Start: 2025-04-09 19:45:31 GMT Package: paleomix Version: 1.3.8-2 Installed-Size: 2006 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-coloredlogs, python3-configargparse, python3-pysam, python3-ruamel.yaml, python3-setproctitle, python3:any, adapterremoval, bedtools, bowtie2, bwa, bcftools, examl, mafft, mapdamage, phylip, picard-tools, r-base-core, radiant, raxml, samtools Description: pipelines and tools for the processing of ancient and modern HTS data Homepage: https://geogenetics.ku.dk/publications/paleomix Description-md5: 7cb3c4aa709e51b480a41a73961d7253 Section: science Priority: optional Filename: pool/main/p/paleomix/paleomix_1.3.8-2_amd64.deb Size: 984108 MD5sum: 002d92f28755caf1c12004da66a7964a SHA256: 56fcce16061450d75d95b3db3d8169aee8f8e810f5ac2a725ea57c7dce44864e 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 paleomix=1.3.8-2 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 paleomix=1.3.8-2 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/tmpuhzqy3e0 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpuhzqy3e0 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', '--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/tmpuhzqy3e0', '--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/tmpuhzqy3e0/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/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/tmpuhzqy3e0/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/tmpuhzqy3e0/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/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/tmpuhzqy3e0/tmp/scripts/ 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts-leftovers to /srv/piuparts.debian.org/tmp/tmpuhzqy3e0/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', '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 (12.9 MB/s) Reading package lists... 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', 'update'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', '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 (156 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/tmpuhzqy3e0', 'apt-get', '-yf', 'dist-upgrade'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.2s DUMP: 31e44ff00e610efb534d9d62a0a21228 - 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.2s INFO: Running scripts post_setup 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', '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/tmpuhzqy3e0', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', '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 (66.3 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/tmpuhzqy3e0', 'tmp/scripts/post_setup_fake-essential'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', '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/tmpuhzqy3e0', 'tmp/scripts/post_setup_forbid_home'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.3s 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' 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_setup_minimize'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_setup_minimize'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_setup_zz_backports'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_setup_zz_backports'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', 'clean'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', 'clean'] 0m4.4s DEBUG: Recording chroot state 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', '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/tmpuhzqy3e0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', '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/tmpuhzqy3e0', 'dpkg-divert', '--list'] 0m4.6s INFO: Running scripts is_testable 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/is_testable_uninstallable'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', '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/tmpuhzqy3e0', 'tmp/scripts/pre_test_exceptions'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_test_exceptions'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', '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/tmpuhzqy3e0', 'tmp/scripts/pre_test_root_password'] 0m4.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0'] 0m4.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0'] 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/tmpuhzqy3e0', 'tmp/scripts/pre_install_database-server'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_database-server'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_exceptions'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_exceptions'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_extras'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_extras'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'show', '--no-all-versions', 'paleomix=1.3.8-2'] 0m5.6s DUMP: Package: paleomix Version: 1.3.8-2 Installed-Size: 2006 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-coloredlogs, python3-configargparse, python3-pysam, python3-ruamel.yaml, python3-setproctitle, python3:any, adapterremoval, bedtools, bowtie2, bwa, bcftools, examl, mafft, mapdamage, phylip, picard-tools, r-base-core, radiant, raxml, samtools Description-en: pipelines and tools for the processing of ancient and modern HTS data The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data: The BAM pipeline processes de-multiplexed reads from one or more samples, through sequence processing and alignment, to generate BAM alignment files useful in downstream analyses; the Phylogenetic pipeline carries out genotyping and phylogenetic inference on BAM alignment files, either produced using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out a suite of analyses on low coverage equine alignments, in order to detect the presence of F1-hybrids in archaeological assemblages. In addition, PALEOMIX aids in metagenomic analysis of the extracts. . The pipelines have been designed with ancient DNA (aDNA) in mind, and includes several features especially useful for the analyses of ancient samples, but can all be for the processing of modern samples, in order to ensure consistent data processing. Description-md5: 7cb3c4aa709e51b480a41a73961d7253 Homepage: https://geogenetics.ku.dk/publications/paleomix Section: science Priority: optional Filename: pool/main/p/paleomix/paleomix_1.3.8-2_amd64.deb Size: 984108 MD5sum: 002d92f28755caf1c12004da66a7964a SHA256: 56fcce16061450d75d95b3db3d8169aee8f8e810f5ac2a725ea57c7dce44864e 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'show', '--no-all-versions', 'paleomix=1.3.8-2'] 0m5.6s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: piuparts developers team Depends: python3-coloredlogs, python3-configargparse, python3-pysam, python3-ruamel.yaml, python3-setproctitle, python3:any, adapterremoval, bedtools, bowtie2, bwa, bcftools, examl, mafft, mapdamage, phylip, picard-tools, r-base-core, radiant, raxml, samtools 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/tmp62t39hrc/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/tmp62t39hrc/piuparts-depends-dummy.deb'. 0m5.6s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmp62t39hrc/piuparts-depends-dummy'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m5.6s DUMP: 3.0.0 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m5.6s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmp62t39hrc/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpuhzqy3e0/tmp 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m26.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adapterremoval adduser adwaita-icon-theme at-spi2-common bcftools bedtools bowtie2 bwa ca-certificates ca-certificates-java dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless examl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme ibverbs-providers java-common junit4 libamd-comgr2 libamdhip64-5 libapache-pom-java libapparmor1 libasound2-data libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libbrotli1 libcairo-gobject2 libcairo2 libcbor0.10 libcloudproviders0 libcolord2 libcom-err2 libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java libcommons-collections4-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm2 libedit2 libelf1t64 libepoxy0 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libezmorph-java libfabric1 libffi8 libfido2-1 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libfuse3-4 libgatk-native-bindings-java libgbm1 libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgkl-java libgl1 libgl1-mesa-dri libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgnutls30t64 libgomp1 libgoogle-gson-java libgraphite2-3 libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libhamcrest-java libharfbuzz0b libhsa-runtime64-1 libhsakmt1 libhts3t64 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libice6 libicu76 libidn2-0 libjaxen-java libjbig0 libjoptsimple-java libjpeg62-turbo libjson-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 liblightcouch-java libllvm17t64 libllvm19 liblog4j2-java libmbedcrypto16 libmbedtls21 libmbedx509-7 libmongodb-java libmunge2 libncbi-ngs3 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenmpi40 libp11-kit0 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0 libpcsclite1 libperl5.40 libpicard-java libpixman-1-0 libpmix2t64 libpng16-16t64 libpsl5t64 libpsm2-2 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librdmacm1t64 libreadline8t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1t64 libsystemd-shared libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libucx0 libunistring5 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxnvctrl0 libxom-java libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libz3-4 littler mafft mapdamage media-types mesa-libgallium mpi-default-bin ncbi-vdb-data netbase ocl-icd-libopencl1 openjdk-21-jre openjdk-21-jre-headless openmpi-bin openmpi-common openssh-client openssl perl perl-modules-5.40 phylip picard-tools python3 python3-coloredlogs python3-configargparse python3-humanfriendly python3-minimal python3-monotonic python3-pysam python3-ruamel.yaml python3-ruamel.yaml.clib python3-setproctitle python3.13 python3.13-minimal r-base-core r-cran-cli r-cran-codetools r-cran-colorspace r-cran-fansi r-cran-farver r-cran-foreach r-cran-gam r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-inline r-cran-isoband r-cran-iterators r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppgsl r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr radiant raxml readline-common samtools seqtk shared-mime-info systemd systemd-sysv unzip x11-common xdg-utils xkb-data zip Suggested packages: liblocale-gettext-perl cron quota adwaita-icon-theme-legacy python3-numpy texlive-latex-recommended bowtie2-examples alsa-utils libasound2-plugins colord libcommons-collections3-java-doc libcommons-collections4-java-doc libasm-java libxz-java libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java cups-common libdom4j-java libjdom1-java libxalan2-java fuse3 gdbm-l10n low-memory-monitor gnutls-bin libgoogle-gson-java-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user gvfs libhwloc-contrib-plugins liblcms2-utils libactivation-java libcommons-csv-java libconversant-disruptor-java libdisruptor-java libgeronimo-jms-1.1-spec-java libjackson2-dataformat-xml-java libjackson2-dataformat-yaml libjansi-java libjctools-java libjeromq-java libmail-java libwoodstox-java libngs-java-doc libcryptsetup12 libtss2-rc0t64 pciutils pcscd rhino lm-sensors libarchive13t64 libbpf1 libdw1t64 libgcrypt20 libip4tc2 libpwquality1 libqrencode4 tcl8.6 tk8.6 libxerces2-java-doc libxml-commons-resolver1.1-java-doc libxom-java-doc opencl-icd libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl phylip-doc python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binutils binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-covr r-cran-knitr r-cran-magick r-cran-rmarkdown r-cran-sf r-cran-getopt r-cran-testthat readline-doc cwltool systemd-container systemd-homed systemd-userdbd systemd-boot systemd-resolved systemd-repart libtss2-tcti-device0 polkitd Recommended packages: librsvg2-common python3-gffutils python3-matplotlib alsa-ucm-conf alsa-topology-conf at-spi2-core libgdk-pixbuf2.0-bin libgkl-jni libglib2.0-data xdg-user-dirs libgtk-3-bin krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules libkmod2 mesa-vulkan-drivers | vulkan-icd blast2 libwww-perl lynx ruby libatk-wrapper-java-jni fonts-dejavu-extra xauth r-recommended r-base-dev r-doc-html r-cran-callr r-cran-covr r-cran-crayon r-cran-digest r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-testthat r-cran-whoami r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-unitizer r-cran-interp r-cran-hexbin r-cran-hmisc r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg r-cran-ragg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 r-cran-dbi r-cran-rsqlite r-cran-waldo r-cran-lintr r-cran-tidyverse r-cran-bit64 r-cran-diagrammer r-cran-formattable r-cran-lubridate r-cran-nanotime r-cran-palmerpenguins r-cran-stringi r-cran-survival r-cran-units r-cran-lobstr r-cran-fs r-cran-usethis r-cran-dichromat r-cran-hms r-cran-bench r-cran-blob r-cran-brio r-cran-evaluate r-cran-here r-cran-pkgbuild r-cran-pkgload r-cran-purrr r-cran-tidyr r-cran-generics r-cran-pkgdown r-cran-zeallot linux-sysctl-defaults systemd-timesyncd | time-daemon systemd-cryptsetup libnss-systemd libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: adapterremoval adduser adwaita-icon-theme at-spi2-common bcftools bedtools bowtie2 bwa ca-certificates ca-certificates-java dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless examl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme ibverbs-providers java-common junit4 libamd-comgr2 libamdhip64-5 libapache-pom-java libapparmor1 libasound2-data libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libbrotli1 libcairo-gobject2 libcairo2 libcbor0.10 libcloudproviders0 libcolord2 libcom-err2 libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java libcommons-collections4-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm2 libedit2 libelf1t64 libepoxy0 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libezmorph-java libfabric1 libffi8 libfido2-1 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libfuse3-4 libgatk-native-bindings-java libgbm1 libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgkl-java libgl1 libgl1-mesa-dri libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgnutls30t64 libgomp1 libgoogle-gson-java libgraphite2-3 libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libhamcrest-java libharfbuzz0b libhsa-runtime64-1 libhsakmt1 libhts3t64 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libice6 libicu76 libidn2-0 libjaxen-java libjbig0 libjoptsimple-java libjpeg62-turbo libjson-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 liblightcouch-java libllvm17t64 libllvm19 liblog4j2-java libmbedcrypto16 libmbedtls21 libmbedx509-7 libmongodb-java libmunge2 libncbi-ngs3 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenmpi40 libp11-kit0 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0 libpcsclite1 libperl5.40 libpicard-java libpixman-1-0 libpmix2t64 libpng16-16t64 libpsl5t64 libpsm2-2 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librdmacm1t64 libreadline8t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1t64 libsystemd-shared libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libucx0 libunistring5 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxnvctrl0 libxom-java libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libz3-4 littler mafft mapdamage media-types mesa-libgallium mpi-default-bin ncbi-vdb-data netbase ocl-icd-libopencl1 openjdk-21-jre openjdk-21-jre-headless openmpi-bin openmpi-common openssh-client openssl perl perl-modules-5.40 phylip picard-tools piuparts-depends-dummy python3 python3-coloredlogs python3-configargparse python3-humanfriendly python3-minimal python3-monotonic python3-pysam python3-ruamel.yaml python3-ruamel.yaml.clib python3-setproctitle python3.13 python3.13-minimal r-base-core r-cran-cli r-cran-codetools r-cran-colorspace r-cran-fansi r-cran-farver r-cran-foreach r-cran-gam r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-inline r-cran-isoband r-cran-iterators r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppgsl r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr radiant raxml readline-common samtools seqtk shared-mime-info systemd systemd-sysv unzip x11-common xdg-utils xkb-data zip 0 upgraded, 343 newly installed, 0 to remove and 0 not upgraded. Need to get 325 MB/325 MB of archives. After this operation, 1293 MB of additional disk space will be used. Get:1 /tmp/piuparts-depends-dummy.deb piuparts-depends-dummy amd64 0.invalid.0 [760 B] Get:2 http://deb.debian.org/debian sid/main amd64 libsystemd-shared amd64 257.5-2 [2142 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libapparmor1 amd64 4.1.0~beta5-6 [43.5 kB] Get:4 http://deb.debian.org/debian sid/main amd64 systemd amd64 257.5-2 [3091 kB] Get:5 http://deb.debian.org/debian sid/main amd64 systemd-sysv amd64 257.5-2 [63.9 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libdbus-1-3 amd64 1.16.2-2 [178 kB] Get:7 http://deb.debian.org/debian sid/main amd64 dbus-bin amd64 1.16.2-2 [80.0 kB] Get:8 http://deb.debian.org/debian sid/main amd64 dbus-session-bus-common all 1.16.2-2 [52.3 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get:10 http://deb.debian.org/debian sid/main amd64 dbus-daemon amd64 1.16.2-2 [159 kB] Get:11 http://deb.debian.org/debian sid/main amd64 adduser all 3.150 [187 kB] Get:12 http://deb.debian.org/debian sid/main amd64 dbus-system-bus-common all 1.16.2-2 [53.5 kB] Get:13 http://deb.debian.org/debian sid/main amd64 dbus amd64 1.16.2-2 [71.6 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.3-1 [861 kB] Get:15 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.3-1 [2210 kB] Get:16 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.13.3-1 [27.2 kB] Get:17 http://deb.debian.org/debian sid/main amd64 media-types all 13.0.0 [29.3 kB] Get:18 http://deb.debian.org/debian sid/main amd64 netbase all 6.5 [12.4 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get:20 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-6 [69.4 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libpython3.13-stdlib amd64 3.13.3-1 [1954 kB] Get:23 http://deb.debian.org/debian sid/main amd64 python3.13 amd64 3.13.3-1 [751 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.13.3-1 [10.2 kB] Get:25 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.13.3-1 [28.2 kB] Get:26 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.5.0-1 [1491 kB] Get:27 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20241223 [164 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libpam-systemd amd64 257.5-2 [296 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libfido2-1 amd64 1.15.0-1+b1 [78.7 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-5 [9316 B] Get:36 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:38 http://deb.debian.org/debian sid/main amd64 openssh-client amd64 1:9.9p2-2 [968 kB] Get:39 http://deb.debian.org/debian sid/main amd64 perl-modules-5.40 all 5.40.1-2 [3017 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libperl5.40 amd64 5.40.1-2 [4315 kB] Get:43 http://deb.debian.org/debian sid/main amd64 perl amd64 5.40.1-2 [267 kB] Get:44 http://deb.debian.org/debian sid/main amd64 adapterremoval amd64 2.3.4-1 [205 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Get:47 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.84.1-1 [1514 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Get:49 http://deb.debian.org/debian sid/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [282 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:54 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.7.0-3 [346 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB] Get:59 http://deb.debian.org/debian sid/main amd64 gtk-update-icon-cache amd64 4.18.4+ds-1 [51.7 kB] Get:60 http://deb.debian.org/debian sid/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get:61 http://deb.debian.org/debian sid/main amd64 adwaita-icon-theme all 48.0-1 [504 kB] Get:62 http://deb.debian.org/debian sid/main amd64 at-spi2-common all 2.56.1-2 [171 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:77 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.13.0-1 [374 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get:82 http://deb.debian.org/debian sid/main amd64 bcftools amd64 1.21-1 [784 kB] Get:83 http://deb.debian.org/debian sid/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get:84 http://deb.debian.org/debian sid/main amd64 bowtie2 amd64 2.5.4-1+b2 [1505 kB] Get:85 http://deb.debian.org/debian sid/main amd64 bwa amd64 0.7.18-1 [212 kB] Get:86 http://deb.debian.org/debian sid/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:87 http://deb.debian.org/debian sid/main amd64 dbus-user-session amd64 1.16.2-2 [52.1 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB] Get:89 http://deb.debian.org/debian sid/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB] Get:90 http://deb.debian.org/debian sid/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB] Get:91 http://deb.debian.org/debian sid/main amd64 java-common all 0.76 [6776 B] Get:92 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libnss3 amd64 2:3.110-1 [1393 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libpcsclite1 amd64 2.3.3-1 [55.2 kB] Get:96 http://deb.debian.org/debian sid/main amd64 openjdk-21-jre-headless amd64 21.0.7~8ea-1 [41.8 MB] Get:97 http://deb.debian.org/debian sid/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get:98 http://deb.debian.org/debian sid/main amd64 libatk1.0-0t64 amd64 2.56.1-2 [51.6 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libatspi2.0-0t64 amd64 2.56.1-2 [80.6 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libatk-bridge2.0-0t64 amd64 2.56.1-2 [68.4 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:109 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:110 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:111 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libcairo-gobject2 amd64 1.18.4-1+b1 [130 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libcloudproviders0 amd64 0.3.6-2 [29.2 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libcolord2 amd64 1.4.7-3 [139 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Get:129 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-2.3 [463 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.56.3-1 [226 kB] Get:134 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [55.6 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [35.7 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libwayland-client0 amd64 1.23.1-3 [26.8 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libwayland-cursor0 amd64 1.23.1-3 [11.9 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libwayland-egl1 amd64 1.23.1-3 [5860 B] Get:139 http://deb.debian.org/debian sid/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get:143 http://deb.debian.org/debian sid/main amd64 libxinerama1 amd64 2:1.1.4-3+b4 [16.0 kB] Get:144 http://deb.debian.org/debian sid/main amd64 xkb-data all 2.42-1 [790 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB] Get:147 http://deb.debian.org/debian sid/main amd64 libgtk-3-common all 3.24.49-3 [4908 kB] Get:148 http://deb.debian.org/debian sid/main amd64 libgtk-3-0t64 amd64 3.24.49-3 [2769 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get:150 http://deb.debian.org/debian sid/main amd64 libdrm-common all 2.4.124-2 [8288 B] Get:151 http://deb.debian.org/debian sid/main amd64 libdrm2 amd64 2.4.124-2 [39.0 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libx11-xcb1 amd64 2:1.8.12-1 [247 kB] Get:153 http://deb.debian.org/debian sid/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get:154 http://deb.debian.org/debian sid/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get:155 http://deb.debian.org/debian sid/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get:156 http://deb.debian.org/debian sid/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get:157 http://deb.debian.org/debian sid/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get:158 http://deb.debian.org/debian sid/main amd64 libdrm-amdgpu1 amd64 2.4.124-2 [22.6 kB] Get:159 http://deb.debian.org/debian sid/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libdrm-intel1 amd64 2.4.124-2 [64.1 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:162 http://deb.debian.org/debian sid/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libllvm19 amd64 1:19.1.7-3 [26.0 MB] Get:164 http://deb.debian.org/debian sid/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get:165 http://deb.debian.org/debian sid/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get:166 http://deb.debian.org/debian sid/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get:167 http://deb.debian.org/debian sid/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get:168 http://deb.debian.org/debian sid/main amd64 libxshmfence1 amd64 1.3.3-1 [10.9 kB] Get:169 http://deb.debian.org/debian sid/main amd64 mesa-libgallium amd64 25.0.3-1 [9624 kB] Get:170 http://deb.debian.org/debian sid/main amd64 libwayland-server0 amd64 1.23.1-3 [34.4 kB] Get:171 http://deb.debian.org/debian sid/main amd64 libgbm1 amd64 25.0.3-1 [44.2 kB] Get:172 http://deb.debian.org/debian sid/main amd64 libvulkan1 amd64 1.4.309.0-1 [130 kB] Get:173 http://deb.debian.org/debian sid/main amd64 libgl1-mesa-dri amd64 25.0.3-1 [45.7 kB] Get:174 http://deb.debian.org/debian sid/main amd64 libglx-mesa0 amd64 25.0.3-1 [143 kB] Get:175 http://deb.debian.org/debian sid/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get:176 http://deb.debian.org/debian sid/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get:177 http://deb.debian.org/debian sid/main amd64 libasound2-data all 1.2.13-1 [21.1 kB] Get:178 http://deb.debian.org/debian sid/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB] Get:179 http://deb.debian.org/debian sid/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get:180 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+24 [217 kB] Get:181 http://deb.debian.org/debian sid/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB] Get:182 http://deb.debian.org/debian sid/main amd64 openjdk-21-jre amd64 21.0.7~8ea-1 [205 kB] Get:183 http://deb.debian.org/debian sid/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get:184 http://deb.debian.org/debian sid/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get:185 http://deb.debian.org/debian sid/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get:186 http://deb.debian.org/debian sid/main amd64 libnl-3-200 amd64 3.7.0-2 [59.4 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libnl-route-3-200 amd64 3.7.0-2 [182 kB] Get:188 http://deb.debian.org/debian sid/main amd64 libibverbs1 amd64 56.0-4 [62.4 kB] Get:189 http://deb.debian.org/debian sid/main amd64 ibverbs-providers amd64 56.0-4 [357 kB] Get:190 http://deb.debian.org/debian sid/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get:191 http://deb.debian.org/debian sid/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:192 http://deb.debian.org/debian sid/main amd64 librdmacm1t64 amd64 56.0-4 [70.2 kB] Get:193 http://deb.debian.org/debian sid/main amd64 libfabric1 amd64 2.0.0-4 [700 kB] Get:194 http://deb.debian.org/debian sid/main amd64 libhwloc15 amd64 2.12.0-1 [164 kB] Get:195 http://deb.debian.org/debian sid/main amd64 libmunge2 amd64 0.5.16-1 [19.7 kB] Get:196 http://deb.debian.org/debian sid/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB] Get:197 http://deb.debian.org/debian sid/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [42.9 kB] Get:198 http://deb.debian.org/debian sid/main amd64 libhwloc-plugins amd64 2.12.0-1 [18.1 kB] Get:199 http://deb.debian.org/debian sid/main amd64 libpmix2t64 amd64 5.0.7-1 [660 kB] Get:200 http://deb.debian.org/debian sid/main amd64 libllvm17t64 amd64 1:17.0.6-21+b1 [23.6 MB] Get:201 http://deb.debian.org/debian sid/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get:202 http://deb.debian.org/debian sid/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB] Get:203 http://deb.debian.org/debian sid/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB] Get:204 http://deb.debian.org/debian sid/main amd64 libamdhip64-5 amd64 5.7.1-5+b1 [8882 kB] Get:205 http://deb.debian.org/debian sid/main amd64 libfuse3-4 amd64 3.17.1-1 [97.7 kB] Get:206 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:207 http://deb.debian.org/debian sid/main amd64 libibumad3 amd64 56.0-4 [29.9 kB] Get:208 http://deb.debian.org/debian sid/main amd64 libibmad5 amd64 56.0-4 [44.5 kB] Get:209 http://deb.debian.org/debian sid/main amd64 libucx0 amd64 1.18.1+ds-2+b1 [1196 kB] Get:210 http://deb.debian.org/debian sid/main amd64 libopenmpi40 amd64 5.0.7-1 [2365 kB] Get:211 http://deb.debian.org/debian sid/main amd64 openmpi-common all 5.0.7-1 [97.2 kB] Get:212 http://deb.debian.org/debian sid/main amd64 openmpi-bin amd64 5.0.7-1 [189 kB] Get:213 http://deb.debian.org/debian sid/main amd64 mpi-default-bin amd64 1.18 [2576 B] Get:214 http://deb.debian.org/debian sid/main amd64 examl amd64 3.0.22-6+b3 [983 kB] Get:215 http://deb.debian.org/debian sid/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get:216 http://deb.debian.org/debian sid/main amd64 junit4 all 4.13.2-5 [350 kB] Get:217 http://deb.debian.org/debian sid/main amd64 libapache-pom-java all 33-2 [5852 B] Get:218 http://deb.debian.org/debian sid/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:219 http://deb.debian.org/debian sid/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get:220 http://deb.debian.org/debian sid/main amd64 libfreemarker-java all 2.3.32-2.1 [1525 kB] Get:221 http://deb.debian.org/debian sid/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get:222 http://deb.debian.org/debian sid/main amd64 libjoptsimple-java all 5.0.4-7 [73.7 kB] Get:223 http://deb.debian.org/debian sid/main amd64 libcommons-codec-java all 1.18.0-1 [304 kB] Get:224 http://deb.debian.org/debian sid/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get:225 http://deb.debian.org/debian sid/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get:226 http://deb.debian.org/debian sid/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get:227 http://deb.debian.org/debian sid/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get:228 http://deb.debian.org/debian sid/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get:229 http://deb.debian.org/debian sid/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get:230 http://deb.debian.org/debian sid/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get:231 http://deb.debian.org/debian sid/main amd64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] Get:232 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:233 http://deb.debian.org/debian sid/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get:234 http://deb.debian.org/debian sid/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get:235 http://deb.debian.org/debian sid/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get:236 http://deb.debian.org/debian sid/main amd64 libcommons-io-java all 2.18.0-1 [509 kB] Get:237 http://deb.debian.org/debian sid/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get:238 http://deb.debian.org/debian sid/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get:239 http://deb.debian.org/debian sid/main amd64 libcommons-math3-java all 3.6.1-4 [2040 kB] Get:240 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.13.0-1 [381 kB] Get:241 http://deb.debian.org/debian sid/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB] Get:242 http://deb.debian.org/debian sid/main amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B] Get:243 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:244 http://deb.debian.org/debian sid/main amd64 libjaxen-java all 1.1.6-5 [214 kB] Get:245 http://deb.debian.org/debian sid/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get:246 http://deb.debian.org/debian sid/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get:247 http://deb.debian.org/debian sid/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get:248 http://deb.debian.org/debian sid/main amd64 libxom-java all 1.3.9-1 [174 kB] Get:249 http://deb.debian.org/debian sid/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get:250 http://deb.debian.org/debian sid/main amd64 libmbedcrypto16 amd64 3.6.3-1 [357 kB] Get:251 http://deb.debian.org/debian sid/main amd64 libmbedx509-7 amd64 3.6.3-1 [149 kB] Get:252 http://deb.debian.org/debian sid/main amd64 libmbedtls21 amd64 3.6.3-1 [236 kB] Get:253 http://deb.debian.org/debian sid/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get:254 http://deb.debian.org/debian sid/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB] Get:255 http://deb.debian.org/debian sid/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7.1 [156 kB] Get:256 http://deb.debian.org/debian sid/main amd64 libngs-jni amd64 3.0.9+dfsg-7.1 [25.6 kB] Get:257 http://deb.debian.org/debian sid/main amd64 libngs-java amd64 3.0.9+dfsg-7.1 [112 kB] Get:258 http://deb.debian.org/debian sid/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get:259 http://deb.debian.org/debian sid/main amd64 libsnappy1v5 amd64 1.2.2-1 [29.3 kB] Get:260 http://deb.debian.org/debian sid/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B] Get:261 http://deb.debian.org/debian sid/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get:262 http://deb.debian.org/debian sid/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get:263 http://deb.debian.org/debian sid/main amd64 libgkl-java all 0.8.11+dfsg-2 [24.7 kB] Get:264 http://deb.debian.org/debian sid/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get:265 http://deb.debian.org/debian sid/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get:266 http://deb.debian.org/debian sid/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get:267 http://deb.debian.org/debian sid/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:268 http://deb.debian.org/debian sid/main amd64 libicu76 amd64 76.1-3 [9721 kB] Get:269 http://deb.debian.org/debian sid/main amd64 libopenblas0-pthread amd64 0.3.29+ds-3 [6740 kB] Get:270 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:271 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get:272 http://deb.debian.org/debian sid/main amd64 libopenblas0 amd64 0.3.29+ds-3 [42.7 kB] Get:273 http://deb.debian.org/debian sid/main amd64 libopenblas-pthread-dev amd64 0.3.29+ds-3 [5063 kB] Get:274 http://deb.debian.org/debian sid/main amd64 libopenblas-dev amd64 0.3.29+ds-3 [57.0 kB] Get:275 http://deb.debian.org/debian sid/main amd64 libpaper2 amd64 2.2.5-0.3+b2 [16.7 kB] Get:276 http://deb.debian.org/debian sid/main amd64 libpaper-utils amd64 2.2.5-0.3+b2 [16.5 kB] Get:277 http://deb.debian.org/debian sid/main amd64 libpicard-java all 3.3.0+dfsg-2 [1778 kB] Get:278 http://deb.debian.org/debian sid/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get:279 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get:280 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.6+ds-1 [11.0 kB] Get:281 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.6+ds-1 [83.3 kB] Get:282 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get:283 http://deb.debian.org/debian sid/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get:284 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get:285 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get:286 http://deb.debian.org/debian sid/main amd64 zip amd64 3.0-14 [233 kB] Get:287 http://deb.debian.org/debian sid/main amd64 unzip amd64 6.0-29 [173 kB] Get:288 http://deb.debian.org/debian sid/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get:289 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.4.3-1+b1 [28.3 MB] Get:290 http://deb.debian.org/debian sid/main amd64 r-cran-littler amd64 0.3.21-1 [107 kB] Get:291 http://deb.debian.org/debian sid/main amd64 littler all 0.3.21-1 [16.9 kB] Get:292 http://deb.debian.org/debian sid/main amd64 mafft amd64 7.505-1 [1078 kB] Get:293 http://deb.debian.org/debian sid/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:294 http://deb.debian.org/debian sid/main amd64 r-cran-iterators all 1.0.14-1 [337 kB] Get:295 http://deb.debian.org/debian sid/main amd64 r-cran-foreach all 1.5.2-1 [122 kB] Get:296 http://deb.debian.org/debian sid/main amd64 r-cran-gam amd64 1.22-5-1 [395 kB] Get:297 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.4-1 [1370 kB] Get:298 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get:299 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.5-1 [1712 kB] Get:300 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:301 http://deb.debian.org/debian sid/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get:302 http://deb.debian.org/debian sid/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:303 http://deb.debian.org/debian sid/main amd64 r-cran-mass amd64 7.3-65-1 [1113 kB] Get:304 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-7-1 [1418 kB] Get:305 http://deb.debian.org/debian sid/main amd64 r-cran-nlme amd64 3.1.168-1 [2329 kB] Get:306 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.7-3-1 [4048 kB] Get:307 http://deb.debian.org/debian sid/main amd64 r-cran-mgcv amd64 1.9-3-1 [3378 kB] Get:308 http://deb.debian.org/debian sid/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get:309 http://deb.debian.org/debian sid/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:310 http://deb.debian.org/debian sid/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get:311 http://deb.debian.org/debian sid/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get:312 http://deb.debian.org/debian sid/main amd64 r-cran-r6 all 2.6.1-1 [106 kB] Get:313 http://deb.debian.org/debian sid/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:314 http://deb.debian.org/debian sid/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:315 http://deb.debian.org/debian sid/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:316 http://deb.debian.org/debian sid/main amd64 r-cran-fansi amd64 1.0.6-1 [629 kB] Get:317 http://deb.debian.org/debian sid/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:318 http://deb.debian.org/debian sid/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:319 http://deb.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:320 http://deb.debian.org/debian sid/main amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] Get:321 http://deb.debian.org/debian sid/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:322 http://deb.debian.org/debian sid/main amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [425 kB] Get:323 http://deb.debian.org/debian sid/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get:324 http://deb.debian.org/debian sid/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get:325 http://deb.debian.org/debian sid/main amd64 r-cran-inline all 0.3.21-1 [132 kB] Get:326 http://deb.debian.org/debian sid/main amd64 seqtk amd64 1.4-2 [34.6 kB] Get:327 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.23.0+ds-1+b1 [3665 kB] Get:328 http://deb.debian.org/debian sid/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get:329 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.14-1 [2080 kB] Get:330 http://deb.debian.org/debian sid/main amd64 r-cran-rcppgsl amd64 0.3.13-1+b1 [203 kB] Get:331 http://deb.debian.org/debian sid/main amd64 mapdamage all 2.2.2+dfsg-1 [42.1 kB] Get:332 http://deb.debian.org/debian sid/main amd64 phylip amd64 1:3.697+dfsg-4 [957 kB] Get:333 http://deb.debian.org/debian sid/main amd64 picard-tools all 3.3.0+dfsg-2 [311 kB] Get:334 http://deb.debian.org/debian sid/main amd64 python3-monotonic all 1.6-3 [5340 B] Get:335 http://deb.debian.org/debian sid/main amd64 python3-humanfriendly all 10.0-6 [85.6 kB] Get:336 http://deb.debian.org/debian sid/main amd64 python3-coloredlogs all 15.0.1-1 [47.4 kB] Get:337 http://deb.debian.org/debian sid/main amd64 python3-configargparse all 1.7-2 [31.4 kB] Get:338 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml.clib amd64 0.2.12+ds-1+b1 [135 kB] Get:339 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml all 0.18.10+ds-1 [147 kB] Get:340 http://deb.debian.org/debian sid/main amd64 python3-setproctitle amd64 1.3.5-1 [18.4 kB] Get:341 http://deb.debian.org/debian sid/main amd64 radiant all 2.8.1+dfsg-2 [181 kB] Get:342 http://deb.debian.org/debian sid/main amd64 raxml amd64 8.2.13+dfsg-2+b1 [1514 kB] Get:343 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.21-1 [667 kB] Preconfiguring packages ... Fetched 325 MB in 2s (145 MB/s) Selecting previously unselected package libsystemd-shared: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 ... 5473 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.5-2_amd64.deb ... Unpacking libsystemd-shared:amd64 (257.5-2) ... Selecting previously unselected package libapparmor1:amd64. Preparing to unpack .../libapparmor1_4.1.0~beta5-6_amd64.deb ... Unpacking libapparmor1:amd64 (4.1.0~beta5-6) ... 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Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' → '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' → '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. [ESC][0;1;39m/usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring.[ESC][0m [ESC][0;1;31m"/home" already exists and is not a directory.[ESC][0m Selecting previously unselected package systemd-sysv. (Reading database ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../6-libpython3.13-stdlib_3.13.3-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.3-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../7-python3.13_3.13.3-1_amd64.deb ... Unpacking python3.13 (3.13.3-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. Unpacking gtk-update-icon-cache (4.18.4+ds-1) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../035-hicolor-icon-theme_0.18-2_all.deb ... Unpacking hicolor-icon-theme (0.18-2) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../036-adwaita-icon-theme_48.0-1_all.deb ... Unpacking adwaita-icon-theme (48.0-1) ... Selecting previously unselected package at-spi2-common. Preparing to unpack .../037-at-spi2-common_2.56.1-2_all.deb ... Unpacking at-spi2-common (2.56.1-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../038-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../039-libunistring5_1.3-2_amd64.deb ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.6+ds-1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../257-libxft2_2.3.6-1+b4_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b4) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../258-libxss1_1%3a1.2.3-1+b3_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../259-libtk8.6_8.6.16-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.16-1) ... Selecting previously unselected package libxt6t64:amd64. Preparing to unpack .../260-libxt6t64_1%3a1.2.1-1.2+b2_amd64.deb ... Unpacking libxt6t64:amd64 (1:1.2.1-1.2+b2) ... 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Setting up libcommons-math3-java (3.6.1-4) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libwayland-egl1:amd64 (1.23.1-3) ... Setting up libicu76:amd64 (76.1-3) ... Setting up libmbedcrypto16:amd64 (3.6.3-1) ... Setting up libpaper2:amd64 (2.2.5-0.3+b2) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjoptsimple-java (5.0.4-7) ... Setting up libfuse3-4:amd64 (3.17.1-1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up dbus-system-bus-common (1.16.2-2) ... Creating group 'messagebus' with GID 997. Creating user 'messagebus' (System Message Bus) with UID 997 and GID 997. Setting up libfido2-1:amd64 (1.15.0-1+b1) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up openssl (3.5.0-1) ... Setting up libdrm-common (2.4.124-2) ... Setting up libsnappy-jni (1.1.10.7-1) ... Setting up libezmorph-java (1.0.6-4) ... Setting up libxcomposite1:amd64 (1:0.4.6-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up bedtools (2.31.1+dfsg-2) ... Setting up libldap2:amd64 (2.6.9+dfsg-2) ... Setting up dbus-bin (1.16.2-2) ... Setting up raxml (8.2.13+dfsg-2+b1) ... Setting up libxkbcommon0:amd64 (1.7.0-2) ... Setting up libwayland-client0:amd64 (1.23.1-3) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libllvm19:amd64 (1:19.1.7-3) ... Setting up libwayland-server0:amd64 (1.23.1-3) ... Setting up libx11-xcb1:amd64 (2:1.8.12-1) ... Setting up libice6:amd64 (2:1.1.1-1) ... 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 libgsl-dev (2.8+dfsg-5) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ... Setting up libopenblas0-pthread:amd64 (0.3.29+ds-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-16) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up libnss3:amd64 (2:3.110-1) ... Setting up dbus-daemon (1.16.2-2) ... Setting up libpaper-utils (2.2.5-0.3+b2) ... Setting up libxom-java (1.3.9-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ... Setting up libnl-route-3-200:amd64 (3.7.0-2) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b2) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libperl5.40:amd64 (5.40.1-2) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... 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) ... Setting up libmbedx509-7:amd64 (3.6.3-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-21+b1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b4) ... Setting up dbus (1.16.2-2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b4) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libxrandr2:amd64 (2:1.5.4-1+b3) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libmbedtls21:amd64 (3.6.3-1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libdrm2:amd64 (2.4.124-2) ... Setting up libopenblas0:amd64 (0.3.29+ds-3) ... Setting up libwayland-cursor0:amd64 (1.23.1-3) ... Setting up libpam-systemd:amd64 (257.5-2) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libharfbuzz0b:amd64 (10.2.0-1+b1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2.3) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-codec-java (1.18.0-1) ... Setting up libsm6:amd64 (2:1.2.6-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.3-1) ... Setting up libavahi-client3:amd64 (0.8-16) ... Setting up libpython3-stdlib:amd64 (3.13.3-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.124-2) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up libopenblas-pthread-dev:amd64 (0.3.29+ds-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up gtk-update-icon-cache (4.18.4+ds-1) ... Setting up libibverbs1:amd64 (56.0-4) ... Setting up fontconfig (2.15.0-2.3) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up libatk1.0-0t64:amd64 (2.56.1-2) ... Setting up openjdk-21-jre-headless:amd64 (21.0.7~8ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libtirpc3t64:amd64 (1.3.6+ds-1) ... Setting up ibverbs-providers:amd64 (56.0-4) ... Setting up python3.13 (3.13.3-1) ... Setting up mafft (7.505-1) ... Setting up libcommons-io-java (2.18.0-1) ... Setting up openssh-client (1:9.9p2-2) ... Setting up libxtst6:amd64 (2:1.2.5-1) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up libxcursor1:amd64 (1:1.2.3-1) ... Setting up libpango-1.0-0:amd64 (1.56.3-1) ... Setting up libdrm-intel1:amd64 (2.4.124-2) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... Setting up libcloudproviders0:amd64 (0.3.6-2) ... Setting up python3 (3.13.3-1) ... Setting up libhwloc-plugins:amd64 (2.12.0-1) ... Setting up libcairo2:amd64 (1.18.4-1+b1) ... Setting up libcolord2:amd64 (1.4.7-3) ... Setting up bowtie2 (2.5.4-1+b2) ... Setting up python3-monotonic (1.6-3) ... Setting up libdconf1:amd64 (0.40.0-5) ... Setting up dbus-user-session (1.16.2-2) ... Setting up libopenblas-dev:amd64 (0.3.29+ds-3) ... Setting up python3-humanfriendly (10.0-6) ... Setting up adwaita-icon-theme (48.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libatspi2.0-0t64:amd64 (2.56.1-2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up python3-setproctitle:amd64 (1.3.5-1) ... Setting up libpmix2t64:amd64 (5.0.7-1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up librdmacm1t64:amd64 (56.0-4) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libcairo-gobject2:amd64 (1.18.4-1+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.56.3-1) ... Setting up python3-coloredlogs (15.0.1-1) ... Setting up libcups2t64:amd64 (2.4.10-2+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libhsakmt1:amd64 (6.2.4+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.56.3-1) ... Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7.1) ... Setting up libatk-bridge2.0-0t64:amd64 (2.56.1-2) ... Setting up python3-configargparse (1.7-2) ... Setting up libfabric1:amd64 (2.0.0-4) ... Setting up mesa-libgallium:amd64 (25.0.3-1) ... Setting up libngs-jni:amd64 (3.0.9+dfsg-7.1) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcurl4t64:amd64 (8.13.0-1) ... Setting up libgbm1:amd64 (25.0.3-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libgl1-mesa-dri:amd64 (25.0.3-1) ... Setting up python3-ruamel.yaml.clib (0.2.12+ds-1+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.13.0-1) ... Setting up dconf-service (0.40.0-5) ... Setting up r-base-core (4.4.3-1+b1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-7-1) ... Setting up r-cran-nlme (3.1.168-1) ... Setting up r-cran-farver (2.1.2-1) ... Setting up python3-ruamel.yaml (0.18.10+ds-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-3) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up libngs-java:amd64 (3.0.9+dfsg-7.1) ... Setting up r-cran-r6 (2.6.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up libbarclay-java (5.0.0+dfsg-1) ... Setting up r-cran-littler (0.3.21-1) ... Setting up r-cran-rcpp (1.0.14-1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-cran-inline (0.3.21-1) ... Setting up r-cran-rlang (1.1.5-1) ... Setting up libglx-mesa0:amd64 (25.0.3-1) ... Setting up python3-pysam (0.23.0+ds-1+b1) ... Setting up littler (0.3.21-1) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up r-cran-iterators (1.0.14-1) ... Setting up bcftools (1.21-1) ... Setting up r-cran-foreach (1.5.2-1) ... Setting up r-cran-fansi (1.0.6-1) ... Setting up r-cran-mass (7.3-65-1) ... Setting up r-cran-glue (1.8.0-1) ... Setting up r-cran-gam (1.22-5-1) ... Setting up r-cran-cli (3.6.4-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up samtools (1.21-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up libamdhip64-5 (5.7.1-5+b1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up r-cran-matrix (1.7-3-1) ... Setting up r-cran-mgcv (1.9-3-1) ... Setting up r-cran-rcppgsl (0.3.13-1+b1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up libgtk-3-common (3.24.49-3) ... Setting up r-cran-pillar (1.10.1+dfsg-1) ... Setting up libucx0:amd64 (1.18.1+ds-2+b1) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-3) ... Setting up libgtk-3-0t64:amd64 (3.24.49-3) ... Setting up r-cran-scales (1.3.0-1) ... Setting up libopenmpi40:amd64 (5.0.7-1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up mapdamage (2.2.2+dfsg-1) ... Setting up openmpi-bin (5.0.7-1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up mpi-default-bin (1.18) ... Setting up examl (3.0.22-6+b3) ... Processing triggers for libc-bin (2.41-6) ... Processing triggers for systemd (257.5-2) ... Processing triggers for procps (2:4.0.4-7) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureSign_Root_CA12.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up junit4 (4.13.2-5) ... Setting up default-jre-headless (2:1.21-76) ... Setting up openjdk-21-jre:amd64 (21.0.7~8ea-1) ... Setting up libjson-java (3.1.0+dfsg-2) ... Setting up libhtsjdk-java (4.1.3+dfsg-2) ... Setting up libgkl-java (0.8.11+dfsg-2) ... Setting up default-jre (2:1.21-76) ... Setting up libpicard-java (3.3.0+dfsg-2) ... Setting up picard-tools (3.3.0+dfsg-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. Processing triggers for ca-certificates-java (20240118) ... done. 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m26.2s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok 0m26.2s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpuhzqy3e0/./tmp/piuparts-depends-dummy.deb 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m26.3s DUMP: piuparts-depends-dummy install ok installed 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m26.3s DUMP: (Reading database ... 24110 files and directories currently installed.) Removing piuparts-depends-dummy (0.invalid.0) ... 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', 'clean'] 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', 'clean'] 0m26.3s DEBUG: Recording chroot state 0m26.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0'] 0m27.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0'] 0m28.6s ERROR: WARN: Broken symlinks: /etc/vconsole.conf -> default/keyboard /etc/default/locale -> ../locale.conf /usr/lib/jvm/java-21-openjdk-amd64/lib/libatk-wrapper.so -> ../../../x86_64-linux-gnu/jni/libatk-wrapper.so 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'policy'] 0m29.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'policy'] 0m29.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'policy', 'paleomix'] 0m29.1s DUMP: paleomix: Installed: (none) Candidate: 1.3.8-2 Version table: 1.3.8-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'policy', 'paleomix'] 0m29.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', '-y', 'install', 'paleomix=1.3.8-2'] 0m29.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: paleomix 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 984 kB of archives. After this operation, 2054 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 paleomix amd64 1.3.8-2 [984 kB] Fetched 984 kB in 0s (6001 kB/s) Selecting previously unselected package paleomix. (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 ... 24110 files and directories currently installed.) Preparing to unpack .../paleomix_1.3.8-2_amd64.deb ... Unpacking paleomix (1.3.8-2) ... Setting up paleomix (1.3.8-2) ... 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', '-y', 'install', 'paleomix=1.3.8-2'] 0m29.9s INFO: Running scripts post_install 0m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_install_exceptions'] 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_install_exceptions'] 0m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'systemd-tmpfiles', '--cat-config'] 0m29.9s DUMP: # /usr/lib/tmpfiles.d/20-systemd-shell-extra.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. L$ /etc/profile.d/70-systemd-shell-extra.sh - - - - /usr/lib/systemd/profile.d/70-systemd-shell-extra.sh # /usr/lib/tmpfiles.d/20-systemd-ssh-generator.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. L$ /etc/ssh/ssh_config.d/20-systemd-ssh-proxy.conf - - - - /usr/lib/systemd/ssh_config.d/20-systemd-ssh-proxy.conf d /run/sshd 0755 # /usr/lib/tmpfiles.d/20-systemd-stub.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # Copy systemd-stub provided metadata such as PCR signature and public key file # from initrd into /run/, so that it will survive the initrd stage C /run/systemd/stub/profile 0444 root root - /.extra/profile C /run/systemd/stub/os-release 0444 root root - /.extra/os-release C /run/systemd/tpm2-pcr-signature.json 0444 root root - /.extra/tpm2-pcr-signature.json C /run/systemd/tpm2-pcr-public-key.pem 0444 root root - /.extra/tpm2-pcr-public-key.pem # /usr/lib/tmpfiles.d/credstore.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. d /etc/credstore 0700 root root d /etc/credstore.encrypted 0700 root root z /run/credstore 0700 root root z /run/credstore.encrypted 0700 root root # /usr/lib/tmpfiles.d/dbus.conf # Fields: type; path; mode; uid; gid; age; argument (symlink target) # Make ${localstatedir}/lib/dbus (required for systemd < 237) # Adjust mode and ownership if it already exists. d /var/lib/dbus 0755 - - - # Make ${localstatedir}/lib/dbus/machine-id a symlink to /etc/machine-id # if it does not already exist L /var/lib/dbus/machine-id - - - - /etc/machine-id # /usr/lib/tmpfiles.d/debian.conf # This file is part of the debianisation of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details # Type Path Mode UID GID Age Argument L /run/shm - - - - /dev/shm d /run/sendsigs.omit.d 0755 root root - d /run/lock 1777 root root - - L+ /etc/mtab - - - - ../proc/self/mounts L+ /etc/default/locale - - - - ../locale.conf L+ /etc/vconsole.conf - - - - default/keyboard # /usr/lib/tmpfiles.d/home.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. Q /home 0755 - - - q /srv 0755 - - - # /usr/lib/tmpfiles.d/journal-nocow.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # Set the NOCOW attribute for directories of journal files. This flag # is inherited by their new files and sub-directories. Matters only # for btrfs filesystems. # # WARNING: Enabling the NOCOW attribute improves journal performance # substantially, but also disables the btrfs checksum logic. In # btrfs RAID filesystems the checksums are needed for rebuilding # corrupted files. Without checksums such rebuilds are not # possible. # # In a single-disk filesystem (or a filesystem without redundancy) # enabling the NOCOW attribute for journal files is safe, because # they have their own checksums and a rebuilding wouldn't be possible # in any case. h /var/log/journal - - - - +C h /var/log/journal/%m - - - - +C h /var/log/journal/remote - - - - +C # /usr/lib/tmpfiles.d/legacy.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # The functionality provided by these files and directories has been replaced # by newer interfaces. Their use is discouraged on legacy-free systems. This # configuration is provided to maintain backward compatibility. d /run/lock 0755 root root - L /var/lock - - - - ../run/lock L$ /var/log/README - - - - ../../usr/share/doc/systemd/README.logs # /run/lock/subsys is used for serializing SysV service execution, and # hence without use on SysV-less systems. d /run/lock/subsys 0755 root root - # /forcefsck, /fastboot and /forcequotacheck are deprecated in favor of the # kernel command line options 'fsck.mode=force', 'fsck.mode=skip' and # 'quotacheck.mode=force' r! /forcefsck r! /fastboot r! /forcequotacheck # /usr/lib/tmpfiles.d/libselinux1.conf # See tmpfiles.d(5) for details # Type Path Mode UID GID Age Argument d /run/setrans 0755 root root - - # /usr/lib/tmpfiles.d/openssh-client.conf x /tmp/ssh-* # /usr/lib/tmpfiles.d/passwd.conf # If a password operation is in progress and we lose power, stale lockfiles # can be left behind. Clear them on boot. r! /etc/gshadow.lock r! /etc/shadow.lock r! /etc/passwd.lock r! /etc/group.lock r! /etc/subuid.lock r! /etc/subgid.lock # /usr/lib/tmpfiles.d/provision.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # Provision additional login messages from credentials, if they are set. Note # that these lines are NOPs if the credentials are not set or if the files # already exist. f^ /etc/motd.d/50-provision.conf - - - - login.motd f^ /etc/issue.d/50-provision.conf - - - - login.issue # Provision a /etc/hosts file from credentials. f^ /etc/hosts - - - - network.hosts # Provision SSH key for root d- /root :0700 root :root - d- /root/.ssh :0700 root :root - f^ /root/.ssh/authorized_keys :0600 root :root - ssh.authorized_keys.root # /usr/lib/tmpfiles.d/systemd-network.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. d$ /run/systemd/netif 0755 systemd-network systemd-network - d$ /run/systemd/netif/links 0755 systemd-network systemd-network - d$ /run/systemd/netif/leases 0755 systemd-network systemd-network - d$ /var/lib/systemd/network 0755 systemd-network systemd-network - # /usr/lib/tmpfiles.d/systemd-nologin.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5), systemd-user-sessions.service(8) and pam_nologin(8). f+! /run/nologin 0644 - - - "System is booting up. Unprivileged users are not permitted to log in yet. Please come back later. For technical details, see pam_nologin(8)." # /usr/lib/tmpfiles.d/systemd-pstore.conf # SPDX-License-Identifier: LGPL-2.1-or-later # # The systemd-pstore.service(1) archives the contents of /sys/fs/pstore # upon boot so that there is room for a subsequent dump. This service # is enabled with: # systemctl enable systemd-pstore # # With the service enabled, the kernel still needs to be configured # to write data into the pstore. The kernel has two parameters, # crash_kexec_post_notifiers and printk.always_kmsg_dump, that # control writes into pstore. # # The crash_kexec_post_notifiers parameter enables the kernel to write # dmesg (including stack trace) into pstore upon a panic even if kdump # is loaded, only needed if you want to use pstore with kdump. Without # this parameter, kdump could block writing to pstore for stability # reason. Note this increases the risk of kdump failure even if pstore # is not available. # # The printk.always_kmsg_dump parameter enables the kernel to write dmesg # upon a normal shutdown (shutdown, reboot, halt). # # To configure the kernel parameters, uncomment the appropriate # lines below. The value written is either 'Y' to enable the # kernel parameter, or 'N' to disable the kernel parameter. # # After making a change to this file, do: # systemd-tmpfiles --create path/to/tmpfiles.d/systemd-pstore.conf # # These changes are automatically applied on future re-boots. d /var/lib/systemd/pstore 0755 root root 14d #w- /sys/module/printk/parameters/always_kmsg_dump - - - - Y #w- /sys/module/kernel/parameters/crash_kexec_post_notifiers - - - - Y # /usr/lib/tmpfiles.d/systemd-tmp.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # Exclude namespace mountpoints created with PrivateTmp=yes x /tmp/systemd-private-%b-* X /tmp/systemd-private-%b-*/tmp x /var/tmp/systemd-private-%b-* X /var/tmp/systemd-private-%b-*/tmp # Remove top-level private temporary directories on each boot R! /tmp/systemd-private-* R! /var/tmp/systemd-private-* # Handle lost systemd-coredump temp files. They could be lost on old filesystems, # for example, after hard reboot. x /var/lib/systemd/coredump/.#core*.%b* r! /var/lib/systemd/coredump/.#* # /usr/lib/tmpfiles.d/systemd.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. d /run/user 0755 root root - d /run/systemd/ask-password 0755 root root - d$ /run/systemd/seats 0755 root root - d$ /run/systemd/sessions 0755 root root - d$ /run/systemd/users 0755 root root - d /run/systemd/machines 0755 root root - d$ /run/systemd/shutdown 0755 root root - d /run/log 0755 root root - z /run/log/journal 2755 root systemd-journal - - Z /run/log/journal/%m ~2750 root systemd-journal - - a+ /run/log/journal - - - - d:group::r-x,d:group:adm:r-x,group::r-x,group:adm:r-x A+ /run/log/journal/%m - - - - d:group:adm:r-x,group:adm:r-X z /var/log/journal 2755 root systemd-journal - - z /var/log/journal/%m 2755 root systemd-journal - - z /var/log/journal/%m/system.journal 0640 root systemd-journal - - a+ /var/log/journal - - - - d:group::r-x,d:group:adm:r-x,group::r-x,group:adm:r-x a+ /var/log/journal/%m - - - - d:group:adm:r-x,group:adm:r-x a+ /var/log/journal/%m/system.journal - - - - group:adm:r-- d /var/lib/systemd 0755 root root - d /var/lib/systemd/coredump 0755 root root 2w # Files and directories in /var/lib/systemd/ephemeral-trees are locked by pid 1 to prevent tmpfiles from # removing them, and tmpfiles is told to clean up anything in /var/lib/systemd/ephemeral-trees that isn't # locked unconditionally. d /var/lib/systemd/ephemeral-trees 0755 root root 0 d /var/lib/private 0700 root root - d /var/log/private 0700 root root - d /var/cache/private 0700 root root - # /usr/lib/tmpfiles.d/tmp.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # Clear tmp directories separately, to make them easier to override q /tmp 1777 root root 10d q /var/tmp 1777 root root 30d # /usr/lib/tmpfiles.d/var.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. q /var 0755 - - - L /var/run - - - - ../run d /var/log 0755 - - - d /var/cache 0755 - - - d /var/lib 0755 - - - d /var/spool 0755 - - - # /usr/lib/tmpfiles.d/x11.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # Make sure these are created by default so that nobody else can # or empty them at startup D! /tmp/.X11-unix 1777 root root 10d D! /tmp/.ICE-unix 1777 root root 10d D! /tmp/.XIM-unix 1777 root root 10d D! /tmp/.font-unix 1777 root root 10d # Unlink the X11 lock files r! /tmp/.X[0-9]*-lock 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'systemd-tmpfiles', '--cat-config'] 0m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', 'remove', 'paleomix'] 0m30.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: adapterremoval adwaita-icon-theme at-spi2-common bcftools bedtools bowtie2 bwa ca-certificates-java dconf-gsettings-backend dconf-service default-jre default-jre-headless examl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme ibverbs-providers java-common junit4 libamd-comgr2 libamdhip64-5 libapache-pom-java libasound2-data libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libbrotli1 libcairo-gobject2 libcairo2 libcloudproviders0 libcolord2 libcom-err2 libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java libcommons-collections4-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm2 libedit2 libepoxy0 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libezmorph-java libfabric1 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libfuse3-4 libgatk-native-bindings-java libgbm1 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgkl-java libgl1 libgl1-mesa-dri libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgnutls30t64 libgomp1 libgoogle-gson-java libgraphite2-3 libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libhamcrest-java libharfbuzz0b libhsa-runtime64-1 libhsakmt1 libhts3t64 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libice6 libicu76 libjaxen-java libjbig0 libjoptsimple-java libjpeg62-turbo libjson-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 liblightcouch-java libllvm17t64 libllvm19 liblog4j2-java libmbedcrypto16 libmbedtls21 libmbedx509-7 libmongodb-java libmunge2 libncbi-ngs3 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenmpi40 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0 libpcsclite1 libpicard-java libpixman-1-0 libpmix2t64 libpng16-16t64 libpsl5t64 libpsm2-2 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librdmacm1t64 libreadline8t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1t64 libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libucx0 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxnvctrl0 libxom-java libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libz3-4 littler mafft mapdamage media-types mesa-libgallium mpi-default-bin ncbi-vdb-data ocl-icd-libopencl1 openjdk-21-jre openjdk-21-jre-headless openmpi-bin openmpi-common openssh-client phylip picard-tools python3 python3-coloredlogs python3-configargparse python3-humanfriendly python3-minimal python3-monotonic python3-pysam python3-ruamel.yaml python3-ruamel.yaml.clib python3-setproctitle python3.13 python3.13-minimal r-base-core r-cran-cli r-cran-codetools r-cran-colorspace r-cran-fansi r-cran-farver r-cran-foreach r-cran-gam r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-inline r-cran-isoband r-cran-iterators r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppgsl r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr radiant raxml readline-common samtools seqtk shared-mime-info unzip x11-common xdg-utils xkb-data zip Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: paleomix 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 2054 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 ... 24355 files and directories currently installed.) Removing paleomix (1.3.8-2) ... 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', 'remove', 'paleomix'] 0m30.4s INFO: Reinstalling after remove 0m30.4s INFO: Running scripts pre_install 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_database-server'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_database-server'] 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_exceptions'] 0m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_exceptions'] 0m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_extras'] 0m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_extras'] 0m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_foreign_architecture'] 0m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_foreign_architecture'] 0m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'policy'] 0m30.5s 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: 0m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'policy'] 0m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'policy', 'paleomix'] 0m30.5s DUMP: paleomix: Installed: (none) Candidate: 1.3.8-2 Version table: 1.3.8-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'policy', 'paleomix'] 0m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', '-y', 'install', 'paleomix=1.3.8-2'] 0m31.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: paleomix 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/984 kB of archives. After this operation, 2054 kB of additional disk space will be used. Selecting previously unselected package paleomix. (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 ... 24110 files and directories currently installed.) Preparing to unpack .../paleomix_1.3.8-2_amd64.deb ... Unpacking paleomix (1.3.8-2) ... Setting up paleomix (1.3.8-2) ... 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', '-y', 'install', 'paleomix=1.3.8-2'] 0m31.2s INFO: Running scripts post_install 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_install_exceptions'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_install_exceptions'] 0m31.2s INFO: Running scripts pre_install 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_database-server'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_database-server'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_exceptions'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_exceptions'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_extras'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_extras'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'policy'] 0m31.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'policy'] 0m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'policy', 'paleomix'] 0m31.3s DUMP: paleomix: Installed: 1.3.8-2 Candidate: 1.3.8-2 Version table: *** 1.3.8-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-cache', 'policy', 'paleomix'] 0m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', '-y', 'install', '--reinstall', 'paleomix=1.3.8-2'] 0m32.0s 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/984 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 ... 24355 files and directories currently installed.) Preparing to unpack .../paleomix_1.3.8-2_amd64.deb ... Unpacking paleomix (1.3.8-2) over (1.3.8-2) ... Setting up paleomix (1.3.8-2) ... 0m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', '-y', 'install', '--reinstall', 'paleomix=1.3.8-2'] 0m32.0s INFO: Running scripts post_install 0m32.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_install_exceptions'] 0m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_install_exceptions'] 0m32.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0'] 0m32.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0'] 0m32.9s INFO: IGNORED broken symlink: /etc/vconsole.conf (flag L+ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 0m32.9s INFO: IGNORED broken symlink: /etc/default/locale (flag L+ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 0m33.9s ERROR: WARN: Broken symlinks: /usr/lib/jvm/java-21-openjdk-amd64/lib/libatk-wrapper.so -> ../../../x86_64-linux-gnu/jni/libatk-wrapper.so (openjdk-21-jre:amd64) 0m34.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', '-ac', '--ignore-obsolete'] 0m37.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', '-ac', '--ignore-obsolete'] 0m37.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m37.6s DUMP: 0.15.6 0m37.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m37.6s INFO: Running adequate version 0.15.6 now. 0m37.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'paleomix'] 0m37.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'paleomix'] 0m37.7s INFO: Running scripts pre_remove 0m37.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m37.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m37.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m37.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m37.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m41.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m41.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m41.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m41.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m41.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m41.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_exceptions'] 0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_exceptions'] 0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_preseed_cleanup'] 0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/pre_remove_preseed_cleanup'] 0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m41.2s DUMP: install ok installed adapterremoval adapterremoval 2.3.4-1 install ok installed adduser adduser 3.150 install ok installed adwaita-icon-theme adwaita-icon-theme 48.0-1 install ok installed apt apt 3.0.0 install ok installed at-spi2-common at-spi2-common 2.56.1-2 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 bcftools bcftools 1.21-1 install ok installed bedtools bedtools 2.31.1+dfsg-2 install ok installed bowtie2 bowtie2 2.5.4-1+b2 install ok installed bsdutils bsdutils 1:2.41-3 install ok installed bwa bwa 0.7.18-1 install ok installed ca-certificates ca-certificates 20241223 install ok installed ca-certificates-java ca-certificates-java 20240118 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 dbus dbus 1.16.2-2 install ok installed dbus-bin dbus-bin 1.16.2-2 install ok installed dbus-daemon dbus-daemon 1.16.2-2 install ok installed dbus-session-bus-common dbus-session-bus-common 1.16.2-2 install ok installed dbus-system-bus-common dbus-system-bus-common 1.16.2-2 install ok installed dbus-user-session dbus-user-session 1.16.2-2 install ok installed dconf-gsettings-backend:amd64 dconf-gsettings-backend 0.40.0-5 install ok installed dconf-service dconf-service 0.40.0-5 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 default-jre default-jre 2:1.21-76 install ok installed default-jre-headless default-jre-headless 2:1.21-76 install ok installed diffutils diffutils 1:3.10-3 install ok installed dpkg dpkg 1.22.18 install ok installed examl examl 3.0.22-6+b3 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig fontconfig 2.15.0-2.3 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 gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gtk-update-icon-cache gtk-update-icon-cache 4.18.4+ds-1 install ok installed gzip gzip 1.13-1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.18-2 install ok installed hostname hostname 3.25 install ok installed ibverbs-providers:amd64 ibverbs-providers 56.0-4 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed java-common java-common 0.76 install ok installed junit4 junit4 4.13.2-5 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libamd-comgr2:amd64 libamd-comgr2 6.0+git20231212.4510c28+dfsg-3+b2 install ok installed libamdhip64-5 libamdhip64-5 5.7.1-5+b1 install ok installed libapache-pom-java libapache-pom-java 33-2 install ok installed libapparmor1:amd64 libapparmor1 4.1.0~beta5-6 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0 install ok installed libasound2-data libasound2-data 1.2.13-1 install ok installed libasound2t64:amd64 libasound2t64 1.2.13-1+b1 install ok installed libatk-bridge2.0-0t64:amd64 libatk-bridge2.0-0t64 2.56.1-2 install ok installed libatk1.0-0t64:amd64 libatk1.0-0t64 2.56.1-2 install ok installed libatomic1:amd64 libatomic1 14.2.0-19 install ok installed libatspi2.0-0t64:amd64 libatspi2.0-0t64 2.56.1-2 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 libavahi-client3:amd64 libavahi-client3 0.8-16 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-16 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-16 install ok installed libbarclay-java libbarclay-java 5.0.0+dfsg-1 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 libcairo-gobject2:amd64 libcairo-gobject2 1.18.4-1+b1 install ok installed libcairo2:amd64 libcairo2 1.18.4-1+b1 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 libcbor0.10:amd64 libcbor0.10 0.10.2-2 install ok installed libcloudproviders0:amd64 libcloudproviders0 0.3.6-2 install ok installed libcolord2:amd64 libcolord2 1.4.7-3 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1+b1 install ok installed libcommons-beanutils-java libcommons-beanutils-java 1.9.4-2 install ok installed libcommons-codec-java libcommons-codec-java 1.18.0-1 install ok installed libcommons-collections3-java libcommons-collections3-java 3.2.2-3 install ok installed libcommons-collections4-java libcommons-collections4-java 4.4-2 install ok installed libcommons-compress-java libcommons-compress-java 1.27.1-2 install ok installed libcommons-io-java libcommons-io-java 2.18.0-1 install ok installed libcommons-jexl2-java libcommons-jexl2-java 2.1.1-6 install ok installed libcommons-lang3-java libcommons-lang3-java 3.17.0-1 install ok installed libcommons-logging-java libcommons-logging-java 1.3.0-1 install ok installed libcommons-math3-java libcommons-math3-java 3.6.1-4 install ok installed libcommons-parent-java libcommons-parent-java 56-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libcups2t64:amd64 libcups2t64 2.4.10-2+b1 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.13.0-1 install ok installed libcurl4t64:amd64 libcurl4t64 8.13.0-1 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3+b1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.16.2-2 install ok installed libdconf1:amd64 libdconf1 0.40.0-5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278 install ok installed libdeflate0:amd64 libdeflate0 1.23-1+b1 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.124-2 install ok installed libdrm-common libdrm-common 2.4.124-2 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.124-2 install ok installed libdrm2:amd64 libdrm2 2.4.124-2 install ok installed libedit2:amd64 libedit2 3.1-20250104-1 install ok installed libelf1t64:amd64 libelf1t64 0.192-4 install ok installed libepoxy0:amd64 libepoxy0 1.5.10-2 install ok installed libevent-core-2.1-7t64:amd64 libevent-core-2.1-7t64 2.1.12-stable-10+b1 install ok installed libevent-pthreads-2.1-7t64:amd64 libevent-pthreads-2.1-7t64 2.1.12-stable-10+b1 install ok installed libexpat1:amd64 libexpat1 2.7.1-1 install ok installed libezmorph-java libezmorph-java 1.0.6-4 install ok installed libfabric1:amd64 libfabric1 2.0.0-4 install ok installed libffi8:amd64 libffi8 3.4.7-1 install ok installed libfido2-1:amd64 libfido2-1 1.15.0-1+b1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-2.3 install ok installed libfreemarker-java libfreemarker-java 2.3.32-2.1 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1 install ok installed libfuse3-4:amd64 libfuse3-4 3.17.1-1 install ok installed libgatk-native-bindings-java libgatk-native-bindings-java 1.0.0+dfsg-2 install ok installed libgbm1:amd64 libgbm1 25.0.3-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgdk-pixbuf-2.0-0:amd64 libgdk-pixbuf-2.0-0 2.42.12+dfsg-2 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.42.12+dfsg-2 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-19 install ok installed libgif7:amd64 libgif7 5.2.2-1+b1 install ok installed libgkl-java libgkl-java 0.8.11+dfsg-2 install ok installed libgl1:amd64 libgl1 1.7.0-1+b2 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 25.0.3-1 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.84.1-1 install ok installed libglvnd0:amd64 libglvnd0 1.7.0-1+b2 install ok installed libglx-mesa0:amd64 libglx-mesa0 25.0.3-1 install ok installed libglx0:amd64 libglx0 1.7.0-1+b2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.9-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-19 install ok installed libgoogle-gson-java libgoogle-gson-java 2.10.1-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgsl-dev libgsl-dev 2.8+dfsg-5 install ok installed libgsl28:amd64 libgsl28 2.8+dfsg-5 install ok installed libgslcblas0:amd64 libgslcblas0 2.8+dfsg-5 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-5 install ok installed libgtk-3-0t64:amd64 libgtk-3-0t64 3.24.49-3 install ok installed libgtk-3-common libgtk-3-common 3.24.49-3 install ok installed libhamcrest-java libhamcrest-java 2.2-2 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.2.0-1+b1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed libhsa-runtime64-1:amd64 libhsa-runtime64-1 6.1.2-3 install ok installed libhsakmt1:amd64 libhsakmt1 6.2.4+ds-1 install ok installed libhts3t64:amd64 libhts3t64 1.21+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-2 install ok installed libhtsjdk-java libhtsjdk-java 4.1.3+dfsg-2 install ok installed libhttpclient-java libhttpclient-java 4.5.14-1 install ok installed libhttpcore-java libhttpcore-java 4.4.16-1 install ok installed libhwloc-plugins:amd64 libhwloc-plugins 2.12.0-1 install ok installed libhwloc15:amd64 libhwloc15 2.12.0-1 install ok installed libibmad5:amd64 libibmad5 56.0-4 install ok installed libibumad3:amd64 libibumad3 56.0-4 install ok installed libibverbs1:amd64 libibverbs1 56.0-4 install ok installed libice6:amd64 libice6 2:1.1.1-1 install ok installed libicu76:amd64 libicu76 76.1-3 install ok installed libidn2-0:amd64 libidn2-0 2.3.8-2 install ok installed libjaxen-java libjaxen-java 1.1.6-5 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjoptsimple-java libjoptsimple-java 5.0.4-7 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3.1 install ok installed libjson-java libjson-java 3.1.0+dfsg-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-5 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-5 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 libldap2:amd64 libldap2 2.6.9+dfsg-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed liblightcouch-java liblightcouch-java 0.2.0-1 install ok installed libllvm17t64:amd64 libllvm17t64 1:17.0.6-21+b1 install ok installed libllvm19:amd64 libllvm19 1:19.1.7-3 install ok installed liblog4j2-java liblog4j2-java 2.19.0-2 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 libmbedcrypto16:amd64 libmbedcrypto16 3.6.3-1 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.3-1 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.3-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmongodb-java libmongodb-java 3.6.3-2 install ok installed libmount1:amd64 libmount1 2.41-3 install ok installed libmunge2:amd64 libmunge2 0.5.16-1 install ok installed libncbi-ngs3:amd64 libncbi-ngs3 3.0.9+dfsg-7.1 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.0.9+dfsg-2 install ok installed libncurses6:amd64 libncurses6 6.5+20250216-2 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.8.0-1 install ok installed libngs-java:amd64 libngs-java 3.0.9+dfsg-7.1 install ok installed libngs-jni:amd64 libngs-jni 3.0.9+dfsg-7.1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.11.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.11.0-1 install ok installed libnl-3-200:amd64 libnl-3-200 3.7.0-2 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.7.0-2 install ok installed libnspr4:amd64 libnspr4 2:4.36-1 install ok installed libnss3:amd64 libnss3 2:3.110-1 install ok installed libnuma1:amd64 libnuma1 2.0.18-1+b1 install ok installed libopenblas-dev:amd64 libopenblas-dev 0.3.29+ds-3 install ok installed libopenblas-pthread-dev:amd64 libopenblas-pthread-dev 0.3.29+ds-3 install ok installed libopenblas0:amd64 libopenblas0 0.3.29+ds-3 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.29+ds-3 install ok installed libopenmpi40:amd64 libopenmpi40 5.0.7-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-3 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 libpam-systemd:amd64 libpam-systemd 257.5-2 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.56.3-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.56.3-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.56.3-1 install ok installed libpaper-utils libpaper-utils 2.2.5-0.3+b2 install ok installed libpaper2:amd64 libpaper2 2.2.5-0.3+b2 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3+b3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libpcsclite1:amd64 libpcsclite1 2.3.3-1 install ok installed libperl5.40:amd64 libperl5.40 5.40.1-2 install ok installed libpicard-java libpicard-java 3.3.0+dfsg-2 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpmix2t64:amd64 libpmix2t64 5.0.7-1 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 libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpsm2-2 libpsm2-2 11.2.185-2.1 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 librdmacm1t64:amd64 librdmacm1t64 56.0-4 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed librhino-java librhino-java 1.7.15-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-9 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-9 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 libsensors-config libsensors-config 1:3.6.0-10 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-10+b1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.5.0-0.1 install ok installed libslf4j-java libslf4j-java 1.7.32-1 install ok installed libsm6:amd64 libsm6 2:1.2.6-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-3 install ok installed libsnappy-java libsnappy-java 1.1.10.7-1 install ok installed libsnappy-jni libsnappy-jni 1.1.10.7-1 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.2.2-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-2 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 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 libsystemd-shared:amd64 libsystemd-shared 257.5-2 install ok installed libsystemd0:amd64 libsystemd0 257.5-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.20.0-2 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 libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2+b1 install ok installed libtiff6:amd64 libtiff6 4.7.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libtirpc-common libtirpc-common 1.3.6+ds-1 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.6+ds-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.16-1 install ok installed libucx0:amd64 libucx0 1.18.1+ds-2+b1 install ok installed libudev1:amd64 libudev1 257.5-2 install ok installed libunistring5:amd64 libunistring5 1.3-2 install ok installed libuuid1:amd64 libuuid1 2.41-3 install ok installed libvulkan1:amd64 libvulkan1 1.4.309.0-1 install ok installed libwayland-client0:amd64 libwayland-client0 1.23.1-3 install ok installed libwayland-cursor0:amd64 libwayland-cursor0 1.23.1-3 install ok installed libwayland-egl1:amd64 libwayland-egl1 1.23.1-3 install ok installed libwayland-server0:amd64 libwayland-server0 1.23.1-3 install ok installed libwebp7:amd64 libwebp7 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 libx11-xcb1:amd64 libx11-xcb1 2:1.8.12-1 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.17.0-2+b1 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.17.0-2+b1 install ok installed libxcb-present0:amd64 libxcb-present0 1.17.0-2+b1 install ok installed libxcb-randr0:amd64 libxcb-randr0 1.17.0-2+b1 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 libxcb-sync1:amd64 libxcb-sync1 1.17.0-2+b1 install ok installed libxcb-xfixes0:amd64 libxcb-xfixes0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxcomposite1:amd64 libxcomposite1 1:0.4.6-1 install ok installed libxcursor1:amd64 libxcursor1 1:1.2.3-1 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.6-1+b2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxerces2-java libxerces2-java 2.12.2-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3 install ok installed libxfixes3:amd64 libxfixes3 1:6.0.0-2+b4 install ok installed libxft2:amd64 libxft2 2.3.6-1+b4 install ok installed libxi6:amd64 libxi6 2:1.8.2-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3+b4 install ok installed libxkbcommon0:amd64 libxkbcommon0 1.7.0-2 install ok installed libxml-commons-external-java libxml-commons-external-java 1.4.01-6 install ok installed libxml-commons-resolver1.1-java libxml-commons-resolver1.1-java 1.2-11 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.4 install ok installed libxnvctrl0:amd64 libxnvctrl0 535.171.04-1+b2 install ok installed libxom-java libxom-java 1.3.9-1 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.4-1+b3 install ok installed libxrender1:amd64 libxrender1 1:0.9.12-1 install ok installed libxshmfence1:amd64 libxshmfence1 1.3.3-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b3 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2+b2 install ok installed libxtst6:amd64 libxtst6 2:1.2.5-1 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b4 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libz3-4:amd64 libz3-4 4.13.3-1 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed littler littler 0.3.21-1 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 mapdamage mapdamage 2.2.2+dfsg-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed media-types media-types 13.0.0 install ok installed mesa-libgallium:amd64 mesa-libgallium 25.0.3-1 install ok installed mount mount 2.41-3 install ok installed mpi-default-bin mpi-default-bin 1.18 install ok installed ncbi-vdb-data ncbi-vdb-data 3.0.9+dfsg-2 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 ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.3.3-1 install ok installed openjdk-21-jre:amd64 openjdk-21-jre 21.0.7~8ea-1 install ok installed openjdk-21-jre-headless:amd64 openjdk-21-jre-headless 21.0.7~8ea-1 install ok installed openmpi-bin openmpi-bin 5.0.7-1 install ok installed openmpi-common openmpi-common 5.0.7-1 install ok installed openssh-client openssh-client 1:9.9p2-2 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 paleomix paleomix 1.3.8-2 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 phylip phylip 1:3.697+dfsg-4 install ok installed picard-tools picard-tools 3.3.0+dfsg-2 install ok installed procps procps 2:4.0.4-7 install ok installed python3 python3 3.13.3-1 install ok installed python3-coloredlogs python3-coloredlogs 15.0.1-1 install ok installed python3-configargparse python3-configargparse 1.7-2 install ok installed python3-humanfriendly python3-humanfriendly 10.0-6 install ok installed python3-minimal python3-minimal 3.13.3-1 install ok installed python3-monotonic python3-monotonic 1.6-3 install ok installed python3-pysam python3-pysam 0.23.0+ds-1+b1 install ok installed python3-ruamel.yaml python3-ruamel.yaml 0.18.10+ds-1 install ok installed python3-ruamel.yaml.clib python3-ruamel.yaml.clib 0.2.12+ds-1+b1 install ok installed python3-setproctitle:amd64 python3-setproctitle 1.3.5-1 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 r-base-core r-base-core 4.4.3-1+b1 install ok installed r-cran-cli r-cran-cli 3.6.4-1 install ok installed r-cran-codetools r-cran-codetools 0.2-20-1 install ok installed r-cran-colorspace r-cran-colorspace 2.1-1+dfsg-1 install ok installed r-cran-fansi r-cran-fansi 1.0.6-1 install ok installed r-cran-farver r-cran-farver 2.1.2-1 install ok installed r-cran-foreach r-cran-foreach 1.5.2-1 install ok installed r-cran-gam r-cran-gam 1.22-5-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.5.1+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.8.0-1 install ok installed r-cran-gtable r-cran-gtable 0.3.6+dfsg-1 install ok installed r-cran-inline r-cran-inline 0.3.21-1 install ok installed r-cran-isoband r-cran-isoband 0.2.7-1 install ok installed r-cran-iterators r-cran-iterators 1.0.14-1 install ok installed r-cran-labeling r-cran-labeling 0.4.3-1 install ok installed r-cran-lattice r-cran-lattice 0.22-7-1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.21-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-mass r-cran-mass 7.3-65-1 install ok installed r-cran-matrix r-cran-matrix 1.7-3-1 install ok installed r-cran-mgcv r-cran-mgcv 1.9-3-1 install ok installed r-cran-munsell r-cran-munsell 0.5.1-1 install ok installed r-cran-nlme r-cran-nlme 3.1.168-1 install ok installed r-cran-pillar r-cran-pillar 1.10.1+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.4-1 install ok installed r-cran-r6 r-cran-r6 2.6.1-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-3-1 install ok installed r-cran-rcpp r-cran-rcpp 1.0.14-1 install ok installed r-cran-rcppgsl r-cran-rcppgsl 0.3.13-1+b1 install ok installed r-cran-rlang r-cran-rlang 1.1.5-1 install ok installed r-cran-scales r-cran-scales 1.3.0-1 install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-3 install ok installed r-cran-utf8 r-cran-utf8 1.2.4-1 install ok installed r-cran-vctrs r-cran-vctrs 0.6.5-1 install ok installed r-cran-viridislite r-cran-viridislite 0.4.2-2 install ok installed r-cran-withr r-cran-withr 3.0.2+dfsg-1 install ok installed radiant radiant 2.8.1+dfsg-2 install ok installed raxml raxml 8.2.13+dfsg-2+b1 install ok installed readline-common readline-common 8.2-6 install ok installed samtools samtools 1.21-1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.24 install ok installed seqtk seqtk 1.4-2 install ok installed shared-mime-info shared-mime-info 2.4-5+b2 install ok installed sqv sqv 1.3.0-1 install ok installed systemd systemd 257.5-2 install ok installed systemd-sysv systemd-sysv 257.5-2 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 unzip unzip 6.0-29 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.41-3 install ok installed x11-common x11-common 1:7.7+24 install ok installed xdg-utils xdg-utils 1.2.1-2 install ok installed xkb-data xkb-data 2.42-1 install ok installed zip zip 3.0-14 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', 'remove', '--allow-remove-essential', 'adapterremoval', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'bcftools', 'bedtools', 'bowtie2', 'bwa', 'ca-certificates', 'ca-certificates-java', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'examl', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'ibverbs-providers:amd64', 'java-common', 'junit4', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libapache-pom-java', 'libapparmor1:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcbor0.10:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcom-err2:amd64', 'libcommons-beanutils-java', 'libcommons-codec-java', 'libcommons-collections3-java', 'libcommons-collections4-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libexpat1:amd64', 'libezmorph-java', 'libfabric1:amd64', 'libffi8:amd64', 'libfido2-1:amd64', 'libfontconfig1:amd64', 'libfreemarker-java', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libfuse3-4:amd64', 'libgatk-native-bindings-java', 'libgbm1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgkl-java', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libhamcrest-java', 'libharfbuzz0b:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu76:amd64', 'libidn2-0:amd64', 'libjaxen-java', 'libjbig0:amd64', 'libjoptsimple-java', 'libjpeg62-turbo:amd64', 'libjson-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'liblightcouch-java', 'libllvm17t64:amd64', 'libllvm19:amd64', 'liblog4j2-java', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmongodb-java', 'libmunge2:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenmpi40:amd64', 'libp11-kit0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpicard-java', 'libpixman-1-0:amd64', 'libpmix2t64:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'librdmacm1t64:amd64', 'libreadline8t64:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libsystemd-shared:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libucx0:amd64', 'libunistring5:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxerces2-java', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml-commons-external-java', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxom-java', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'mesa-libgallium:amd64', 'mpi-default-bin', 'ncbi-vdb-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'perl', 'perl-modules-5.40', 'phylip', 'picard-tools', 'python3', 'python3-coloredlogs', 'python3-configargparse', 'python3-humanfriendly', 'python3-minimal', 'python3-monotonic', 'python3-pysam', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib', 'python3-setproctitle:amd64', 'python3.13', 'python3.13-minimal', 'r-base-core', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-gam', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-inline', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcppgsl', 'r-cran-rlang', 'r-cran-scales', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'radiant', 'raxml', 'readline-common', 'samtools', 'seqtk', 'shared-mime-info', 'systemd', 'systemd-sysv', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'zip', 'paleomix'] 0m43.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adapterremoval adduser adwaita-icon-theme at-spi2-common bcftools bedtools bowtie2 bwa ca-certificates ca-certificates-java dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless examl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme ibverbs-providers java-common junit4 libamd-comgr2 libamdhip64-5 libapache-pom-java libapparmor1 libasound2-data libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libbrotli1 libcairo-gobject2 libcairo2 libcbor0.10 libcloudproviders0 libcolord2 libcom-err2 libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java libcommons-collections4-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm2 libedit2 libelf1t64 libepoxy0 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libezmorph-java libfabric1 libffi8 libfido2-1 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libfuse3-4 libgatk-native-bindings-java libgbm1 libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgkl-java libgl1 libgl1-mesa-dri libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgnutls30t64 libgomp1 libgoogle-gson-java libgraphite2-3 libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libhamcrest-java libharfbuzz0b libhsa-runtime64-1 libhsakmt1 libhts3t64 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libice6 libicu76 libidn2-0 libjaxen-java libjbig0 libjoptsimple-java libjpeg62-turbo libjson-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 liblightcouch-java libllvm17t64 libllvm19 liblog4j2-java libmbedcrypto16 libmbedtls21 libmbedx509-7 libmongodb-java libmunge2 libncbi-ngs3 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenmpi40 libp11-kit0 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0 libpcsclite1 libperl5.40 libpicard-java libpixman-1-0 libpmix2t64 libpng16-16t64 libpsl5t64 libpsm2-2 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librdmacm1t64 libreadline8t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1t64 libsystemd-shared libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libucx0 libunistring5 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxnvctrl0 libxom-java libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libz3-4 littler mafft mapdamage media-types mesa-libgallium mpi-default-bin ncbi-vdb-data netbase ocl-icd-libopencl1 openjdk-21-jre openjdk-21-jre-headless openmpi-bin openmpi-common openssh-client openssl paleomix perl perl-modules-5.40 phylip picard-tools python3 python3-coloredlogs python3-configargparse python3-humanfriendly python3-minimal python3-monotonic python3-pysam python3-ruamel.yaml python3-ruamel.yaml.clib python3-setproctitle python3.13 python3.13-minimal r-base-core r-cran-cli r-cran-codetools r-cran-colorspace r-cran-fansi r-cran-farver r-cran-foreach r-cran-gam r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-inline r-cran-isoband r-cran-iterators r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppgsl r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr radiant raxml readline-common samtools seqtk shared-mime-info systemd systemd-sysv unzip x11-common xdg-utils xkb-data zip WARNING: The following essential packages will be removed. This should NOT be done unless you know exactly what you are doing! systemd-sysv systemd (due to systemd-sysv) 0 upgraded, 0 newly installed, 343 to remove and 0 not upgraded. After this operation, 1295 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 ... 24355 files and directories currently installed.) Removing paleomix (1.3.8-2) ... Removing adapterremoval (2.3.4-1) ... Removing examl (3.0.22-6+b3) ... Removing mpi-default-bin (1.18) ... Removing openmpi-bin (5.0.7-1) ... Removing libopenmpi40:amd64 (5.0.7-1) ... Removing libucx0:amd64 (1.18.1+ds-2+b1) ... Removing libfabric1:amd64 (2.0.0-4) ... Removing ibverbs-providers:amd64 (56.0-4) ... Removing librdmacm1t64:amd64 (56.0-4) ... Removing libibverbs1:amd64 (56.0-4) ... Removing openssh-client (1:9.9p2-2) ... Removing adduser (3.150) ... Removing picard-tools (3.3.0+dfsg-2) ... Removing default-jre (2:1.21-76) ... Removing openjdk-21-jre:amd64 (21.0.7~8ea-1) ... Removing libgtk-3-0t64:amd64 (3.24.49-3) ... Removing adwaita-icon-theme (48.0-1) ... Removing libatk-bridge2.0-0t64:amd64 (2.56.1-2) ... Removing libatk1.0-0t64:amd64 (2.56.1-2) ... Removing at-spi2-common (2.56.1-2) ... Removing bcftools (1.21-1) ... Removing bedtools (2.31.1+dfsg-2) ... Removing bowtie2 (2.5.4-1+b2) ... Removing bwa (0.7.18-1) ... Removing mapdamage (2.2.2+dfsg-1) ... Removing r-cran-ggplot2 (3.5.1+dfsg-1) ... Removing r-cran-mgcv (1.9-3-1) ... Removing r-cran-matrix (1.7-3-1) ... Removing r-cran-rcppgsl (0.3.13-1+b1) ... Removing r-cran-rcpp (1.0.14-1) ... Removing r-cran-scales (1.3.0-1) ... Removing r-cran-rcolorbrewer (1.1-3-1) ... Removing r-cran-withr (3.0.2+dfsg-1) ... Removing libpicard-java (3.3.0+dfsg-2) ... Removing default-jre-headless (2:1.21-76) ... Removing libgtk-3-common (3.24.49-3) ... Removing dconf-gsettings-backend:amd64 (0.40.0-5) ... Removing dconf-service (0.40.0-5) ... Removing dbus-user-session (1.16.2-2) ... Removing libpam-systemd:amd64 (257.5-2) ... Removing dbus (1.16.2-2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Removing dbus-daemon (1.16.2-2) ... Removing dbus-bin (1.16.2-2) ... Removing dbus-session-bus-common (1.16.2-2) ... Removing dbus-system-bus-common (1.16.2-2) ... Removing libcairo-gobject2:amd64 (1.18.4-1+b1) ... Removing gtk-update-icon-cache (4.18.4+ds-1) ... Removing hicolor-icon-theme (0.18-2) ... Removing libamdhip64-5 (5.7.1-5+b1) ... Removing libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Removing libbarclay-java (5.0.0+dfsg-1) ... dpkg: warning: overriding problem because --force enabled: dpkg: warning: this is a protected package; it should not be removed Removing systemd-sysv (257.5-2) ... Removing systemd (257.5-2) ... Removing libapparmor1:amd64 (4.1.0~beta5-6) ... Removing libasound2t64:amd64 (1.2.13-1+b1) ... Removing libasound2-data (1.2.13-1) ... Removing libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... Removing shared-mime-info (2.4-5+b2) ... Removing libcloudproviders0:amd64 (0.3.6-2) ... Removing libatspi2.0-0t64:amd64 (2.56.1-2) ... Removing libcups2t64:amd64 (2.4.10-2+b1) ... Removing libavahi-client3:amd64 (0.8-16) ... Removing libavahi-common3:amd64 (0.8-16) ... Removing libavahi-common-data:amd64 (0.8-16) ... Removing r-cran-gam (1.22-5-1) ... Removing liblapack3:amd64 (3.12.1-2) ... Removing libblas3:amd64 (3.12.1-2) ... Removing libfido2-1:amd64 (1.15.0-1+b1) ... Removing libcbor0.10:amd64 (0.10.2-2) ... Removing libcolord2:amd64 (1.4.7-3) ... Removing samtools (1.21-1) ... Removing libgkl-java (0.8.11+dfsg-2) ... Removing liblog4j2-java (2.19.0-2) ... Removing liblightcouch-java (0.2.0-1) ... Removing libhttpclient-java (4.5.14-1) ... Removing libcommons-math3-java (3.6.1-4) ... Removing libdbus-1-3:amd64 (1.16.2-2) ... Removing libdconf1:amd64 (0.40.0-5) ... Removing libhsa-runtime64-1:amd64 (6.1.2-3) ... Removing libhsakmt1:amd64 (6.2.4+ds-1) ... Removing libgl1:amd64 (1.7.0-1+b2) ... Removing libglx0:amd64 (1.7.0-1+b2) ... Removing libglx-mesa0:amd64 (25.0.3-1) ... Removing libllvm17t64:amd64 (1:17.0.6-21+b1) ... Removing libepoxy0:amd64 (1.5.10-2) ... Removing libpmix2t64:amd64 (5.0.7-1) ... Removing libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Removing libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Removing python3-ruamel.yaml (0.18.10+ds-1) ... Removing python3-ruamel.yaml.clib (0.2.12+ds-1+b1) ... Removing python3-setproctitle:amd64 (1.3.5-1) ... Removing python3-coloredlogs (15.0.1-1) ... Removing python3-humanfriendly (10.0-6) ... Removing python3-pysam (0.23.0+ds-1+b1) ... Removing python3-monotonic (1.6-3) ... Removing libgl1-mesa-dri:amd64 (25.0.3-1) ... Removing libgbm1:amd64 (25.0.3-1) ... Removing libwayland-server0:amd64 (1.23.1-3) ... Removing libwayland-cursor0:amd64 (1.23.1-3) ... Removing libwayland-client0:amd64 (1.23.1-3) ... Removing libfreemarker-java (2.3.32-2.1) ... Removing libfuse3-4:amd64 (3.17.1-1) ... Removing libgatk-native-bindings-java (1.0.0+dfsg-2) ... 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 libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... Removing libopenblas-dev:amd64 (0.3.29+ds-3) ... Removing libopenblas-pthread-dev:amd64 (0.3.29+ds-3) ... Removing libopenblas0:amd64 (0.3.29+ds-3) ... Removing libgif7:amd64 (5.2.2-1+b1) ... Removing libglvnd0:amd64 (1.7.0-1+b2) ... Removing libgoogle-gson-java (2.10.1-1) ... Removing libgsl-dev (2.8+dfsg-5) ... Removing libgsl28:amd64 (2.8+dfsg-5) ... Removing libgslcblas0:amd64 (2.8+dfsg-5) ... Removing libhttpcore-java (4.4.16-1) ... Removing libhwloc-plugins:amd64 (2.12.0-1) ... Removing libhwloc15:amd64 (2.12.0-1) ... Removing libibmad5:amd64 (56.0-4) ... Removing libibumad3:amd64 (56.0-4) ... Removing libjoptsimple-java (5.0.4-7) ... Removing libmongodb-java (3.6.3-2) ... Removing libmunge2:amd64 (0.5.16-1) ... Removing libncurses6:amd64 (6.5+20250216-2) ... Removing libnl-route-3-200:amd64 (3.7.0-2) ... Removing libnl-3-200:amd64 (3.7.0-2) ... Removing libpsm2-2 (11.2.185-2.1) ... Removing libnuma1:amd64 (2.0.18-1+b1) ... Removing libsystemd-shared:amd64 (257.5-2) ... Removing libvulkan1:amd64 (1.4.309.0-1) ... Removing libwayland-egl1:amd64 (1.23.1-3) ... Removing libxxf86vm1:amd64 (1:1.1.4-1+b4) ... Removing libxtst6:amd64 (2:1.2.5-1) ... Removing libxcb-glx0:amd64 (1.17.0-2+b1) ... Removing libxcomposite1:amd64 (1:0.4.6-1) ... Removing libxcursor1:amd64 (1:1.2.3-1) ... Removing libxdamage1:amd64 (1:1.1.6-1+b2) ... Removing libxfixes3:amd64 (1:6.0.0-2+b4) ... Removing libxi6:amd64 (2:1.8.2-1) ... Removing libxinerama1:amd64 (2:1.1.4-3+b4) ... Removing libxkbcommon0:amd64 (1.7.0-2) ... Removing libxnvctrl0:amd64 (535.171.04-1+b2) ... Removing libxrandr2:amd64 (2:1.5.4-1+b3) ... Removing littler (0.3.21-1) ... Removing ocl-icd-libopencl1:amd64 (2.3.3-1) ... Removing openmpi-common (5.0.7-1) ... Removing perl-modules-5.40 (5.40.1-2) ... Removing phylip (1:3.697+dfsg-4) ... Removing python3-configargparse (1.7-2) ... Removing r-cran-tibble (3.2.1+dfsg-3) ... Removing r-cran-pillar (1.10.1+dfsg-1) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-gtable (0.3.6+dfsg-1) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-cli (3.6.4-1) ... Removing r-cran-foreach (1.5.2-1) ... Removing r-cran-codetools (0.2-20-1) ... Removing r-cran-munsell (0.5.1-1) ... Removing r-cran-colorspace (2.1-1+dfsg-1) ... Removing r-cran-fansi (1.0.6-1) ... Removing r-cran-farver (2.1.2-1) ... Removing r-cran-glue (1.8.0-1) ... Removing r-cran-inline (0.3.21-1) ... Removing r-cran-isoband (0.2.7-1) ... Removing r-cran-iterators (1.0.14-1) ... Removing r-cran-labeling (0.4.3-1) ... Removing r-cran-nlme (3.1.168-1) ... Removing r-cran-lattice (0.22-7-1) ... Removing r-cran-littler (0.3.21-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-65-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-pkgkitten (0.2.4-1) ... Removing r-cran-r6 (2.6.1-1) ... Removing r-cran-rlang (1.1.5-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing r-cran-viridislite (0.4.2-2) ... Removing radiant (2.8.1+dfsg-2) ... Removing raxml (8.2.13+dfsg-2+b1) ... Removing seqtk (1.4-2) ... Removing xkb-data (2.42-1) ... Removing r-base-core (4.4.3-1+b1) ... Removing libhtsjdk-java (4.1.3+dfsg-2) ... Removing libjson-java (3.1.0+dfsg-2) ... Removing junit4 (4.13.2-5) ... Removing openjdk-21-jre-headless:amd64 (21.0.7~8ea-1) ... Removing ca-certificates-java (20240118) ... Removing ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.56.3-1) ... Removing libpangoft2-1.0-0:amd64 (1.56.3-1) ... Removing libpango-1.0-0:amd64 (1.56.3-1) ... Removing fontconfig (2.15.0-2.3) ... Removing libtk8.6:amd64 (8.6.16-1) ... Removing libxft2:amd64 (2.3.6-1+b4) ... 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-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing java-common (0.76) ... Removing libcommons-beanutils-java (1.9.4-2) ... Removing libcommons-jexl2-java (2.1.1-6) ... Removing libcommons-logging-java (1.3.0-1) ... Removing libcommons-lang3-java (3.17.0-1) ... Removing libharfbuzz0b:amd64 (10.2.0-1+b1) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libcurl4t64:amd64 (8.13.0-1) ... Removing libtirpc3t64:amd64 (1.3.6+ds-1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libhts3t64:amd64 (1.21+ds-1) ... Removing libcurl3t64-gnutls:amd64 (8.13.0-1) ... Removing libgssapi-krb5-2:amd64 (1.21.3-5) ... Removing libkrb5-3:amd64 (1.21.3-5) ... Removing libcom-err2:amd64 (1.47.2-1+b1) ... Removing libcommons-compress-java (1.27.1-2) ... Removing libcommons-codec-java (1.18.0-1) ... Removing libcommons-collections3-java (3.2.2-3) ... Removing libcommons-collections4-java (4.4-2) ... Removing libcommons-io-java (2.18.0-1) ... Removing libthai0:amd64 (0.1.29-2+b1) ... Removing libdatrie1:amd64 (0.2.13-3+b1) ... Removing libtiff6:amd64 (4.7.0-3) ... Removing libdeflate0:amd64 (1.23-1+b1) ... Removing mesa-libgallium:amd64 (25.0.3-1) ... Removing libdrm-intel1:amd64 (2.4.124-2) ... Removing libllvm19:amd64 (1:19.1.7-3) ... Removing libedit2:amd64 (3.1-20250104-1) ... Removing libelf1t64:amd64 (0.192-4) ... 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 libezmorph-java (1.0.6-4) ... Removing libfribidi0:amd64 (1.0.16-1) ... Removing libopenblas0-pthread:amd64 (0.3.29+ds-3) ... Removing libgfortran5:amd64 (14.2.0-19) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Removing libgnutls30t64:amd64 (3.8.9-2) ... Removing libgomp1:amd64 (14.2.0-19) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libhamcrest-java (2.2-2) ... Removing libhtscodecs2:amd64 (1.6.1-2) ... Removing libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Removing libsm6:amd64 (2:1.2.6-1) ... Removing libice6:amd64 (2:1.1.1-1) ... Removing libicu76:amd64 (76.1-3) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libidn2-0:amd64 (2.3.8-2) ... Removing libxom-java (1.3.9-1) ... Removing libjaxen-java (1.1.6-5) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3.1) ... Removing libk5crypto3:amd64 (1.21.3-5) ... Removing libkeyutils1:amd64 (1.6.3-5) ... Removing libkrb5support0:amd64 (1.21.3-5) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing libldap2:amd64 (2.6.9+dfsg-2) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing libngs-java:amd64 (3.0.9+dfsg-7.1) ... Removing libngs-jni:amd64 (3.0.9+dfsg-7.1) ... Removing libncbi-ngs3:amd64 (3.0.9+dfsg-7.1) ... Removing libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... Removing libmbedtls21:amd64 (3.6.3-1) ... Removing libmbedx509-7:amd64 (3.6.3-1) ... Removing libmbedcrypto16:amd64 (3.6.3-1) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libnghttp3-9:amd64 (1.8.0-1) ... Removing libngtcp2-16:amd64 (1.11.0-1) ... Removing libnss3:amd64 (2:3.110-1) ... Removing libnspr4:amd64 (2:4.36-1) ... Removing libp11-kit0:amd64 (0.25.5-3) ... Removing libpaper-utils (2.2.5-0.3+b2) ... Removing libpaper2:amd64 (2.2.5-0.3+b2) ... Removing libpciaccess0:amd64 (0.17-3+b3) ... Removing libpcsclite1:amd64 (2.3.3-1) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libpng16-16t64:amd64 (1.6.47-1.1) ... 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 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 librhino-java (1.7.15-1) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Removing libsensors5:amd64 (1:3.6.0-10+b1) ... Removing libsensors-config (1:3.6.0-10) ... Removing libwebp7:amd64 (1.5.0-0.1) ... Removing libsharpyuv0:amd64 (1.5.0-0.1) ... Removing libslf4j-java (1.7.32-1) ... Removing libsnappy-java (1.1.10.7-1) ... Removing libsnappy-jni (1.1.10.7-1) ... Removing libsnappy1v5:amd64 (1.2.2-1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libtasn1-6:amd64 (4.20.0-2) ... Removing libtcl8.6:amd64 (8.6.16+dfsg-1) ... Removing libthai-data (0.1.29-2) ... Removing libtirpc-common (1.3.6+ds-1) ... Removing libunistring5:amd64 (1.3-2) ... Removing libx11-xcb1:amd64 (2:1.8.12-1) ... Removing libxcb-xfixes0:amd64 (1.17.0-2+b1) ... Removing libxcb-sync1:amd64 (1.17.0-2+b1) ... Removing libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Removing libxcb-present0:amd64 (1.17.0-2+b1) ... Removing libxcb-randr0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxerces2-java (2.12.2-1) ... Removing libxss1:amd64 (1:1.2.3-1+b3) ... Removing libxext6:amd64 (2:1.3.4-1+b3) ... Removing libxml-commons-external-java (1.4.01-6) ... Removing libxml-commons-resolver1.1-java (1.2-11) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Removing libxrender1:amd64 (1:0.9.12-1) ... Removing libxshmfence1:amd64 (1.3.3-1) ... Removing libz3-4:amd64 (4.13.3-1) ... Removing media-types (13.0.0) ... Removing ncbi-vdb-data (3.0.9+dfsg-2) ... Removing netbase (6.5) ... Removing openssl (3.5.0-1) ... Removing readline-common (8.2-6) ... Removing unzip (6.0-29) ... 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 xdg-utils (1.2.1-2) ... Removing zip (3.0-14) ... Removing libcommons-parent-java (56-1) ... Removing libapache-pom-java (33-2) ... Removing libglib2.0-0t64:amd64 (2.84.1-1) ... Removing libatomic1:amd64 (14.2.0-19) ... Removing libbrotli1:amd64 (1.1.0-2+b7) ... Removing libdrm-amdgpu1:amd64 (2.4.124-2) ... Removing libdrm2:amd64 (2.4.124-2) ... Removing libdrm-common (2.4.124-2) ... Removing libffi8:amd64 (3.4.7-1) ... 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) ... Processing triggers for procps (2:4.0.4-7) ... Processing triggers for libc-bin (2.41-6) ... 0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', 'remove', '--allow-remove-essential', 'adapterremoval', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'bcftools', 'bedtools', 'bowtie2', 'bwa', 'ca-certificates', 'ca-certificates-java', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'examl', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'ibverbs-providers:amd64', 'java-common', 'junit4', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libapache-pom-java', 'libapparmor1:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcbor0.10:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcom-err2:amd64', 'libcommons-beanutils-java', 'libcommons-codec-java', 'libcommons-collections3-java', 'libcommons-collections4-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libexpat1:amd64', 'libezmorph-java', 'libfabric1:amd64', 'libffi8:amd64', 'libfido2-1:amd64', 'libfontconfig1:amd64', 'libfreemarker-java', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libfuse3-4:amd64', 'libgatk-native-bindings-java', 'libgbm1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgkl-java', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libhamcrest-java', 'libharfbuzz0b:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu76:amd64', 'libidn2-0:amd64', 'libjaxen-java', 'libjbig0:amd64', 'libjoptsimple-java', 'libjpeg62-turbo:amd64', 'libjson-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'liblightcouch-java', 'libllvm17t64:amd64', 'libllvm19:amd64', 'liblog4j2-java', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmongodb-java', 'libmunge2:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenmpi40:amd64', 'libp11-kit0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpicard-java', 'libpixman-1-0:amd64', 'libpmix2t64:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'librdmacm1t64:amd64', 'libreadline8t64:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libsystemd-shared:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libucx0:amd64', 'libunistring5:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxerces2-java', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml-commons-external-java', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxom-java', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'mesa-libgallium:amd64', 'mpi-default-bin', 'ncbi-vdb-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'perl', 'perl-modules-5.40', 'phylip', 'picard-tools', 'python3', 'python3-coloredlogs', 'python3-configargparse', 'python3-humanfriendly', 'python3-minimal', 'python3-monotonic', 'python3-pysam', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib', 'python3-setproctitle:amd64', 'python3.13', 'python3.13-minimal', 'r-base-core', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-gam', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-inline', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcppgsl', 'r-cran-rlang', 'r-cran-scales', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'radiant', 'raxml', 'readline-common', 'samtools', 'seqtk', 'shared-mime-info', 'systemd', 'systemd-sysv', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'zip', 'paleomix'] 0m43.5s INFO: Running scripts post_remove 0m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_remove_cleanup'] 0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_remove_cleanup'] 0m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_remove_exceptions'] 0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_remove_exceptions'] 0m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg', '--purge', 'adapterremoval', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'bcftools', 'bedtools', 'bowtie2', 'bwa', 'ca-certificates', 'ca-certificates-java', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'examl', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'ibverbs-providers:amd64', 'java-common', 'junit4', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libapache-pom-java', 'libapparmor1:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcbor0.10:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcom-err2:amd64', 'libcommons-beanutils-java', 'libcommons-codec-java', 'libcommons-collections3-java', 'libcommons-collections4-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libexpat1:amd64', 'libezmorph-java', 'libfabric1:amd64', 'libffi8:amd64', 'libfido2-1:amd64', 'libfontconfig1:amd64', 'libfreemarker-java', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libfuse3-4:amd64', 'libgatk-native-bindings-java', 'libgbm1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgkl-java', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libhamcrest-java', 'libharfbuzz0b:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu76:amd64', 'libidn2-0:amd64', 'libjaxen-java', 'libjbig0:amd64', 'libjoptsimple-java', 'libjpeg62-turbo:amd64', 'libjson-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'liblightcouch-java', 'libllvm17t64:amd64', 'libllvm19:amd64', 'liblog4j2-java', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmongodb-java', 'libmunge2:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenmpi40:amd64', 'libp11-kit0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpicard-java', 'libpixman-1-0:amd64', 'libpmix2t64:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'librdmacm1t64:amd64', 'libreadline8t64:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libsystemd-shared:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libucx0:amd64', 'libunistring5:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxerces2-java', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml-commons-external-java', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxom-java', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'mesa-libgallium:amd64', 'mpi-default-bin', 'ncbi-vdb-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'perl', 'perl-modules-5.40', 'phylip', 'picard-tools', 'python3', 'python3-coloredlogs', 'python3-configargparse', 'python3-humanfriendly', 'python3-minimal', 'python3-monotonic', 'python3-pysam', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib', 'python3-setproctitle:amd64', 'python3.13', 'python3.13-minimal', 'r-base-core', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-gam', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-inline', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcppgsl', 'r-cran-rlang', 'r-cran-scales', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'radiant', 'raxml', 'readline-common', 'samtools', 'seqtk', 'shared-mime-info', 'systemd', 'systemd-sysv', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'zip'] 0m43.8s DUMP: dpkg: warning: ignoring request to remove adapterremoval which isn't installed (Reading database ... 5628 files and directories currently installed.) Purging configuration files for adduser (3.150) ... Purging configuration files for adwaita-icon-theme (48.0-1) ... dpkg: warning: ignoring request to remove at-spi2-common which isn't installed dpkg: warning: ignoring request to remove bcftools which isn't installed dpkg: warning: ignoring request to remove bedtools which isn't installed dpkg: warning: ignoring request to remove bowtie2 which isn't installed dpkg: warning: ignoring request to remove bwa which isn't installed Purging configuration files for ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20240118) ... Purging configuration files for dbus (1.16.2-2) ... rmdir: failed to remove '/var/run/dbus': No such file or directory rmdir: failed to remove '/var/lib/dbus': Directory not empty dpkg: warning: while removing dbus, directory '/var/lib/dbus' not empty so not removed dpkg: warning: ignoring request to remove dbus-bin which isn't installed Purging configuration files for dbus-daemon (1.16.2-2) ... dpkg: warning: ignoring request to remove dbus-session-bus-common which isn't installed dpkg: warning: ignoring request to remove dbus-system-bus-common which isn't installed Purging configuration files for dbus-user-session (1.16.2-2) ... dpkg: warning: ignoring request to remove dconf-gsettings-backend which isn't installed dpkg: warning: ignoring request to remove dconf-service which isn't installed dpkg: warning: ignoring request to remove default-jre which isn't installed dpkg: warning: ignoring request to remove default-jre-headless which isn't installed dpkg: warning: ignoring request to remove examl which isn't installed Purging configuration files for fontconfig (2.15.0-2.3) ... 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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 Purging configuration files for libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... dpkg: warning: ignoring request to remove libgdk-pixbuf2.0-common which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgif7 which isn't installed dpkg: warning: ignoring request to remove libgkl-java which isn't installed dpkg: warning: ignoring request to remove libgl1 which isn't installed Purging configuration files for libgl1-mesa-dri:amd64 (25.0.3-1) ... 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remove libpaper-utils which isn't installed Purging configuration files for libpaper2:amd64 (2.2.5-0.3+b2) ... dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpcsclite1 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libpicard-java which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpmix2t64 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpsm2-2 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 librdmacm1t64 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove librhino-java which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed Purging configuration files for libsensors-config (1:3.6.0-10) ... dpkg: warning: ignoring request to remove libsensors5 which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libslf4j-java which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libsnappy-java which isn't installed dpkg: warning: ignoring request to remove libsnappy-jni which isn't installed dpkg: warning: ignoring request to remove libsnappy1v5 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libsystemd-shared which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.6+ds-1) ... Purging configuration files for libtirpc3t64:amd64 (1.3.6+ds-1) ... dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libucx0 which isn't installed dpkg: warning: ignoring request to remove libunistring5 which isn't installed dpkg: warning: ignoring request to remove libvulkan1 which isn't installed dpkg: warning: ignoring request to remove libwayland-client0 which isn't installed dpkg: warning: ignoring request to remove libwayland-cursor0 which isn't installed dpkg: warning: ignoring request to remove libwayland-egl1 which isn't installed dpkg: warning: ignoring request to remove libwayland-server0 which isn't installed dpkg: warning: ignoring request to remove libwebp7 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 libx11-xcb1 which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-dri3-0 which isn't installed dpkg: warning: ignoring request to remove libxcb-glx0 which isn't installed dpkg: warning: ignoring request to remove libxcb-present0 which isn't installed dpkg: warning: ignoring request to remove libxcb-randr0 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 libxcb-sync1 which isn't installed dpkg: warning: ignoring request to remove libxcb-xfixes0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxcomposite1 which isn't installed dpkg: warning: ignoring request to remove libxcursor1 which isn't installed dpkg: warning: ignoring request to remove libxdamage1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxerces2-java which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxfixes3 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxi6 which isn't installed dpkg: warning: ignoring request to remove libxinerama1 which isn't installed dpkg: warning: ignoring request to remove libxkbcommon0 which isn't installed dpkg: warning: ignoring request to remove libxml-commons-external-java which isn't installed Purging configuration files for libxml-commons-resolver1.1-java (1.2-11) ... dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxnvctrl0 which isn't installed dpkg: warning: ignoring request to remove libxom-java which isn't installed dpkg: warning: ignoring request to remove libxrandr2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxshmfence1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6t64 which isn't installed dpkg: warning: ignoring request to remove libxtst6 which isn't installed dpkg: warning: ignoring request to remove libxxf86vm1 which isn't installed dpkg: warning: ignoring request to remove libz3-4 which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed dpkg: warning: ignoring request to remove mafft which isn't installed dpkg: warning: ignoring request to remove mapdamage which isn't installed Purging configuration files for media-types (13.0.0) ... dpkg: warning: ignoring request to remove mesa-libgallium which isn't installed dpkg: warning: ignoring request to remove mpi-default-bin which isn't installed dpkg: warning: ignoring request to remove ncbi-vdb-data which isn't installed Purging configuration files for netbase (6.5) ... dpkg: warning: ignoring request to remove ocl-icd-libopencl1 which isn't installed dpkg: warning: ignoring request to remove openjdk-21-jre which isn't installed Purging configuration files for openjdk-21-jre-headless:amd64 (21.0.7~8ea-1) ... Purging configuration files for openmpi-bin (5.0.7-1) ... dpkg: warning: ignoring request to remove openmpi-common which isn't installed Purging configuration files for openssh-client (1:9.9p2-2) ... 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 phylip which isn't installed dpkg: warning: ignoring request to remove picard-tools which isn't installed Purging configuration files for python3 (3.13.3-1) ... dpkg: warning: ignoring request to remove python3-coloredlogs which isn't installed dpkg: warning: ignoring request to remove python3-configargparse which isn't installed dpkg: warning: ignoring request to remove python3-humanfriendly which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-monotonic which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-ruamel.yaml which isn't installed dpkg: warning: ignoring request to remove python3-ruamel.yaml.clib which isn't installed dpkg: warning: ignoring request to remove python3-setproctitle 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) ... Purging configuration files for r-base-core (4.4.3-1+b1) ... dpkg: warning: ignoring request to remove r-cran-cli which isn't installed dpkg: warning: ignoring request to remove r-cran-codetools which isn't installed dpkg: warning: ignoring request to remove r-cran-colorspace which isn't installed dpkg: warning: ignoring request to remove r-cran-fansi which isn't installed dpkg: warning: ignoring request to remove r-cran-farver which isn't installed dpkg: warning: ignoring request to remove r-cran-foreach which isn't installed dpkg: warning: ignoring request to remove r-cran-gam which isn't installed dpkg: warning: ignoring request to remove r-cran-ggplot2 which isn't installed dpkg: warning: ignoring request to remove r-cran-glue which isn't installed dpkg: warning: ignoring request to remove r-cran-gtable which isn't installed dpkg: warning: ignoring request to remove r-cran-inline which isn't installed dpkg: warning: ignoring request to remove r-cran-isoband which isn't installed dpkg: warning: ignoring request to remove r-cran-iterators which isn't installed dpkg: warning: ignoring request to remove r-cran-labeling which isn't installed dpkg: warning: ignoring request to remove r-cran-lattice which isn't installed dpkg: warning: ignoring request to remove r-cran-lifecycle which isn't installed dpkg: warning: ignoring request to remove r-cran-littler which isn't installed dpkg: warning: ignoring request to remove r-cran-magrittr which isn't installed dpkg: warning: ignoring request to remove r-cran-mass which isn't installed dpkg: warning: ignoring request to remove r-cran-matrix which isn't installed dpkg: warning: ignoring request to remove r-cran-mgcv which isn't installed dpkg: warning: ignoring request to remove r-cran-munsell which isn't installed dpkg: warning: ignoring request to remove r-cran-nlme which isn't installed dpkg: warning: ignoring request to remove r-cran-pillar which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgconfig which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgkitten which isn't installed dpkg: warning: ignoring request to remove r-cran-r6 which isn't installed dpkg: warning: ignoring request to remove r-cran-rcolorbrewer which isn't installed dpkg: warning: ignoring request to remove r-cran-rcpp which isn't installed dpkg: warning: ignoring request to remove r-cran-rcppgsl which isn't installed dpkg: warning: ignoring request to remove r-cran-rlang which isn't installed dpkg: warning: ignoring request to remove r-cran-scales which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-cran-utf8 which isn't installed dpkg: warning: ignoring request to remove r-cran-vctrs which isn't installed dpkg: warning: ignoring request to remove r-cran-viridislite which isn't installed dpkg: warning: ignoring request to remove r-cran-withr which isn't installed Purging configuration files for radiant (2.8.1+dfsg-2) ... 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 samtools which isn't installed dpkg: warning: ignoring request to remove seqtk which isn't installed Purging configuration files for shared-mime-info (2.4-5+b2) ... Purging configuration files for systemd (257.5-2) ... dpkg: warning: ignoring request to remove systemd-sysv which isn't installed dpkg: warning: ignoring request to remove unzip which isn't installed Purging configuration files for x11-common (1:7.7+24) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove xkb-data which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg', '--purge', 'adapterremoval', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'bcftools', 'bedtools', 'bowtie2', 'bwa', 'ca-certificates', 'ca-certificates-java', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'examl', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'ibverbs-providers:amd64', 'java-common', 'junit4', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libapache-pom-java', 'libapparmor1:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcbor0.10:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcom-err2:amd64', 'libcommons-beanutils-java', 'libcommons-codec-java', 'libcommons-collections3-java', 'libcommons-collections4-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libexpat1:amd64', 'libezmorph-java', 'libfabric1:amd64', 'libffi8:amd64', 'libfido2-1:amd64', 'libfontconfig1:amd64', 'libfreemarker-java', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libfuse3-4:amd64', 'libgatk-native-bindings-java', 'libgbm1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgkl-java', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libhamcrest-java', 'libharfbuzz0b:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu76:amd64', 'libidn2-0:amd64', 'libjaxen-java', 'libjbig0:amd64', 'libjoptsimple-java', 'libjpeg62-turbo:amd64', 'libjson-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'liblightcouch-java', 'libllvm17t64:amd64', 'libllvm19:amd64', 'liblog4j2-java', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmongodb-java', 'libmunge2:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenmpi40:amd64', 'libp11-kit0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpicard-java', 'libpixman-1-0:amd64', 'libpmix2t64:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'librdmacm1t64:amd64', 'libreadline8t64:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libsystemd-shared:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libucx0:amd64', 'libunistring5:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxerces2-java', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml-commons-external-java', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxom-java', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'mesa-libgallium:amd64', 'mpi-default-bin', 'ncbi-vdb-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'perl', 'perl-modules-5.40', 'phylip', 'picard-tools', 'python3', 'python3-coloredlogs', 'python3-configargparse', 'python3-humanfriendly', 'python3-minimal', 'python3-monotonic', 'python3-pysam', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib', 'python3-setproctitle:amd64', 'python3.13', 'python3.13-minimal', 'r-base-core', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-gam', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-inline', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcppgsl', 'r-cran-rlang', 'r-cran-scales', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'radiant', 'raxml', 'readline-common', 'samtools', 'seqtk', 'shared-mime-info', 'systemd', 'systemd-sysv', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'zip'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg', '--purge', 'paleomix'] 0m43.8s DUMP: dpkg: warning: ignoring request to remove paleomix which isn't installed 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg', '--purge', 'paleomix'] 0m43.8s INFO: Running scripts post_purge 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_purge_exceptions'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_purge_exceptions'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_purge_manual_cleanup'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_purge_manual_cleanup'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg', '--purge', '--pending'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg', '--purge', '--pending'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg', '--remove', '--pending'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg', '--remove', '--pending'] 0m43.8s INFO: Running scripts post_test 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_test_exceptions'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'tmp/scripts/post_test_exceptions'] 0m43.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0'] 0m44.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0'] 0m44.1s INFO: IGNORED broken symlink: /etc/vconsole.conf (flag L+ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 0m44.1s INFO: IGNORED broken symlink: /etc/default/locale (flag L+ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 0m44.3s DEBUG: No broken symlinks as far as we can find. 0m44.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg-divert', '--list'] 0m44.3s 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 0m44.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'dpkg-divert', '--list'] 0m44.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', 'clean'] 0m44.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0', 'apt-get', 'clean'] 0m44.3s DEBUG: Recording chroot state 0m44.6s INFO: IGNORED PATH@1: /var/lib/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 0m44.6s INFO: IGNORED PATH@1: /var/lib/systemd/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 0m44.6s INFO: IGNORED PATH@1: /var/cache/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 0m44.6s INFO: IGNORED PATH@1: /var/log/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 0m44.6s INFO: IGNORED PATH@1: /var/spool/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 0m44.6s INFO: IGNORED PATH@1: /root/ (flag d- systemd-tmpfiles snippet /usr/lib/tmpfiles.d/provision.conf) 0m44.6s INFO: IGNORED PATH@1: /run/lock/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/legacy.conf) 0m44.6s INFO: IGNORED PATH@2: /var/lib/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 0m44.6s INFO: IGNORED PATH@2: /var/lib/private/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 0m44.6s INFO: IGNORED PATH@2: /var/lib/systemd/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 0m44.6s INFO: IGNORED PATH@2: /var/cache/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 0m44.6s INFO: IGNORED PATH@2: /var/cache/private/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 0m44.6s INFO: IGNORED PATH@2: /var/log/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 0m44.6s INFO: IGNORED PATH@2: /var/log/private/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 0m44.6s INFO: IGNORED PATH@2: /var/spool/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 0m44.6s INFO: IGNORED PATH@2: /etc/vconsole.conf (flag L+ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 0m44.6s INFO: IGNORED PATH@2: /etc/default/locale (flag L+ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 0m44.7s INFO: IGNORED PATH@2: /root/ (flag d- systemd-tmpfiles snippet /usr/lib/tmpfiles.d/provision.conf) 0m44.7s INFO: IGNORED PATH@2: /root/.ssh/ (flag d- systemd-tmpfiles snippet /usr/lib/tmpfiles.d/provision.conf) 0m44.7s INFO: IGNORED PATH@2: /run/log/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 0m44.7s INFO: IGNORED PATH@2: /run/user/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 0m44.7s INFO: IGNORED PATH@2: /run/systemd/shutdown/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 0m44.7s INFO: IGNORED PATH@2: /run/systemd/machines/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 0m44.7s INFO: IGNORED PATH@2: /run/systemd/users/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 0m44.7s INFO: IGNORED PATH@2: /run/systemd/sessions/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 0m44.7s INFO: IGNORED PATH@2: /run/systemd/seats/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 0m44.7s INFO: IGNORED PATH@2: /run/systemd/ask-password/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 0m44.7s INFO: IGNORED PATH@2: /run/systemd/netif/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd-network.conf) 0m44.7s INFO: IGNORED PATH@2: /run/systemd/netif/leases/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd-network.conf) 0m44.7s INFO: IGNORED PATH@2: /run/systemd/netif/links/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd-network.conf) 0m44.7s INFO: IGNORED PATH@2: /run/sendsigs.omit.d/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 0m44.7s INFO: IGNORED PATH@2: /run/sshd/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/20-systemd-ssh-generator.conf) 0m44.7s INFO: IGNORED PATH@2: /run/lock/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/legacy.conf) 0m44.7s INFO: IGNORED PATH@2: /run/lock/subsys/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/legacy.conf) 0m45.2s INFO: PASS: Installation and purging test. 0m45.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/shm'] 0m45.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/shm'] 0m45.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/console'] 0m45.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/console'] 0m45.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/ptmx'] 0m45.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/ptmx'] 0m45.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/pts'] 0m45.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/dev/pts'] 0m45.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/proc'] 0m45.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0/proc'] 0m45.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0'] 0m45.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpuhzqy3e0'] 0m45.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpuhzqy3e0 0m45.5s INFO: PASS: All tests. 0m45.5s INFO: piuparts run ends. ret=0 End: 2025-04-09 19:46:17 GMT