Start: 2025-04-09 14:57:51 GMT Package: augur Version: 24.4.0-1 Installed-Size: 1056 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_24.4.0-1_all.deb Size: 261232 MD5sum: b572f222840d0090638ca16dde37b5e6 SHA256: 54cf77ceaea54e677ac39643f62ead613bbd628037ce9c203f3d64cfe727f5f0 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --install-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt augur=24.4.0-1 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 1.5.2~202503162239~1.5.1-10-g345d5865 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --install-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt augur=24.4.0-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-34-amd64 #1 SMP Debian 5.10.234-1 (2025-02-24) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp6m2t5qhr 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp6m2t5qhr 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp6m2t5qhr/tmp/scripts/ 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts-leftovers to /srv/piuparts.debian.org/tmp/tmp6m2t5qhr/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', 'update'] 0m2.1s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.2 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7417 kB] Fetched 17.8 MB in 1s (12.4 MB/s) Reading package lists... 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', 'update'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', '-yf', 'dist-upgrade'] 0m3.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: bash coreutils libssl3t64 openssl-provider-legacy 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7251 kB of archives. After this operation, 824 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.37-2 [1500 kB] Get:2 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.7-1 [3012 kB] Get:3 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.5.0-1 [307 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.5.0-1 [2432 kB] Fetched 7251 kB in 0s (164 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 ... 4927 files and directories currently installed.) Preparing to unpack .../bash_5.2.37-2_amd64.deb ... Unpacking bash (5.2.37-2) over (5.2.37-1.1+b2) ... Setting up bash (5.2.37-2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4926 files and directories currently installed.) Preparing to unpack .../coreutils_9.7-1_amd64.deb ... Unpacking coreutils (9.7-1) over (9.6-2) ... Setting up coreutils (9.7-1) ... (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 ... 4926 files and directories currently installed.) Preparing to unpack .../openssl-provider-legacy_3.5.0-1_amd64.deb ... Unpacking openssl-provider-legacy (3.5.0-1) over (3.4.1-1) ... Setting up openssl-provider-legacy (3.5.0-1) ... (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 ... 4926 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.5.0-1_amd64.deb ... Unpacking libssl3t64:amd64 (3.5.0-1) over (3.4.1-1) ... Setting up libssl3t64:amd64 (3.5.0-1) ... Processing triggers for debianutils (5.21) ... Processing triggers for libc-bin (2.41-6) ... 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', '-yf', 'dist-upgrade'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.2s DUMP: 31e44ff00e610efb534d9d62a0a21228 - 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.2s INFO: Running scripts post_setup 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s 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 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_fake-essential'] 0m4.3s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... Reading state information... init-system-helpers is already the newest version (1.68). The following additional packages will be installed: libncursesw6 libproc2-0 libtext-charwidth-perl libtext-wrapi18n-perl procps sensible-utils ucf Suggested packages: dbconfig-mysql | dbconfig-pgsql | dbconfig-sqlite3 | dbconfig-no-thanks Recommended packages: libgpm2 psmisc linux-sysctl-defaults The following NEW packages will be installed: dbconfig-common libncursesw6 libproc2-0 libtext-charwidth-perl libtext-wrapi18n-perl procps sensible-utils ucf 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. Need to get 1757 kB of archives. After this operation, 4947 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get:3 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get:4 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get:6 http://deb.debian.org/debian sid/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get:7 http://deb.debian.org/debian sid/main amd64 ucf all 3.0051 [42.8 kB] Get:8 http://deb.debian.org/debian sid/main amd64 dbconfig-common all 2.0.24 [592 kB] Preconfiguring packages ... Fetched 1757 kB in 0s (67.5 MB/s) Selecting previously unselected package libncursesw6: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 ... 4925 files and directories currently installed.) Preparing to unpack .../0-libncursesw6_6.5+20250216-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.5+20250216-2) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../1-libproc2-0_2%3a4.0.4-7_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-7) ... Selecting previously unselected package procps. Preparing to unpack .../2-procps_2%3a4.0.4-7_amd64.deb ... Unpacking procps (2:4.0.4-7) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../3-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libtext-charwidth-perl:amd64. Preparing to unpack .../4-libtext-charwidth-perl_0.04-11+b4_amd64.deb ... Unpacking libtext-charwidth-perl:amd64 (0.04-11+b4) ... Selecting previously unselected package libtext-wrapi18n-perl. Preparing to unpack .../5-libtext-wrapi18n-perl_0.06-10_all.deb ... Unpacking libtext-wrapi18n-perl (0.06-10) ... Selecting previously unselected package ucf. Preparing to unpack .../6-ucf_3.0051_all.deb ... Moving old data out of the way Unpacking ucf (3.0051) ... Selecting previously unselected package dbconfig-common. Preparing to unpack .../7-dbconfig-common_2.0.24_all.deb ... Unpacking dbconfig-common (2.0.24) ... Setting up libtext-charwidth-perl:amd64 (0.04-11+b4) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libproc2-0:amd64 (2:4.0.4-7) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up sensible-utils (0.0.24) ... Setting up procps (2:4.0.4-7) ... Setting up ucf (3.0051) ... Setting up dbconfig-common (2.0.24) ... Creating config file /etc/dbconfig-common/config with new version Processing triggers for libc-bin (2.41-6) ... 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_fake-essential'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_forbid_home'] 0m4.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_forbid_home'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.4s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_minimize'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_minimize'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_zz_backports'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_setup_zz_backports'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', 'clean'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', 'clean'] 0m4.4s DEBUG: Recording chroot state 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.6s DUMP: install ok installed apt apt 3.0.0 install ok installed base-files base-files 13.7 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2 install ok installed bsdutils bsdutils 1:2.41-3 install ok installed coreutils coreutils 9.7-1 install ok installed dash dash 0.5.12-12 install ok installed dbconfig-common dbconfig-common 2.0.24 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-3 install ok installed dpkg dpkg 1.22.18 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-3 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 2.41-6 install ok installed libc6:amd64 libc6 2.41-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-4 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 0.278 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-3 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-3 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-7 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 2.41-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-2 install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.5-2 install ok installed libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b4 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.5-2 install ok installed libuuid1:amd64 libuuid1 2.41-3 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-3 install ok installed login.defs login.defs 1:4.17.4-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-3 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 3.5.0-1 install ok installed passwd passwd 1:4.17.4-1 install ok installed perl-base perl-base 5.40.1-2 install ok installed procps procps 2:4.0.4-7 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.24 install ok installed sqv sqv 1.3.0-1 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-1 install ok installed ucf ucf 3.0051 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.41-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg-divert', '--list'] 0m4.6s 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 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg-divert', '--list'] 0m4.6s INFO: Running scripts is_testable 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/is_testable_uninstallable'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/is_testable_uninstallable'] 0m4.6s INFO: apt-cache does not know about any of the requested packages 0m4.6s INFO: Running scripts pre_test 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_test_exceptions'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_test_exceptions'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_test_root_password'] 0m4.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_test_root_password'] 0m4.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr'] 0m4.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr'] 0m5.1s DEBUG: No broken symlinks as far as we can find. 0m5.1s INFO: Running scripts pre_install 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_database-server'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_database-server'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_exceptions'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_exceptions'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_extras'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_extras'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'show', '--no-all-versions', 'augur=24.4.0-1'] 0m5.6s DUMP: Package: augur Version: 24.4.0-1 Installed-Size: 1056 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-en: pipeline components for real-time virus analysis The nextstrain project is an attempt to make flexible informatic pipelines and visualization tools to track ongoing pathogen evolution as sequence data emerges. The nextstrain project derives from nextflu, which was specific to influenza evolution. . nextstrain is comprised of three components: . * fauna: database and IO scripts for sequence and serological data * augur: informatic pipelines to conduct inferences from raw data * auspice: web app to visualize resulting inferences Description-md5: e2aaa44840d7b632d0e95700bc100196 Homepage: https://github.com/nextstrain/augur Section: science Priority: optional Filename: pool/main/a/augur/augur_24.4.0-1_all.deb Size: 261232 MD5sum: b572f222840d0090638ca16dde37b5e6 SHA256: 54cf77ceaea54e677ac39643f62ead613bbd628037ce9c203f3d64cfe727f5f0 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'show', '--no-all-versions', 'augur=24.4.0-1'] 0m5.6s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: all Maintainer: piuparts developers team 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 Description: Dummy package to satisfy dependencies - created by piuparts This package was created automatically by piuparts and can safely be removed 0m5.6s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmp2e2f3v2m/piuparts-depends-dummy'] 0m5.6s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmp2e2f3v2m/piuparts-depends-dummy.deb'. 0m5.6s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmp2e2f3v2m/piuparts-depends-dummy'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m5.6s DUMP: 3.0.0 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m5.6s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmp2e2f3v2m/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmp6m2t5qhr/tmp 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m54.7s 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 libamd3 libatomic1 libblas3 libbrotli1 libcairo2 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdeflate0 libdsdp-5.8t64 libexpat1 libffi8 libfftw3-double3 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglpk40 libgomp1 libgpg-error0 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui liblapack3 liblcms2-2 liblerc4 libltdl7 libopenjp2-7 libperl5.40 libpixman-1-0 libpng16-16t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 libsharpyuv0 libsuitesparseconfig7 libtcl8.6 libtiff6 libtk8.6 libumfpack6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 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-cffi-backend 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-importlib-metadata 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 libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc 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: libglib2.0-data shared-mime-info xdg-user-dirs libgpg-error-l10n javascript-common blast2 libwww-perl lynx ruby python-biopython-doc ncbi-blast+ 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: blt ca-certificates fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libamd3 libatomic1 libblas3 libbrotli1 libcairo2 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdeflate0 libdsdp-5.8t64 libexpat1 libffi8 libfftw3-double3 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglpk40 libgomp1 libgpg-error0 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui liblapack3 liblcms2-2 liblerc4 libltdl7 libopenjp2-7 libperl5.40 libpixman-1-0 libpng16-16t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 libsharpyuv0 libsuitesparseconfig7 libtcl8.6 libtiff6 libtk8.6 libumfpack6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libzopfli1 mafft media-types netbase openssl perl perl-modules-5.40 pigz piuparts-depends-dummy 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-cffi-backend 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-importlib-metadata 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, 197 newly installed, 0 to remove and 0 not upgraded. Need to get 160 MB/160 MB of archives. After this operation, 748 MB of additional disk space will be used. Get:1 /tmp/piuparts-depends-dummy.deb piuparts-depends-dummy all 0.invalid.0 [846 B] Get:2 http://deb.debian.org/debian sid/main amd64 pigz amd64 2.8-1 [62.7 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.3-1 [861 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get:5 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.3-1 [2210 kB] Get:6 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.13.3-1 [27.2 kB] Get:7 http://deb.debian.org/debian sid/main amd64 media-types all 13.0.0 [29.3 kB] Get:8 http://deb.debian.org/debian sid/main amd64 netbase all 6.5 [12.4 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get:10 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-6 [69.4 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libpython3.13-stdlib amd64 3.13.3-1 [1954 kB] Get:13 http://deb.debian.org/debian sid/main amd64 python3.13 amd64 3.13.3-1 [751 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.13.3-1 [10.2 kB] Get:15 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.13.3-1 [28.2 kB] Get:16 http://deb.debian.org/debian sid/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:19 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:20 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get:21 http://deb.debian.org/debian sid/main amd64 sgml-base all 1.31 [15.4 kB] Get:22 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.5.0-1 [1491 kB] Get:23 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20241223 [164 kB] Get:24 http://deb.debian.org/debian sid/main amd64 perl-modules-5.40 all 5.40.1-2 [3017 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libperl5.40 amd64 5.40.1-2 [4315 kB] Get:28 http://deb.debian.org/debian sid/main amd64 perl amd64 5.40.1-2 [267 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [282 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:33 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:34 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get:36 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+24 [217 kB] Get:37 http://deb.debian.org/debian sid/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:38 http://deb.debian.org/debian sid/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get:39 http://deb.debian.org/debian sid/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:40 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get:52 http://deb.debian.org/debian sid/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get:53 http://deb.debian.org/debian sid/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get:54 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:55 http://deb.debian.org/debian sid/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get:56 http://deb.debian.org/debian sid/main amd64 fonts-lyx all 2.4.3-1 [190 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libsuitesparseconfig7 amd64 1:7.10.1+dfsg-1 [32.3 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libamd3 amd64 1:7.10.1+dfsg-1 [49.2 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Get:60 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libcamd3 amd64 1:7.10.1+dfsg-1 [45.9 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libccolamd3 amd64 1:7.10.1+dfsg-1 [47.7 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libcolamd3 amd64 1:7.10.1+dfsg-1 [41.0 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libcholmod5 amd64 1:7.10.1+dfsg-1 [648 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libdsdp-5.8t64 amd64 5.8-10.1 [181 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.51-4 [82.1 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.84.1-1 [1514 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libltdl7 amd64 2.5.4-4 [416 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libglpk40 amd64 5.0-1+b2 [401 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:86 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:87 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.3-2 [204 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.7.0-3 [346 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libumfpack6 amd64 1:7.10.1+dfsg-1 [288 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libxslt1.1 amd64 1.1.35-1.2 [233 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get:100 http://deb.debian.org/debian sid/main amd64 mafft amd64 7.505-1 [1078 kB] Get:101 http://deb.debian.org/debian sid/main amd64 python-matplotlib-data all 3.10.1+dfsg1-2 [2736 kB] Get:102 http://deb.debian.org/debian sid/main amd64 python3-asttokens all 3.0.0-1 [20.1 kB] Get:103 http://deb.debian.org/debian sid/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get:104 http://deb.debian.org/debian sid/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:105 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get:106 http://deb.debian.org/debian sid/main amd64 python3.13-tk amd64 3.13.3-1 [107 kB] Get:107 http://deb.debian.org/debian sid/main amd64 python3-tk amd64 3.13.3-1 [9548 B] Get:108 http://deb.debian.org/debian sid/main amd64 python3-pil.imagetk amd64 11.1.0-5+b1 [81.6 kB] Get:109 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB] Get:110 http://deb.debian.org/debian sid/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get:111 http://deb.debian.org/debian sid/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get:112 http://deb.debian.org/debian sid/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:113 http://deb.debian.org/debian sid/main amd64 python3-reportlab all 4.3.1-1 [1158 kB] Get:114 http://deb.debian.org/debian sid/main amd64 xml-core all 0.19 [20.1 kB] Get:115 http://deb.debian.org/debian sid/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:116 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.85+dfsg-2+b1 [1672 kB] Get:117 http://deb.debian.org/debian sid/main amd64 python3-six all 1.17.0-1 [16.5 kB] Get:118 http://deb.debian.org/debian sid/main amd64 python3-bcbio-gff all 0.7.1-2 [33.7 kB] Get:119 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get:120 http://deb.debian.org/debian sid/main amd64 python3-jmespath all 1.0.1-1 [21.1 kB] Get:121 http://deb.debian.org/debian sid/main amd64 python3-urllib3 all 2.3.0-2 [114 kB] Get:122 http://deb.debian.org/debian sid/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get:123 http://deb.debian.org/debian sid/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB] Get:124 http://deb.debian.org/debian sid/main amd64 python3-idna all 3.10-1 [42.0 kB] Get:125 http://deb.debian.org/debian sid/main amd64 python3-requests all 2.32.3+dfsg-5 [72.2 kB] Get:126 http://deb.debian.org/debian sid/main amd64 python3-botocore all 1.37.9+repack-1 [7311 kB] Get:127 http://deb.debian.org/debian sid/main amd64 python3-s3transfer all 0.11.4-1 [57.7 kB] Get:128 http://deb.debian.org/debian sid/main amd64 python3-boto3 all 1.37.9-1 [339 kB] Get:129 http://deb.debian.org/debian sid/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get:130 http://deb.debian.org/debian sid/main amd64 python3-cffi-backend amd64 1.17.1-2+b2 [93.6 kB] Get:131 http://deb.debian.org/debian sid/main amd64 python3-contourpy amd64 1.3.1-1+b1 [216 kB] Get:132 http://deb.debian.org/debian sid/main amd64 python3-cvxopt amd64 1.3.0+dfsg-1+b9 [265 kB] Get:133 http://deb.debian.org/debian sid/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:134 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.2.1-1 [32.9 kB] Get:135 http://deb.debian.org/debian sid/main amd64 python3-dendropy all 4.6.1-2 [277 kB] Get:136 http://deb.debian.org/debian sid/main amd64 python3-executing all 2.2.0-0.1 [24.5 kB] Get:137 http://deb.debian.org/debian sid/main amd64 python3-platformdirs all 4.3.7-1 [16.6 kB] Get:138 http://deb.debian.org/debian sid/main amd64 python3-fs all 2.4.16-7 [95.2 kB] Get:139 http://deb.debian.org/debian sid/main amd64 python3-lxml amd64 5.3.2-1 [1297 kB] Get:140 http://deb.debian.org/debian sid/main amd64 python3-lz4 amd64 4.4.0+dfsg-2 [25.3 kB] Get:141 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.15.2-7 [16.3 MB] Get:142 http://deb.debian.org/debian sid/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:143 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.13.3-5 [4148 kB] Get:144 http://deb.debian.org/debian sid/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get:145 http://deb.debian.org/debian sid/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b4 [299 kB] Get:146 http://deb.debian.org/debian sid/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get:147 http://deb.debian.org/debian sid/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:148 http://deb.debian.org/debian sid/main amd64 python3-fonttools amd64 4.57.0-1 [1438 kB] Get:149 http://deb.debian.org/debian sid/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get:150 http://deb.debian.org/debian sid/main amd64 python3-importlib-metadata all 8.6.1-1 [21.4 kB] Get:151 http://deb.debian.org/debian sid/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get:152 http://deb.debian.org/debian sid/main amd64 python3-typing-extensions all 4.13.1-1 [90.2 kB] Get:153 http://deb.debian.org/debian sid/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get:154 http://deb.debian.org/debian sid/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:155 http://deb.debian.org/debian sid/main amd64 python3-parso all 0.8.4-1 [67.8 kB] Get:156 http://deb.debian.org/debian sid/main amd64 python3-typeshed all 0.0~git20241223.ea91db2-1 [1530 kB] Get:157 http://deb.debian.org/debian sid/main amd64 python3-jedi all 0.19.1+ds1-1 [691 kB] Get:158 http://deb.debian.org/debian sid/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get:159 http://deb.debian.org/debian sid/main amd64 python3-matplotlib-inline all 0.1.7-1 [9032 B] Get:160 http://deb.debian.org/debian sid/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB] Get:161 http://deb.debian.org/debian sid/main amd64 python3-prompt-toolkit all 3.0.50-1 [278 kB] Get:162 http://deb.debian.org/debian sid/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get:163 http://deb.debian.org/debian sid/main amd64 python3-pure-eval all 0.2.3-1 [11.2 kB] Get:164 http://deb.debian.org/debian sid/main amd64 python3-stack-data all 0.6.3-1 [21.6 kB] Get:165 http://deb.debian.org/debian sid/main amd64 python3-ptyprocess all 0.7.0-6 [14.5 kB] Get:166 http://deb.debian.org/debian sid/main amd64 python3-pexpect all 4.9-3 [55.6 kB] Get:167 http://deb.debian.org/debian sid/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get:168 http://deb.debian.org/debian sid/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:169 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB] Get:170 http://deb.debian.org/debian sid/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get:171 http://deb.debian.org/debian sid/main amd64 python3-setuptools all 75.8.0-1 [724 kB] Get:172 http://deb.debian.org/debian sid/main amd64 python3-ipython all 8.30.0-2 [568 kB] Get:173 http://deb.debian.org/debian sid/main amd64 python3-ipdb all 0.13.13-3 [17.5 kB] Get:174 http://deb.debian.org/debian sid/main amd64 python3-isodate all 0.7.0-1 [19.4 kB] Get:175 http://deb.debian.org/debian sid/main amd64 python3-rpds-py amd64 0.21.0-2+b1 [257 kB] Get:176 http://deb.debian.org/debian sid/main amd64 python3-referencing all 0.36.2-1 [23.7 kB] Get:177 http://deb.debian.org/debian sid/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get:178 http://deb.debian.org/debian sid/main amd64 python3-jsonschema all 4.19.2-6 [71.4 kB] Get:179 http://deb.debian.org/debian sid/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get:180 http://deb.debian.org/debian sid/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:181 http://deb.debian.org/debian sid/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:182 http://deb.debian.org/debian sid/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-2 [23.8 MB] Get:183 http://deb.debian.org/debian sid/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get:184 http://deb.debian.org/debian sid/main amd64 python3-pytz all 2025.2-1 [151 kB] Get:185 http://deb.debian.org/debian sid/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-9 [4595 kB] Get:186 http://deb.debian.org/debian sid/main amd64 python3-pandas all 2.2.3+dfsg-9 [3097 kB] Get:187 http://deb.debian.org/debian sid/main amd64 python3-pyfaidx all 0.8.1.3-1 [29.1 kB] Get:188 http://deb.debian.org/debian sid/main amd64 python3-pyfastx amd64 2.2.0-1+b1 [58.1 kB] Get:189 http://deb.debian.org/debian sid/main amd64 python3-pygtrie all 2.2-3 [17.1 kB] Get:190 http://deb.debian.org/debian sid/main amd64 python3-schedule all 1.2.2-1 [14.9 kB] Get:191 http://deb.debian.org/debian sid/main amd64 python3-seaborn all 0.13.2-5 [215 kB] Get:192 http://deb.debian.org/debian sid/main amd64 python3-treetime all 0.11.4-1 [938 kB] Get:193 http://deb.debian.org/debian sid/main amd64 python3-xopen all 1.7.0-3 [16.8 kB] Get:194 http://deb.debian.org/debian sid/main amd64 python3-zstandard amd64 0.23.0-4 [351 kB] Get:195 http://deb.debian.org/debian sid/main amd64 raxml amd64 8.2.13+dfsg-2+b1 [1514 kB] Get:196 http://deb.debian.org/debian sid/main amd64 seqmagick all 0.8.6-3 [40.1 kB] Get:197 http://deb.debian.org/debian sid/main amd64 vcftools amd64 0.1.16-3+b1 [431 kB] Preconfiguring packages ... Fetched 160 MB in 3s (57.0 MB/s) Selecting previously unselected package pigz. (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 ... 5473 files and directories currently installed.) Preparing to unpack .../archives/pigz_2.8-1_amd64.deb ... Unpacking pigz (2.8-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.3-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.3-1) ... 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Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up libgpg-error0:amd64 (1.51-4) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up fonts-lyx (2.4.3-1) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up libgcrypt20:amd64 (1.11.0-7) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b2) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libgomp1:amd64 (14.2.0-19) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up unicode-data (15.1.0-1) ... Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-3.1) ... Setting up libzopfli1 (1.0.3-3) ... Setting up libx11-data (2:1.8.12-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.47-1.1) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Setting up libatomic1:amd64 (14.2.0-19) ... Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libltdl7:amd64 (2.5.4-4) ... Setting up libfftw3-double3:amd64 (3.3.10-2+b1) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up perl-modules-5.40 (5.40.1-2) ... Setting up pigz (2.8-1) ... Setting up libtiff6:amd64 (4.7.0-3) ... Setting up libsuitesparseconfig7:amd64 (1:7.10.1+dfsg-1) ... Setting up libopenjp2-7:amd64 (2.5.3-2) ... 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) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up python-matplotlib-data (3.10.1+dfsg1-2) ... Setting up openssl (3.5.0-1) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up raxml (8.2.13+dfsg-2+b1) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libamd3:amd64 (1:7.10.1+dfsg-1) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up libcolamd3:amd64 (1:7.10.1+dfsg-1) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libcamd3:amd64 (1:7.10.1+dfsg-1) ... Setting up libperl5.40:amd64 (5.40.1-2) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up perl (5.40.1-2) ... Setting up libglib2.0-0t64:amd64 (2.84.1-1) ... No schema files found: doing nothing. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libglpk40:amd64 (5.0-1+b2) ... Setting up libccolamd3:amd64 (1:7.10.1+dfsg-1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.2) ... Setting up libharfbuzz0b:amd64 (10.2.0-1+b1) ... Setting up libdsdp-5.8t64 (5.8-10.1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2.3) ... Setting up libpython3.13-stdlib:amd64 (3.13.3-1) ... Setting up libpython3-stdlib:amd64 (3.13.3-1) ... Setting up vcftools (0.1.16-3+b1) ... Setting up libcholmod5:amd64 (1:7.10.1+dfsg-1) ... Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up python3.13 (3.13.3-1) ... Setting up mafft (7.505-1) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up python3 (3.13.3-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... 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 (3.13.3-1) ... Setting up python3-platformdirs (4.3.7-1) ... Setting up python3-zopfli (0.2.3.post1-1+b1) ... Setting up python3-fs (2.4.16-7) ... Setting up python3-six (1.17.0-1) ... Setting up python3-isodate (0.7.0-1) ... Setting up python3-decorator (5.2.1-1) ... 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-packaging (24.2-1) ... 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.ea91db2-1) ... Setting up python3-jmespath (1.0.1-1) ... Setting up python3-brotli (1.1.0-2+b7) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.7-3+b1) ... Setting up python3-idna (3.10-1) ... Setting up python3-typing-extensions (4.13.1-1) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up python3-urllib3 (2.3.0-2) ... Setting up python3-rpds-py (0.21.0-2+b1) ... Setting up libumfpack6:amd64 (1:7.10.1+dfsg-1) ... Setting up python3-lxml:amd64 (5.3.2-1) ... Setting up python3-traitlets (5.14.3+really5.14.3-1) ... Setting up python3-dateutil (2.9.0-4) ... Setting up python3-contourpy (1.3.1-1+b1) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-dendropy (4.6.1-2) ... Setting up python3-cffi-backend:amd64 (1.17.1-2+b2) ... Setting up python3-ptyprocess (0.7.0-6) ... Setting up python3-prompt-toolkit (3.0.50-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-schedule (1.2.2-1) ... Setting up python3-sympy (1.13.3-5) ... 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 (1.15.2-7) ... Setting up python3-cairo (1.27.0-2) ... Setting up python3-importlib-metadata (8.6.1-1) ... 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 (4.4.0+dfsg-2) ... Setting up python3-asttokens (3.0.0-1) ... Setting up python3-charset-normalizer (3.4.1-1+b1) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b4) ... Setting up blt (2.5.3+dfsg-8) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-9) ... Setting up python3-typeguard (4.4.2-1) ... Setting up python3-tk:amd64 (3.13.3-1) ... Setting up python3-pytz (2025.2-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-matplotlib-inline (0.1.7-1) ... Setting up python3-pil:amd64 (11.1.0-5+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-zstandard (0.23.0-4) ... Setting up python3-pandas (2.2.3+dfsg-9) ... Setting up python3-pil.imagetk:amd64 (11.1.0-5+b1) ... Setting up python3-executing (2.2.0-0.1) ... 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 (2.32.3+dfsg-5) ... Setting up python3-reportlab (4.3.1-1) ... Setting up python3-stack-data (0.6.3-1) ... Setting up python3-referencing (0.36.2-1) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up python3-pyfaidx (0.8.1.3-1) ... Setting up python3-setuptools (75.8.0-1) ... Setting up python3-jedi (0.19.1+ds1-1) ... Setting up python3-pyfastx (2.2.0-1+b1) ... Setting up python3-networkx (3.2.1-5) ... Setting up python3-ipython (8.30.0-2) ... 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 (4.57.0-1) ... Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... Setting up python3-matplotlib (3.10.1+dfsg1-2) ... Setting up python3-seaborn (0.13.2-5) ... Processing triggers for libc-bin (2.41-6) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-2+b1) ... 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 piuparts-depends-dummy (0.invalid.0) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m54.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m54.7s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok 0m54.7s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmp6m2t5qhr/./tmp/piuparts-depends-dummy.deb 0m54.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m54.7s DUMP: piuparts-depends-dummy install ok installed 0m54.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m54.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m54.8s DUMP: (Reading database ... 40555 files and directories currently installed.) Removing piuparts-depends-dummy (0.invalid.0) ... 0m54.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m54.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', 'clean'] 0m54.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', 'clean'] 0m54.8s DEBUG: Recording chroot state 0m55.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr'] 0m56.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr'] 0m59.0s ERROR: WARN: Broken symlinks: /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-Italic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-Italic.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-BoldItalic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-BoldItalic.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-Bold.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-Bold.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerif-Italic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerif-BoldItalic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-Oblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-Oblique.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-BoldOblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-BoldOblique.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-Bold.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-Bold.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-Oblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-ExtraLight.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-ExtraLight.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-BoldOblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuMathTeXGyre.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuMathTeXGyre.ttf /usr/share/doc/python3-networkx/html/_static/sphinx_highlight.js -> ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js /usr/share/doc/python3-networkx/html/_static/searchtools.js -> ../../../../javascript/sphinxdoc/1.0/searchtools.js /usr/share/doc/python3-networkx/html/_static/language_data.js -> ../../../../javascript/sphinxdoc/1.0/language_data.js /usr/share/doc/python3-networkx/html/_static/doctools.js -> ../../../../javascript/sphinxdoc/1.0/doctools.js 0m59.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'policy'] 0m59.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m59.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'policy'] 0m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'policy', 'augur'] 0m59.5s DUMP: augur: Installed: (none) Candidate: 24.4.0-1 Version table: 24.4.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m59.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'policy', 'augur'] 0m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', '-y', 'install', 'augur=24.4.0-1'] 1m0.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Recommended packages: iqtree The following NEW packages will be installed: augur 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 261 kB of archives. After this operation, 1081 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 augur all 24.4.0-1 [261 kB] Fetched 261 kB in 0s (1689 kB/s) Selecting previously unselected package augur. (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 ... 40555 files and directories currently installed.) Preparing to unpack .../augur_24.4.0-1_all.deb ... Unpacking augur (24.4.0-1) ... Setting up augur (24.4.0-1) ... 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', '-y', 'install', 'augur=24.4.0-1'] 1m0.3s INFO: Running scripts post_install 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_install_exceptions'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_install_exceptions'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'systemd-tmpfiles', '--cat-config'] 1m0.3s DUMP: chroot: failed to run command 'systemd-tmpfiles': No such file or directory 1m0.3s DEBUG: Command failed (status=127), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'systemd-tmpfiles', '--cat-config'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', 'remove', 'augur'] 1m0.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: blt fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libamd3 libatomic1 libblas3 libbrotli1 libcairo2 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdeflate0 libdsdp-5.8t64 libexpat1 libffi8 libfftw3-double3 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libglpk40 libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui liblapack3 liblcms2-2 liblerc4 libltdl7 libopenjp2-7 libpixman-1-0 libpng16-16t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 libsharpyuv0 libsuitesparseconfig7 libtcl8.6 libtiff6 libtk8.6 libumfpack6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libzopfli1 mafft media-types 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-cffi-backend 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-importlib-metadata 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 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: augur 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 1081 kB 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 ... 40657 files and directories currently installed.) Removing augur (24.4.0-1) ... 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', 'remove', 'augur'] 1m0.8s INFO: Reinstalling after remove 1m0.8s INFO: Running scripts pre_install 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_database-server'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_database-server'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_exceptions'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_exceptions'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_extras'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_extras'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_foreign_architecture'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_foreign_architecture'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'policy'] 1m0.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'policy'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'policy', 'augur'] 1m0.9s DUMP: augur: Installed: (none) Candidate: 24.4.0-1 Version table: 24.4.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 1m0.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'policy', 'augur'] 1m0.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', '-y', 'install', 'augur=24.4.0-1'] 1m1.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Recommended packages: iqtree The following NEW packages will be installed: augur 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/261 kB of archives. After this operation, 1081 kB of additional disk space will be used. Selecting previously unselected package augur. (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 ... 40555 files and directories currently installed.) Preparing to unpack .../augur_24.4.0-1_all.deb ... Unpacking augur (24.4.0-1) ... Setting up augur (24.4.0-1) ... 1m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', '-y', 'install', 'augur=24.4.0-1'] 1m1.5s INFO: Running scripts post_install 1m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_install_exceptions'] 1m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_install_exceptions'] 1m1.5s INFO: Running scripts pre_install 1m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_database-server'] 1m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_database-server'] 1m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_exceptions'] 1m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_exceptions'] 1m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_extras'] 1m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_extras'] 1m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_foreign_architecture'] 1m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_foreign_architecture'] 1m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'policy'] 1m1.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'policy'] 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'policy', 'augur'] 1m1.6s DUMP: augur: Installed: 24.4.0-1 Candidate: 24.4.0-1 Version table: *** 24.4.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-cache', 'policy', 'augur'] 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', '-y', 'install', '--reinstall', 'augur=24.4.0-1'] 1m2.2s DUMP: Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/261 kB of archives. After this operation, 0 B of additional disk space will be used. (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 ... 40657 files and directories currently installed.) Preparing to unpack .../augur_24.4.0-1_all.deb ... Unpacking augur (24.4.0-1) over (24.4.0-1) ... Setting up augur (24.4.0-1) ... 1m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', '-y', 'install', '--reinstall', 'augur=24.4.0-1'] 1m2.2s INFO: Running scripts post_install 1m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_install_exceptions'] 1m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_install_exceptions'] 1m2.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr'] 1m3.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr'] 1m6.3s 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) 1m7.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', '-ac', '--ignore-obsolete'] 1m10.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', '-ac', '--ignore-obsolete'] 1m10.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m10.3s DUMP: 0.15.6 1m10.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m10.3s INFO: Running adequate version 0.15.6 now. 1m10.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'augur'] 1m10.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'augur'] 1m10.3s INFO: Running scripts pre_remove 1m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_exceptions'] 1m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_exceptions'] 1m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_preseed_cleanup'] 1m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/pre_remove_preseed_cleanup'] 1m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m12.4s DUMP: install ok installed apt apt 3.0.0 install ok installed augur augur 24.4.0-1 install ok installed base-files base-files 13.7 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2 install ok installed blt blt 2.5.3+dfsg-8 install ok installed bsdutils bsdutils 1:2.41-3 install ok installed ca-certificates ca-certificates 20241223 install ok installed coreutils coreutils 9.7-1 install ok installed dash dash 0.5.12-12 install ok installed dbconfig-common dbconfig-common 2.0.24 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-3 install ok installed dpkg dpkg 1.22.18 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 2.15.0-2.3 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 2.4.3-1 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libamd3:amd64 libamd3 1:7.10.1+dfsg-1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0 install ok installed libatomic1:amd64 libatomic1 14.2.0-19 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblas3:amd64 libblas3 3.12.1-2 install ok installed libblkid1:amd64 libblkid1 2.41-3 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 2.41-6 install ok installed libc6:amd64 libc6 2.41-6 install ok installed libcairo2:amd64 libcairo2 1.18.4-1+b1 install ok installed libcamd3:amd64 libcamd3 1:7.10.1+dfsg-1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-4 install ok installed libccolamd3:amd64 libccolamd3 1:7.10.1+dfsg-1 install ok installed libcholmod5:amd64 libcholmod5 1:7.10.1+dfsg-1 install ok installed libcolamd3:amd64 libcolamd3 1:7.10.1+dfsg-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278 install ok installed libdeflate0:amd64 libdeflate0 1.23-1+b1 install ok installed libdsdp-5.8t64 libdsdp-5.8t64 5.8-10.1 install ok installed libexpat1:amd64 libexpat1 2.7.1-1 install ok installed libffi8:amd64 libffi8 3.4.7-1 install ok installed libfftw3-double3:amd64 libfftw3-double3 3.3.10-2+b1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-2.3 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1+b2 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-7 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-19 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.84.1-1 install ok installed libglpk40:amd64 libglpk40 5.0-1+b2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgomp1:amd64 libgomp1 14.2.0-19 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-4 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgsl28:amd64 libgsl28 2.8+dfsg-5 install ok installed libgslcblas0:amd64 libgslcblas0 2.8+dfsg-5 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.2.0-1+b1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1+b2 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3.1 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed liblapack3:amd64 liblapack3 3.12.1-2 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-3 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 2.5.4-4 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-3 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 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libperl5.40:amd64 libperl5.40 5.40.1-2 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.47-1.1 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-7 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.3-1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.3-1 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.3-1 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b2 install ok installed libraqm0:amd64 libraqm0 0.10.2-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 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 2.41-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-2 install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsuitesparseconfig7:amd64 libsuitesparseconfig7 1:7.10.1+dfsg-1 install ok installed libsystemd0:amd64 libsystemd0 257.5-2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.16+dfsg-1 install ok installed libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b4 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10 install ok installed libtiff6:amd64 libtiff6 4.7.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libtk8.6:amd64 libtk8.6 8.6.16-1 install ok installed libudev1:amd64 libudev1 257.5-2 install ok installed libumfpack6:amd64 libumfpack6 1:7.10.1+dfsg-1 install ok installed libuuid1:amd64 libuuid1 2.41-3 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:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.4 install ok installed libxrender1:amd64 libxrender1 1:0.9.12-1 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1.2 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 libzopfli1 libzopfli1 1.0.3-3 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-3 install ok installed login.defs login.defs 1:4.17.4-1 install ok installed mafft mafft 7.505-1 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 2.41-3 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 3.5.0-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1 install ok installed passwd passwd 1:4.17.4-1 install ok installed perl perl 5.40.1-2 install ok installed perl-base perl-base 5.40.1-2 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.1-2 install ok installed pigz pigz 2.8-1 install ok installed procps procps 2:4.0.4-7 install ok installed python-matplotlib-data python-matplotlib-data 3.10.1+dfsg1-2 install ok installed python3 python3 3.13.3-1 install ok installed python3-asttokens python3-asttokens 3.0.0-1 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-2+b1 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-cffi-backend:amd64 python3-cffi-backend 1.17.1-2+b2 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-2 install ok installed python3-charset-normalizer python3-charset-normalizer 3.4.1-1+b1 install ok installed python3-contourpy python3-contourpy 1.3.1-1+b1 install ok installed python3-cvxopt python3-cvxopt 1.3.0+dfsg-1+b9 install ok installed python3-cycler python3-cycler 0.12.1-1 install ok installed python3-dateutil python3-dateutil 2.9.0-4 install ok installed python3-decorator python3-decorator 5.2.1-1 install ok installed python3-dendropy python3-dendropy 4.6.1-2 install ok installed python3-executing python3-executing 2.2.0-0.1 install ok installed python3-fonttools python3-fonttools 4.57.0-1 install ok installed python3-freetype python3-freetype 2.5.1-1 install ok installed python3-fs python3-fs 2.4.16-7 install ok installed python3-idna python3-idna 3.10-1 install ok installed python3-importlib-metadata python3-importlib-metadata 8.6.1-1 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-ipdb python3-ipdb 0.13.13-3 install ok installed python3-ipython python3-ipython 8.30.0-2 install ok installed python3-isodate python3-isodate 0.7.0-1 install ok installed python3-jaraco.context python3-jaraco.context 6.0.1-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-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 5.3.2-1 install ok installed python3-lz4 python3-lz4 4.4.0+dfsg-2 install ok installed python3-matplotlib python3-matplotlib 3.10.1+dfsg1-2 install ok installed python3-matplotlib-inline python3-matplotlib-inline 0.1.7-1 install ok installed python3-minimal python3-minimal 3.13.3-1 install ok installed python3-more-itertools python3-more-itertools 10.6.0-1 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 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.4+ds-1 install ok installed python3-packaging python3-packaging 24.2-1 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 11.1.0-5+b1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 11.1.0-5+b1 install ok installed python3-pkg-resources python3-pkg-resources 75.8.0-1 install ok installed python3-platformdirs python3-platformdirs 4.3.7-1 install ok installed python3-prompt-toolkit python3-prompt-toolkit 3.0.50-1 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 0.8.1.3-1 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 2025.2-1 install ok installed python3-referencing python3-referencing 0.36.2-1 install ok installed python3-reportlab python3-reportlab 4.3.1-1 install ok installed python3-requests python3-requests 2.32.3+dfsg-5 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 1.15.2-7 install ok installed python3-seaborn python3-seaborn 0.13.2-5 install ok installed python3-setuptools python3-setuptools 75.8.0-1 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 1.13.3-5 install ok installed python3-tk:amd64 python3-tk 3.13.3-1 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 4.4.2-1 install ok installed python3-typeshed python3-typeshed 0.0~git20241223.ea91db2-1 install ok installed python3-typing-extensions python3-typing-extensions 4.13.1-1 install ok installed python3-ufolib2 python3-ufolib2 0.17.1+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b4 install ok installed python3-urllib3 python3-urllib3 2.3.0-2 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 3.21.0-1 install ok installed python3-zopfli python3-zopfli 0.2.3.post1-1+b1 install ok installed python3-zstandard python3-zstandard 0.23.0-4 install ok installed python3.13 python3.13 3.13.3-1 install ok installed python3.13-minimal python3.13-minimal 3.13.3-1 install ok installed python3.13-tk python3.13-tk 3.13.3-1 install ok installed raxml raxml 8.2.13+dfsg-2+b1 install ok installed readline-common readline-common 8.2-6 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.24 install ok installed seqmagick seqmagick 0.8.6-3 install ok installed sgml-base sgml-base 1.31 install ok installed sqv sqv 1.3.0-1 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-1 install ok installed ucf ucf 3.0051 install ok installed unicode-data unicode-data 15.1.0-1 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.41-3 install ok installed vcftools vcftools 0.1.16-3+b1 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+24 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+7 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 1m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', 'remove', '--allow-remove-essential', 'blt', 'ca-certificates', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libamd3:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcamd3:amd64', 'libccolamd3:amd64', 'libcholmod5:amd64', 'libcolamd3:amd64', 'libdeflate0:amd64', 'libdsdp-5.8t64', 'libexpat1:amd64', 'libffi8:amd64', 'libfftw3-double3:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0: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', 'libjs-jquery', 'libjs-jquery-ui', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libltdl7: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', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsuitesparseconfig7: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:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1: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-cffi-backend:amd64', '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-importlib-metadata', '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'] 1m35.2s 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 libamd3 libatomic1 libblas3 libbrotli1 libcairo2 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdeflate0 libdsdp-5.8t64 libexpat1 libffi8 libfftw3-double3 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglpk40 libgomp1 libgpg-error0 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui liblapack3 liblcms2-2 liblerc4 libltdl7 libopenjp2-7 libperl5.40 libpixman-1-0 libpng16-16t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 libsharpyuv0 libsuitesparseconfig7 libtcl8.6 libtiff6 libtk8.6 libumfpack6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 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-cffi-backend 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-importlib-metadata 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, 197 to remove and 0 not upgraded. After this operation, 749 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 ... 40657 files and directories currently installed.) Removing augur (24.4.0-1) ... 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+dfsg1-2) ... Removing python3-pil.imagetk:amd64 (11.1.0-5+b1) ... Removing python3-tk:amd64 (3.13.3-1) ... 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 (2.32.3+dfsg-5) ... Removing python3-certifi (2025.1.31+ds-1) ... Removing ca-certificates (20241223) ... 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 (3.13.3-1) ... Removing libtk8.6:amd64 (8.6.16-1) ... Removing libxft2:amd64 (2.3.6-1+b4) ... Removing python-matplotlib-data (3.10.1+dfsg1-2) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-lyx (2.4.3-1) ... Removing python3-cvxopt (1.3.0+dfsg-1+b9) ... Removing libumfpack6:amd64 (1:7.10.1+dfsg-1) ... Removing libcholmod5:amd64 (1:7.10.1+dfsg-1) ... Removing python3-pandas (2.2.3+dfsg-9) ... Removing python3-pandas-lib:amd64 (2.2.3+dfsg-9) ... Removing libdsdp-5.8t64 (5.8-10.1) ... Removing libcamd3:amd64 (1:7.10.1+dfsg-1) ... Removing libccolamd3:amd64 (1:7.10.1+dfsg-1) ... Removing libglpk40:amd64 (5.0-1+b2) ... Removing libcolamd3:amd64 (1:7.10.1+dfsg-1) ... 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 (8.30.0-2) ... Removing python3-prompt-toolkit (3.0.50-1) ... Removing python3-wcwidth (0.2.13+dfsg1-1) ... Removing python3-networkx (3.2.1-5) ... Removing python3-setuptools (75.8.0-1) ... Removing python3-jaraco.text (4.0.0-1) ... Removing python3-zstandard (0.23.0-4) ... Removing python3-jedi (0.19.1+ds1-1) ... Removing python3-typeshed (0.0~git20241223.ea91db2-1) ... Removing python3-cffi-backend:amd64 (1.17.1-2+b2) ... Removing libfftw3-double3:amd64 (3.3.10-2+b1) ... Removing vcftools (0.1.16-3+b1) ... Removing mafft (7.505-1) ... Removing perl (5.40.1-2) ... Removing libperl5.40:amd64 (5.40.1-2) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgsl28:amd64 (2.8+dfsg-5) ... Removing libgslcblas0:amd64 (2.8+dfsg-5) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libltdl7:amd64 (2.5.4-4) ... Removing libqhull-r8.0:amd64 (2020.2-6+b2) ... Removing libtcl8.6:amd64 (8.6.16+dfsg-1) ... Removing libxss1:amd64 (1:1.2.3-1+b3) ... Removing openssl (3.5.0-1) ... Removing perl-modules-5.40 (5.40.1-2) ... Removing python3-xopen (1.7.0-3) ... Removing pigz (2.8-1) ... Removing python3-stack-data (0.6.3-1) ... Removing python3-executing (2.2.0-0.1) ... Removing python3-asttokens (3.0.0-1) ... Removing python3-bcbio-gff (0.7.1-2) ... Removing python3-charset-normalizer (3.4.1-1+b1) ... Removing python3-contourpy (1.3.1-1+b1) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-4) ... Removing python3-dendropy (4.6.1-2) ... Removing python3-idna (3.10-1) ... Removing python3-pyfastx (2.2.0-1+b1) ... Removing python3-pyfaidx (0.8.1.3-1) ... Removing python3-importlib-metadata (8.6.1-1) ... Removing python3-isodate (0.7.0-1) ... 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-packaging (24.2-1) ... 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 (2025.2-1) ... 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 (2.3.0-2) ... Removing python3-zipp (3.21.0-1) ... Removing raxml (8.2.13+dfsg-2+b1) ... Removing python3-biopython (1.85+dfsg-2+b1) ... Removing python3-reportlab (4.3.1-1) ... Removing python3-pil:amd64 (11.1.0-5+b1) ... 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 (2.15.0-2.3) ... Removing fontconfig-config (2.15.0-2.3) ... Removing fonts-urw-base35 (20200910-8) ... Removing libamd3:amd64 (1:7.10.1+dfsg-1) ... Removing libraqm0:amd64 (0.10.2-1) ... Removing libharfbuzz0b:amd64 (10.2.0-1+b1) ... Removing libglib2.0-0t64:amd64 (2.84.1-1) ... Removing libatomic1:amd64 (14.2.0-19) ... Removing xfonts-utils (1:7.7+7) ... Removing python3-freetype (2.5.1-1) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libbrotli1:amd64 (1.1.0-2+b7) ... Removing libtiff6:amd64 (4.7.0-3) ... Removing libdeflate0:amd64 (1.23-1+b1) ... Removing python3-pkg-resources (75.8.0-1) ... Removing python3-jaraco.context (6.0.1-1) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.2-1) ... Removing libfontenc1:amd64 (1:1.1.8-1+b2) ... Removing libfribidi0:amd64 (1.0.16-1) ... Removing libsuitesparseconfig7:amd64 (1:7.10.1+dfsg-1) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libgomp1:amd64 (14.2.0-19) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3.1) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing libopenjp2-7:amd64 (2.5.3-2) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libpng16-16t64:amd64 (1.6.47-1.1) ... 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 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-chardet (5.2.0+dfsg-2) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-more-itertools (10.6.0-1) ... Removing python3-typing-extensions (4.13.1-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libx11-6:amd64 (2:1.8.12-1) ... 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 (4.57.0-1) ... Removing python3-scipy (1.15.2-7) ... Removing python3-numpy (1:2.2.4+ds-1) ... Removing liblapack3:amd64 (3.12.1-2) ... Removing libblas3:amd64 (3.12.1-2) ... Removing python3-lxml:amd64 (5.3.2-1) ... Removing libxslt1.1:amd64 (1.1.35-1.2) ... Removing libgcrypt20:amd64 (1.11.0-7) ... Removing libgfortran5:amd64 (14.2.0-19) ... Removing libgpg-error0:amd64 (1.51-4) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... 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 (5.2.1-1) ... Removing python3-fs (2.4.16-7) ... Removing python3-lz4 (4.4.0+dfsg-2) ... Removing python3-sympy (1.13.3-5) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Removing python3-platformdirs (4.3.7-1) ... Removing python3-unicodedata2 (15.1.0+ds-1+b4) ... Removing unicode-data (15.1.0-1) ... Removing python3-ufolib2 (0.17.1+dfsg1-1) ... Removing python3-attr (25.3.0-1) ... Removing python3 (3.13.3-1) ... Removing python3-minimal (3.13.3-1) ... Removing python3.13 (3.13.3-1) ... Removing python3.13-minimal (3.13.3-1) ... Removing libexpat1:amd64 (2.7.1-1) ... Removing libpython3-stdlib:amd64 (3.13.3-1) ... Removing libpython3.13-stdlib:amd64 (3.13.3-1) ... find: '/usr/lib/python3': No such file or directory Removing libffi8:amd64 (3.4.7-1) ... Removing libpython3.13-minimal:amd64 (3.13.3-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-6) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing media-types (13.0.0) ... Removing netbase (6.5) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.41-6) ... 1m35.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', 'remove', '--allow-remove-essential', 'blt', 'ca-certificates', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libamd3:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcamd3:amd64', 'libccolamd3:amd64', 'libcholmod5:amd64', 'libcolamd3:amd64', 'libdeflate0:amd64', 'libdsdp-5.8t64', 'libexpat1:amd64', 'libffi8:amd64', 'libfftw3-double3:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0: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', 'libjs-jquery', 'libjs-jquery-ui', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libltdl7: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', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsuitesparseconfig7: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:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1: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-cffi-backend:amd64', '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-importlib-metadata', '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'] 1m35.2s INFO: Running scripts post_remove 1m35.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_remove_cleanup'] 1m35.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_remove_cleanup'] 1m35.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_remove_exceptions'] 1m35.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_remove_exceptions'] 1m35.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libamd3:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcamd3:amd64', 'libccolamd3:amd64', 'libcholmod5:amd64', 'libcolamd3:amd64', 'libdeflate0:amd64', 'libdsdp-5.8t64', 'libexpat1:amd64', 'libffi8:amd64', 'libfftw3-double3:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0: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', 'libjs-jquery', 'libjs-jquery-ui', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libltdl7: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', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsuitesparseconfig7: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:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1: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-cffi-backend:amd64', '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-importlib-metadata', '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'] 1m35.5s DUMP: dpkg: warning: ignoring request to remove blt which isn't installed (Reading database ... 5536 files and directories currently installed.) Purging configuration files for ca-certificates (20241223) ... 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 (2.15.0-2.3) ... 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 libamd3 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove 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 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 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 (2.84.1-1) ... 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 Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove 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 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 (3.13.3-1) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsuitesparseconfig7 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 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 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 (3.5.0-1) ... Purging configuration files for perl (5.40.1-2) ... 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+dfsg1-2) ... Purging configuration files for python3 (3.13.3-1) ... 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-cffi-backend 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-importlib-metadata 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) ... 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 (1.13.3-5) ... 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 (3.13.3-1) ... 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 (8.2-6) ... dpkg: warning: ignoring request to remove seqmagick which isn't installed Purging configuration files for sgml-base (1.31) ... 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+24) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+7) ... Purging configuration files for xml-core (0.19) ... 1m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libamd3:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcamd3:amd64', 'libccolamd3:amd64', 'libcholmod5:amd64', 'libcolamd3:amd64', 'libdeflate0:amd64', 'libdsdp-5.8t64', 'libexpat1:amd64', 'libffi8:amd64', 'libfftw3-double3:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0: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', 'libjs-jquery', 'libjs-jquery-ui', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libltdl7: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', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsuitesparseconfig7: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:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1: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-cffi-backend:amd64', '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-importlib-metadata', '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'] 1m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg', '--purge', 'augur'] 1m35.5s DUMP: dpkg: warning: ignoring request to remove augur which isn't installed 1m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg', '--purge', 'augur'] 1m35.5s INFO: Running scripts post_purge 1m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_purge_exceptions'] 1m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_purge_exceptions'] 1m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_purge_manual_cleanup'] 1m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_purge_manual_cleanup'] 1m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg', '--purge', '--pending'] 1m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg', '--purge', '--pending'] 1m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg', '--remove', '--pending'] 1m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg', '--remove', '--pending'] 1m35.5s INFO: Running scripts post_test 1m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_test_exceptions'] 1m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'tmp/scripts/post_test_exceptions'] 1m35.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr'] 1m35.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr'] 1m36.0s DEBUG: No broken symlinks as far as we can find. 1m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg-divert', '--list'] 1m36.0s 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 1m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'dpkg-divert', '--list'] 1m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', 'clean'] 1m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr', 'apt-get', 'clean'] 1m36.0s DEBUG: Recording chroot state 1m37.2s INFO: PASS: Installation and purging test. 1m37.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/shm'] 1m37.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/shm'] 1m37.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/console'] 1m37.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/console'] 1m37.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/ptmx'] 1m37.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/ptmx'] 1m37.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/pts'] 1m37.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/dev/pts'] 1m37.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/proc'] 1m37.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr/proc'] 1m37.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr'] 1m37.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp6m2t5qhr'] 1m37.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp6m2t5qhr 1m37.5s INFO: PASS: All tests. 1m37.5s INFO: piuparts run ends. ret=0 End: 2025-04-09 14:59:29 GMT