seaborn (0.13.2-5) ... Removing python3-matplotlib (3.10.1+dfsg1-5) ... Removing python3-pil.imagetk:amd64 (11.3.0-1) ... Removing python3-tk:amd64 (3.13.5-1) ... Removing blt (2.5.3+dfsg-8) ... Removing python3-boto3 (1.37.9-1) ... Removing python3-s3transfer (0.11.4-1) ... Removing python3-botocore (1.37.9+repack-1) ... Removing python3-requests (2.32.5+dfsg-1) ... Removing python3-certifi (2025.1.31+ds-1) ... Removing ca-certificates (20250419) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing fasttree (2.1.11-2) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-8) ... Removing python3.13-tk (3.13.7-1) ... Removing libtk8.6:amd64 (8.6.17-1) ... Removing libxft2:amd64 (2.3.6-1+b4) ... Removing python-matplotlib-data (3.10.1+dfsg1-5) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-lyx (2.4.4-1) ... Removing python3-cvxopt (1.3.0+dfsg-1+b9) ... Removing libumfpack6:amd64 (1:7.11.0+dfsg-2) ... Removing libcholmod5:amd64 (1:7.11.0+dfsg-2) ... Removing python3-pandas (2.2.3+dfsg-9) ... Removing python3-pandas-lib:amd64 (2.2.3+dfsg-9) ... Removing libdsdp-5.8t64 (5.8-11) ... Removing libcamd3:amd64 (1:7.11.0+dfsg-2) ... Removing libccolamd3:amd64 (1:7.11.0+dfsg-2) ... Removing libglpk40:amd64 (5.0-2) ... Removing libcolamd3:amd64 (1:7.11.0+dfsg-2) ... Removing python3-jsonschema (4.19.2-6) ... Removing python3-jsonschema-specifications (2023.12.1-2) ... Removing python3-referencing (0.36.2-1) ... Removing python3-rpds-py (0.21.0-2+b1) ... Removing python3-ipdb (0.13.13-3) ... Removing python3-ipython (8.35.0-2) ... Removing python3-prompt-toolkit (3.0.52-1) ... Removing python3-wcwidth (0.2.13+dfsg1-1) ... Removing python3-networkx (3.2.1-5) ... Removing python3-setuptools (78.1.1-0.1) ... Removing python3-jaraco.text (4.0.0-1) ... Removing python3-zstandard (0.24.0-1) ... Removing python3-jedi (0.19.1+ds1-1) ... Removing python3-typeshed (0.0~git20241223.ea91db2-4) ... Removing libfftw3-double3:amd64 (3.3.10-2+b1) ... Removing vcftools (0.1.17-1) ... Removing mafft (7.525-1) ... Removing perl (5.40.1-6) ... Removing libperl5.40:amd64 (5.40.1-6) ... Removing libgdbm-compat4t64:amd64 (1.26-1) ... Removing libgdbm6t64:amd64 (1.26-1) ... Removing libgsl28:amd64 (2.8+dfsg-5.1) ... Removing libgslcblas0:amd64 (2.8+dfsg-5.1) ... Removing libltdl7:amd64 (2.5.4-5) ... Removing libqhull-r8.0:amd64 (2020.2-7) ... Removing libtcl8.6:amd64 (8.6.17+dfsg-1) ... Removing libxss1:amd64 (1:1.2.3-1+b3) ... Removing openssl (3.5.2-1) ... Removing perl-modules-5.40 (5.40.1-6) ... Removing python3-xopen (1.7.0-3) ... Removing pigz (2.8-1) ... Removing python3-stack-data (0.6.3-1) ... Removing python3-executing (2.2.0-0.3) ... Removing python3-asttokens (3.0.0-2) ... Removing python3-bcbio-gff (0.7.1-2) ... Removing python3-chardet (5.2.0+dfsg-2) ... Removing python3-contourpy (1.3.1-2) ... Removing python3-cycler (0.12.1-2) ... Removing python3-dateutil (2.9.0-4) ... Removing python3-dendropy (4.6.1-2) ... Removing python3-idna (3.10-1) ... Removing python3-isodate (0.7.2-1) ... Removing python3-jmespath (1.0.1-1) ... Removing python3-kiwisolver (1.4.7-3+b1) ... Removing python3-matplotlib-inline (0.1.7-1) ... Removing python3-pyfastx (2.2.0-1+b1) ... Removing python3-pyfaidx (0.8.1.3-2) ... Removing python3-packaging (25.0-1) ... Removing python3-parso (0.8.4-1) ... Removing python3-pexpect (4.9-3) ... Removing python3-ptyprocess (0.7.0-6) ... Removing python3-pure-eval (0.2.3-1) ... Removing python3-pygments (2.18.0+dfsg-2) ... Removing python3-pygtrie (2.2-3) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-pytz (2025.2-3) ... Removing python3-schedule (1.2.2-1) ... Removing python3-six (1.17.0-1) ... Removing python3-traitlets (5.14.3+really5.14.3-1) ... Removing python3-urllib3 (2.5.0-1) ... Removing python3-zipp (3.23.0-1) ... Removing raxml (8.2.13+dfsg-2+b1) ... Removing python3-biopython (1.85+dfsg-5) ... Removing python3-reportlab (4.4.3-1) ... Removing python3-pil:amd64 (11.3.0-1) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.27.0-2) ... Removing libcairo2:amd64 (1.18.4-1+b1) ... Removing libfontconfig1:amd64 (2.15.0-2.4) ... Removing fontconfig-config (2.15.0-2.4) ... Removing fonts-urw-base35 (20200910-8) ... Removing libavif16:amd64 (1.3.0-1) ... Removing libgav1-1:amd64 (0.19.0-3+b1) ... Removing libabsl20240722:amd64 (20240722.0-4) ... Removing libamd3:amd64 (1:7.11.0+dfsg-2) ... Removing libaom3:amd64 (3.12.1-1) ... Removing libraqm0:amd64 (0.10.3-1) ... Removing libharfbuzz0b:amd64 (11.4.5-1) ... Removing libglib2.0-0t64:amd64 (2.84.4-3) ... Removing libatomic1:amd64 (15.2.0-4) ... Removing xfonts-utils (1:7.7+7) ... Removing python3-freetype (2.5.1-2) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libbrotli1:amd64 (1.1.0-2+b7) ... Removing libdav1d7:amd64 (1.5.1-1) ... Removing libtiff6:amd64 (4.7.0-5) ... Removing libdeflate0:amd64 (1.23-2) ... Removing python3-pkg-resources (78.1.1-0.1) ... Removing python3-jaraco.context (6.0.1-1) ... Removing python3-inflect (7.5.0-1) ... Removing python3-typeguard (4.4.4-1) ... Removing libfontenc1:amd64 (1:1.1.8-1+b2) ... Removing libfribidi0:amd64 (1.0.16-1) ... Removing libsuitesparseconfig7:amd64 (1:7.11.0+dfsg-2) ... Removing libgomp1:amd64 (15.2.0-4) ... Removing libgraphite2-3:amd64 (1.3.14-3) ... Removing libimagequant0:amd64 (4.4.0-3) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libyuv0:amd64 (0.0.1916.20250814-1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-4) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing libopenjp2-7:amd64 (2.5.3-2.1) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libpng16-16t64:amd64 (1.6.50-1) ... Removing librav1e0.7:amd64 (0.7.1-9+b2) ... Removing libwebpmux3:amd64 (1.5.0-0.1) ... Removing libwebpdemux2:amd64 (1.5.0-0.1) ... Removing libwebp7:amd64 (1.5.0-0.1) ... Removing libsharpyuv0:amd64 (1.5.0-0.1) ... Removing libsvtav1enc2:amd64 (2.3.0+dfsg-1) ... Removing libxrender1:amd64 (1:0.9.12-1) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing libxext6:amd64 (2:1.3.4-1+b3) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-charset-normalizer (3.4.3-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-more-itertools (10.8.0-1) ... Removing python3-typing-extensions (4.15.0-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31+nmu1) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+25) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libx11-6:amd64 (2:1.8.12-1) ... Removing libx11-data (2:1.8.12-1) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.5-1) ... Removing python3-fonttools (4.57.0-2) ... Removing python3-scipy (1.15.3-1.1) ... Removing python3-numpy (1:2.2.4+ds-1.2) ... Removing liblapack3:amd64 (3.12.1-7) ... Removing libblas3:amd64 (3.12.1-7) ... Removing python3-lxml:amd64 (6.0.1-1) ... Removing libxslt1.1:amd64 (1.1.43-0.2) ... Removing libgcrypt20:amd64 (1.11.2-2) ... Removing libgfortran5:amd64 (15.2.0-4) ... Removing libgpg-error0:amd64 (1.55-2) ... Removing libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Removing python3-zopfli (0.2.3.post1-1+b1) ... Removing libzopfli1 (1.0.3-3) ... Removing python3-brotli (1.1.0-2+b7) ... Removing python3-decorator (5.2.1-2) ... Removing python3-fs (2.4.16-8) ... Removing python3-lz4 (4.4.4+dfsg-1) ... Removing python3-sympy (1.14.0-2) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-numpy-dev:amd64 (1:2.2.4+ds-1.2) ... Removing python3-platformdirs (4.4.0-1) ... Removing python3-unicodedata2 (16.0.0+ds-1) ... Removing unicode-data (16.0.0-1) ... Removing python3-ufolib2 (0.17.1+dfsg1-1) ... Removing python3-attr (25.3.0-1) ... Removing python3 (3.13.7-1) ... Removing python3-minimal (3.13.7-1) ... Removing python3.13 (3.13.7-1) ... Removing python3.13-minimal (3.13.7-1) ... Removing libexpat1:amd64 (2.7.1-2) ... Removing libpython3-stdlib:amd64 (3.13.7-1) ... Removing libpython3.13-stdlib:amd64 (3.13.7-1) ... find: '/usr/lib/python3': No such file or directory Removing libffi8:amd64 (3.5.2-2) ... Removing libncursesw6:amd64 (6.5+20250216-2) ... Removing libpython3.13-minimal:amd64 (3.13.7-1) ... 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 (13.0.0) ... Removing netbase (6.5) ... Removing readline-common (8.3-3) ... Processing triggers for libc-bin (2.41-12) ... 3m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-get', 'remove', '--allow-remove-essential', 'blt', 'ca-certificates', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libabsl20240722:amd64', 'libamd3:amd64', 'libaom3:amd64', 'libatomic1:amd64', 'libavif16:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcamd3:amd64', 'libccolamd3:amd64', 'libcholmod5:amd64', 'libcolamd3:amd64', 'libdav1d7:amd64', 'libdeflate0:amd64', 'libdsdp-5.8t64', 'libexpat1:amd64', 'libffi8:amd64', 'libfftw3-double3:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgav1-1:amd64', 'libgcrypt20:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libltdl7:amd64', 'libncursesw6:amd64', 'libopenjp2-7:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'librav1e0.7:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsuitesparseconfig7:amd64', 'libsvtav1enc2:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libumfpack6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2-16:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libyuv0:amd64', 'libzopfli1', 'mafft', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'pigz', 'python-matplotlib-data', 'python3', 'python3-asttokens', 'python3-attr', 'python3-autocommand', 'python3-bcbio-gff', 'python3-biopython', 'python3-boto3', 'python3-botocore', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cvxopt', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-executing', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-idna', 'python3-inflect', 'python3-ipdb', 'python3-ipython', 'python3-isodate', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jaraco.text', 'python3-jedi', 'python3-jmespath', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-matplotlib-inline', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-parso', 'python3-pexpect', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-prompt-toolkit', 'python3-ptyprocess', 'python3-pure-eval', 'python3-pyfaidx', 'python3-pyfastx', 'python3-pygments', 'python3-pygtrie', 'python3-pyparsing', 'python3-pytz', 'python3-referencing', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-rpds-py', 'python3-s3transfer', 'python3-schedule', 'python3-scipy', 'python3-seaborn', 'python3-setuptools', 'python3-six', 'python3-stack-data', 'python3-sympy', 'python3-tk:amd64', 'python3-traitlets', 'python3-treetime', 'python3-typeguard', 'python3-typeshed', 'python3-typing-extensions', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wcwidth', 'python3-xopen', 'python3-zipp', 'python3-zopfli', 'python3-zstandard', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'raxml', 'readline-common', 'seqmagick', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'vcftools', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'augur'] 3m19.6s INFO: Running scripts post_remove 3m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_remove_exceptions'] 3m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_remove_exceptions'] 3m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libabsl20240722:amd64', 'libamd3:amd64', 'libaom3:amd64', 'libatomic1:amd64', 'libavif16:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcamd3:amd64', 'libccolamd3:amd64', 'libcholmod5:amd64', 'libcolamd3:amd64', 'libdav1d7:amd64', 'libdeflate0:amd64', 'libdsdp-5.8t64', 'libexpat1:amd64', 'libffi8:amd64', 'libfftw3-double3:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgav1-1:amd64', 'libgcrypt20:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libltdl7:amd64', 'libncursesw6:amd64', 'libopenjp2-7:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'librav1e0.7:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsuitesparseconfig7:amd64', 'libsvtav1enc2:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libumfpack6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2-16:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libyuv0:amd64', 'libzopfli1', 'mafft', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'pigz', 'python-matplotlib-data', 'python3', 'python3-asttokens', 'python3-attr', 'python3-autocommand', 'python3-bcbio-gff', 'python3-biopython', 'python3-boto3', 'python3-botocore', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cvxopt', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-executing', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-idna', 'python3-inflect', 'python3-ipdb', 'python3-ipython', 'python3-isodate', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jaraco.text', 'python3-jedi', 'python3-jmespath', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-matplotlib-inline', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-parso', 'python3-pexpect', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-prompt-toolkit', 'python3-ptyprocess', 'python3-pure-eval', 'python3-pyfaidx', 'python3-pyfastx', 'python3-pygments', 'python3-pygtrie', 'python3-pyparsing', 'python3-pytz', 'python3-referencing', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-rpds-py', 'python3-s3transfer', 'python3-schedule', 'python3-scipy', 'python3-seaborn', 'python3-setuptools', 'python3-six', 'python3-stack-data', 'python3-sympy', 'python3-tk:amd64', 'python3-traitlets', 'python3-treetime', 'python3-typeguard', 'python3-typeshed', 'python3-typing-extensions', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wcwidth', 'python3-xopen', 'python3-zipp', 'python3-zopfli', 'python3-zstandard', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'raxml', 'readline-common', 'seqmagick', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'vcftools', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 3m20.4s DUMP: dpkg: warning: ignoring request to remove blt which isn't installed (Reading database ... 5009 files and directories currently installed.) Purging configuration files for ca-certificates (20250419) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove fasttree which isn't installed Purging configuration files for fontconfig-config (2.15.0-2.4) ... Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: ignoring request to remove fonts-lyx which isn't installed Purging configuration files for fonts-urw-base35 (20200910-8) ... dpkg: warning: ignoring request to remove libabsl20240722 which isn't installed dpkg: warning: ignoring request to remove libamd3 which isn't installed dpkg: warning: ignoring request to remove libaom3 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libavif16 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcamd3 which isn't installed dpkg: warning: ignoring request to remove libccolamd3 which isn't installed dpkg: warning: ignoring request to remove libcholmod5 which isn't installed dpkg: warning: ignoring request to remove libcolamd3 which isn't installed dpkg: warning: ignoring request to remove libdav1d7 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdsdp-5.8t64 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 libfftw3-double3 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgav1-1 which isn't installed dpkg: warning: ignoring request to remove libgcrypt20 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 Purging configuration files for libglib2.0-0t64:amd64 (2.84.4-3) ... dpkg: warning: ignoring request to remove libglpk40 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgpg-error0 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libgsl28 which isn't installed dpkg: warning: ignoring request to remove libgslcblas0 which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libltdl7 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.13-minimal:amd64 (3.13.7-1) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed dpkg: warning: ignoring request to remove librav1e0.7 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.3-3) ... dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsuitesparseconfig7 which isn't installed dpkg: warning: ignoring request to remove libsvtav1enc2 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libumfpack6 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2-16 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libyuv0 which isn't installed dpkg: warning: ignoring request to remove libzopfli1 which isn't installed dpkg: warning: ignoring request to remove mafft which isn't installed Purging configuration files for media-types (13.0.0) ... Purging configuration files for netbase (6.5) ... Purging configuration files for openssl (3.5.2-1) ... Purging configuration files for perl (5.40.1-6) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed dpkg: warning: ignoring request to remove pigz which isn't installed Purging configuration files for python-matplotlib-data (3.10.1+dfsg1-5) ... Purging configuration files for python3 (3.13.7-1) ... dpkg: warning: ignoring request to remove python3-asttokens which isn't installed dpkg: warning: ignoring request to remove python3-attr which isn't installed dpkg: warning: ignoring request to remove python3-autocommand which isn't installed dpkg: warning: ignoring request to remove python3-bcbio-gff which isn't installed dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-boto3 which isn't installed dpkg: warning: ignoring request to remove python3-botocore which isn't installed dpkg: warning: ignoring request to remove python3-brotli which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-certifi which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-charset-normalizer which isn't installed dpkg: warning: ignoring request to remove python3-contourpy which isn't installed dpkg: warning: ignoring request to remove python3-cvxopt which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-dendropy which isn't installed dpkg: warning: ignoring request to remove python3-executing which isn't installed dpkg: warning: ignoring request to remove python3-fonttools which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-fs which isn't installed dpkg: warning: ignoring request to remove python3-idna which isn't installed dpkg: warning: ignoring request to remove python3-inflect which isn't installed dpkg: warning: ignoring request to remove python3-ipdb which isn't installed dpkg: warning: ignoring request to remove python3-ipython which isn't installed dpkg: warning: ignoring request to remove python3-isodate 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-jaraco.text which isn't installed dpkg: warning: ignoring request to remove python3-jedi which isn't installed dpkg: warning: ignoring request to remove python3-jmespath which isn't installed Purging configuration files for python3-jsonschema (4.19.2-6) ... dpkg: warning: ignoring request to remove python3-jsonschema-specifications which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-lxml which isn't installed dpkg: warning: ignoring request to remove python3-lz4 which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib-inline 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-mpmath which isn't installed dpkg: warning: ignoring request to remove python3-networkx which isn't installed Purging configuration files for python3-numpy (1:2.2.4+ds-1.2) ... 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-parso which isn't installed dpkg: warning: ignoring request to remove python3-pexpect which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pil.imagetk which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-platformdirs which isn't installed dpkg: warning: ignoring request to remove python3-prompt-toolkit which isn't installed dpkg: warning: ignoring request to remove python3-ptyprocess which isn't installed dpkg: warning: ignoring request to remove python3-pure-eval which isn't installed dpkg: warning: ignoring request to remove python3-pyfaidx which isn't installed dpkg: warning: ignoring request to remove python3-pyfastx which isn't installed dpkg: warning: ignoring request to remove python3-pygments which isn't installed dpkg: warning: ignoring request to remove python3-pygtrie which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pytz which isn't installed dpkg: warning: ignoring request to remove python3-referencing which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-requests which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-rpds-py which isn't installed dpkg: warning: ignoring request to remove python3-s3transfer which isn't installed dpkg: warning: ignoring request to remove python3-schedule which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-seaborn which isn't installed dpkg: warning: ignoring request to remove python3-setuptools which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-stack-data which isn't installed Purging configuration files for python3-sympy (1.14.0-2) ... dpkg: warning: ignoring request to remove python3-tk which isn't installed dpkg: warning: ignoring request to remove python3-traitlets which isn't installed dpkg: warning: ignoring request to remove python3-treetime which isn't installed dpkg: warning: ignoring request to remove python3-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typeshed which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3-ufolib2 which isn't installed dpkg: warning: ignoring request to remove python3-unicodedata2 which isn't installed dpkg: warning: ignoring request to remove python3-urllib3 which isn't installed dpkg: warning: ignoring request to remove python3-wcwidth which isn't installed dpkg: warning: ignoring request to remove python3-xopen which isn't installed dpkg: warning: ignoring request to remove python3-zipp which isn't installed dpkg: warning: ignoring request to remove python3-zopfli which isn't installed dpkg: warning: ignoring request to remove python3-zstandard which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.7-1) ... dpkg: warning: ignoring request to remove python3.13-tk which isn't installed dpkg: warning: ignoring request to remove raxml which isn't installed Purging configuration files for readline-common (8.3-3) ... dpkg: warning: ignoring request to remove seqmagick which isn't installed Purging configuration files for sgml-base (1.31+nmu1) ... dpkg: warning: ignoring request to remove tk8.6-blt2.5 which isn't installed dpkg: warning: ignoring request to remove unicode-data which isn't installed dpkg: warning: ignoring request to remove vcftools which isn't installed Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+25) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+7) ... Purging configuration files for xml-core (0.19) ... 3m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libabsl20240722:amd64', 'libamd3:amd64', 'libaom3:amd64', 'libatomic1:amd64', 'libavif16:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcamd3:amd64', 'libccolamd3:amd64', 'libcholmod5:amd64', 'libcolamd3:amd64', 'libdav1d7:amd64', 'libdeflate0:amd64', 'libdsdp-5.8t64', 'libexpat1:amd64', 'libffi8:amd64', 'libfftw3-double3:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgav1-1:amd64', 'libgcrypt20:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libltdl7:amd64', 'libncursesw6:amd64', 'libopenjp2-7:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'librav1e0.7:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsuitesparseconfig7:amd64', 'libsvtav1enc2:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libumfpack6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2-16:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libyuv0:amd64', 'libzopfli1', 'mafft', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'pigz', 'python-matplotlib-data', 'python3', 'python3-asttokens', 'python3-attr', 'python3-autocommand', 'python3-bcbio-gff', 'python3-biopython', 'python3-boto3', 'python3-botocore', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cvxopt', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-executing', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-idna', 'python3-inflect', 'python3-ipdb', 'python3-ipython', 'python3-isodate', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jaraco.text', 'python3-jedi', 'python3-jmespath', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-matplotlib-inline', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-parso', 'python3-pexpect', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-prompt-toolkit', 'python3-ptyprocess', 'python3-pure-eval', 'python3-pyfaidx', 'python3-pyfastx', 'python3-pygments', 'python3-pygtrie', 'python3-pyparsing', 'python3-pytz', 'python3-referencing', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-rpds-py', 'python3-s3transfer', 'python3-schedule', 'python3-scipy', 'python3-seaborn', 'python3-setuptools', 'python3-six', 'python3-stack-data', 'python3-sympy', 'python3-tk:amd64', 'python3-traitlets', 'python3-treetime', 'python3-typeguard', 'python3-typeshed', 'python3-typing-extensions', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wcwidth', 'python3-xopen', 'python3-zipp', 'python3-zopfli', 'python3-zstandard', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'raxml', 'readline-common', 'seqmagick', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'vcftools', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 3m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg', '--purge', 'augur'] 3m20.4s DUMP: dpkg: warning: ignoring request to remove augur which isn't installed 3m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg', '--purge', 'augur'] 3m20.4s INFO: Running scripts post_purge 3m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_purge_exceptions'] 3m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_purge_exceptions'] 3m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg', '--purge', '--pending'] 3m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg', '--purge', '--pending'] 3m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg', '--remove', '--pending'] 3m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg', '--remove', '--pending'] 3m20.4s INFO: Running scripts post_test 3m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_test_exceptions'] 3m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'tmp/scripts/post_test_exceptions'] 3m20.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm'] 3m20.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm'] 3m21.0s DEBUG: No broken symlinks as far as we can find. 3m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg-divert', '--list'] 3m21.0s 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 3m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'dpkg-divert', '--list'] 3m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-get', 'clean'] 3m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm', 'apt-get', 'clean'] 3m21.1s DEBUG: Recording chroot state 3m21.6s INFO: PASS: Installation and purging test. 3m22.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/shm'] 3m22.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/shm'] 3m22.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/console'] 3m22.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/console'] 3m22.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/ptmx'] 3m22.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/ptmx'] 3m22.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/pts'] 3m22.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/dev/pts'] 3m22.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/proc'] 3m22.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm/proc'] 3m22.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm'] 3m22.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpmml3a1xm'] 3m22.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpmml3a1xm 3m22.3s INFO: PASS: All tests. 3m22.3s INFO: piuparts run ends. ret=0 End: 2025-09-18 03:51:19 GMT