Start: 2024-02-25 06:41:38 GMT Package: paleomix Version: 1.3.8-1 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_1.3.8-1_amd64.deb Size: 983864 MD5sum: 5f5fdaf6a3957756e162048d7dfa0362 SHA256: 1962b954a2ab038bd6339542265e1f9720eba2aeaded3066749bda681a7424ba Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt paleomix=1.3.8-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.3.1~202401311821~1.3-2-g28295102 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt paleomix=1.3.8-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp8pqt8b8n 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp8pqt8b8n 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmp8pqt8b8n/tmp/scripts/ 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp8pqt8b8n/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-get', 'update'] 0m5.1s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9750 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7154 kB] Fetched 17.1 MB in 3s (5036 kB/s) Reading package lists... 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-get', 'update'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-get', '-yf', 'dist-upgrade'] 0m6.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libpcre2-8-0 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 262 kB of archives. After this operation, 1024 B of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 262 kB in 0s (6866 kB/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 ... 5224 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.42-4+b1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-4+b1) over (10.42-4) ... Setting up libpcre2-8-0:amd64 (10.42-4+b1) ... Processing triggers for libc-bin (2.37-15) ... 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-get', '-yf', 'dist-upgrade'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.8s DUMP: 96e7054ed1dbeae3f1e3d79f505b1fc9 - 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.8s INFO: Running scripts post_setup 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_setup_dummy_users'] 0m7.6s 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 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_setup_dummy_users'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_setup_forbid_home'] 0m7.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_setup_forbid_home'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.7s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_setup_minimize'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_setup_minimize'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_setup_zz_backports'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_setup_zz_backports'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-get', 'clean'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-get', 'clean'] 0m7.7s DEBUG: Recording chroot state 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.3s DUMP: install ok installed apt apt 2.7.12 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.39.3-6 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.16 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.4 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240201-3 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.12 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2 install ok installed libblkid1:amd64 libblkid1 2.39.3-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-15 install ok installed libc6:amd64 libc6 2.37-15 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240201-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30:amd64 libgnutls30 3.8.3-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.4.5-0.3 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-6 install ok installed libnettle8:amd64 libnettle8 3.9.1-2+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1+b1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-6 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssl3:amd64 libssl3 3.1.5-1 install ok installed libstdc++6:amd64 libstdc++6 14-20240201-3 install ok installed libsystemd0:amd64 libsystemd0 255.3-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.3-2 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-6 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2+b1 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.39.3-6 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.08-6 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.39.3-6 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3+b1 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg-divert', '--list'] 0m8.3s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg-divert', '--list'] 0m8.3s INFO: Running scripts is_testable 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/is_testable_uninstallable'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/is_testable_uninstallable'] 0m8.3s INFO: apt-cache does not know about any of the requested packages 0m8.3s INFO: Running scripts pre_test 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_test_exceptions'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_test_exceptions'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_test_root_password'] 0m8.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_test_root_password'] 0m8.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n'] 0m8.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n'] 0m9.5s DEBUG: No broken symlinks as far as we can find. 0m9.5s INFO: Running scripts pre_install 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_install_database-server'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_install_database-server'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_install_exceptions'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_install_exceptions'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_install_extras'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_install_extras'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_install_log_alternatives'] 0m9.5s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_install_log_alternatives'] 0m9.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n'] 0m10.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n'] 0m10.7s DEBUG: No broken symlinks as far as we can find. 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-cache', 'policy'] 0m11.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-cache', 'policy'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-cache', 'policy', 'paleomix'] 0m11.8s DUMP: paleomix: Installed: (none) Candidate: 1.3.8-1 Version table: 1.3.8-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-cache', 'policy', 'paleomix'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-get', '-y', 'install', 'paleomix=1.3.8-1'] 0m59.7s 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 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 libapache-pom-java libasound2 libasound2-data libatk1.0-0 libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libbrotli1 libbsd0 libcairo2 libcbor0.10 libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfido2-1 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libgatk-native-bindings-java libgdbm-compat4 libgdbm6 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgkl-java libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgoogle-gson-java libgraphite2-3 libgsl-dev libgsl27 libgslcblas0 libgssapi-krb5-2 libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhts3 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibverbs1 libice6 libicu72 libjbig0 libjoptsimple-java libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 liblightcouch-java libllvm17 liblog4j2-java libmbedcrypto7 libmbedtls14 libmbedx509-1 libmjson-java libmongodb-java libmunge2 libncbi-ngs3 libncbi-vdb3 libncurses6 libncursesw6 libnghttp2-14 libngs-java libngs-jni libnl-3-200 libnl-route-3-200 libnsl2 libnspr4 libnss3 libnuma1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenmpi3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.38 libpicard-java libpixman-1-0 libpmix2 libpng16-16 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librdmacm1 libreadline8 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsqlite3-0 libssh2-1 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3 libtk8.6 libucx0 libvulkan1 libwebp7 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml2 libxnvctrl0 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxxf86vm1 libz3-4 littler mafft mapdamage media-types ncbi-vdb-data netbase ocl-icd-libopencl1 openjdk-17-jre openjdk-17-jre-headless openmpi-bin openmpi-common openssh-client openssl perl perl-modules-5.38 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 python3.11 python3.11-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 sensible-utils seqtk shared-mime-info ucf unzip x11-common xdg-utils zip Suggested packages: liblocale-gettext-perl cron quota python3-numpy python3-matplotlib texlive-latex-recommended bowtie2-examples libasound2-plugins alsa-utils libasm-java libxz-java libcommons-io-java-doc libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java cups-common jython libdom4j-java libjaxen-java libjdom1-java libxalan2-java gdbm-l10n low-memory-monitor libgoogle-gson-java-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user gvfs libhwloc-contrib-plugins libjoptsimple-java-doc 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 pciutils pcscd rhino lm-sensors tcl8.6 tk8.6 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 python3.11-venv python3.11-doc binutils binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 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-knitr r-cran-rmarkdown r-cran-viridis r-cran-covr r-cran-magick r-cran-sf r-cran-getopt r-cran-bit64 r-cran-dbi r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-stringi r-cran-survival r-cran-units r-cran-vdiffr r-cran-testthat r-cran-bench r-cran-blob r-cran-brio r-cran-callr r-cran-crayon r-cran-evaluate r-cran-here r-cran-hms r-cran-htmltools r-cran-pkgbuild r-cran-pkgload r-cran-purrr r-cran-tidyr readline-doc cwltool Recommended packages: librsvg2-common alsa-ucm-conf alsa-topology-conf dbus libgdk-pixbuf2.0-bin libgkl-jni libglib2.0-data xdg-user-dirs libgail-common libgtk2.0-bin krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules 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-mockery r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-testthat r-cran-whoami r-cran-unitizer r-cran-interp r-cran-dplyr 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-lubridate r-cran-fs r-cran-usethis r-cran-bit64 r-cran-dichromat r-cran-hms r-cran-stringi r-cran-data.table r-cran-mockr r-cran-formattable r-cran-generics r-cran-pkgdown r-cran-zeallot 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 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 libapache-pom-java libasound2 libasound2-data libatk1.0-0 libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libbrotli1 libbsd0 libcairo2 libcbor0.10 libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfido2-1 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libgatk-native-bindings-java libgdbm-compat4 libgdbm6 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgkl-java libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgoogle-gson-java libgraphite2-3 libgsl-dev libgsl27 libgslcblas0 libgssapi-krb5-2 libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhts3 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibverbs1 libice6 libicu72 libjbig0 libjoptsimple-java libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 liblightcouch-java libllvm17 liblog4j2-java libmbedcrypto7 libmbedtls14 libmbedx509-1 libmjson-java libmongodb-java libmunge2 libncbi-ngs3 libncbi-vdb3 libncurses6 libncursesw6 libnghttp2-14 libngs-java libngs-jni libnl-3-200 libnl-route-3-200 libnsl2 libnspr4 libnss3 libnuma1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenmpi3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.38 libpicard-java libpixman-1-0 libpmix2 libpng16-16 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librdmacm1 libreadline8 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsqlite3-0 libssh2-1 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3 libtk8.6 libucx0 libvulkan1 libwebp7 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml2 libxnvctrl0 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxxf86vm1 libz3-4 littler mafft mapdamage media-types ncbi-vdb-data netbase ocl-icd-libopencl1 openjdk-17-jre openjdk-17-jre-headless openmpi-bin openmpi-common openssh-client openssl paleomix perl perl-modules-5.38 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 python3.11 python3.11-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 sensible-utils seqtk shared-mime-info ucf unzip x11-common xdg-utils zip 0 upgraded, 296 newly installed, 0 to remove and 0 not upgraded. Need to get 257 MB of archives. After this operation, 976 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3 [2899 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.23-5+b1 [72.8 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.23-5+b1 [48.5 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libperl5.38 amd64 5.38.2-3 [4275 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3 [236 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.8-1 [817 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.0-1 [101 kB] Get:8 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.8-1 [2037 kB] Get:9 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.6-1 [26.2 kB] Get:10 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:11 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5+b1 [33.2 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5+b1 [80.0 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:16 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-5+b1 [333 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-5+b1 [135 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1 [10.7 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:21 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.2-3+b1 [167 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.1-1 [894 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.8-1 [1825 kB] Get:25 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.8-1 [597 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get:27 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get:28 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:29 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:30 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.1.5-1 [1241 kB] Get:31 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.11.8-1 [125 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libedit2 amd64 3.1-20230828-1 [93.1 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libcbor0.10 amd64 0.10.2-1.2 [28.2 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libfido2-1 amd64 1.14.0-1 [77.4 kB] Get:36 http://deb.debian.org/debian sid/main amd64 openssh-client amd64 1:9.6p1-3 [975 kB] Get:37 http://deb.debian.org/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:38 http://deb.debian.org/debian sid/main amd64 adapterremoval amd64 2.3.3-2 [191 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.78.4-1 [1452 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:43 http://deb.debian.org/debian sid/main amd64 shared-mime-info amd64 2.4-1 [751 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libpng16-16 amd64 1.6.42-1 [277 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.19-1 [41.4 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:48 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [108 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.4 [308 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-3+b1 [138 kB] Get:53 http://deb.debian.org/debian sid/main amd64 gtk-update-icon-cache amd64 3.24.41-1 [45.7 kB] Get:54 http://deb.debian.org/debian sid/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get:55 http://deb.debian.org/debian sid/main amd64 adwaita-icon-theme all 46~beta-4 [614 kB] Get:56 http://deb.debian.org/debian sid/main amd64 at-spi2-common all 2.50.0-1 [163 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.59.0-1 [74.3 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libpsl5 amd64 0.21.2-1+b1 [59.1 kB] Get:63 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libssh2-1 amd64 1.11.0-4 [215 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libcurl3-gnutls amd64 8.6.0-3 [421 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libhts3 amd64 1.19+ds-1 [447 kB] Get:68 http://deb.debian.org/debian sid/main amd64 bcftools amd64 1.19-1 [738 kB] Get:69 http://deb.debian.org/debian sid/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get:70 http://deb.debian.org/debian sid/main amd64 bowtie2 amd64 2.5.2-1 [1438 kB] Get:71 http://deb.debian.org/debian sid/main amd64 bwa amd64 0.7.17-7+b3 [212 kB] Get:72 http://deb.debian.org/debian sid/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:73 http://deb.debian.org/debian sid/main amd64 java-common all 0.75 [6640 B] Get:74 http://deb.debian.org/debian sid/main amd64 libavahi-common-data amd64 0.8-13+b1 [111 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libavahi-common3 amd64 0.8-13+b1 [43.3 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libdbus-1-3 amd64 1.14.10-4 [203 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libavahi-client3 amd64 0.8-13+b1 [47.1 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libcups2 amd64 2.4.7-1+b1 [247 kB] Get:79 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b1 [439 kB] Get:81 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:82 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:83 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1 [317 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1 [388 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libnss3 amd64 2:3.98-1 [1382 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libasound2-data all 1.2.10-3 [20.7 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libasound2 amd64 1.2.10-3 [368 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2 [2213 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libpcsclite1 amd64 2.0.1-1+b1 [51.1 kB] Get:92 http://deb.debian.org/debian sid/main amd64 openjdk-17-jre-headless amd64 17.0.10+7-1 [43.7 MB] Get:93 http://deb.debian.org/debian sid/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get:94 http://deb.debian.org/debian sid/main amd64 libgtk2.0-common all 2.24.33-3 [2659 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libatk1.0-0 amd64 2.50.0-1+b1 [50.1 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-1+b1 [531 kB] Get:107 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1 [462 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [215 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [47.3 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [35.1 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libgtk2.0-0 amd64 2.24.33-3 [1816 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libglvnd0 amd64 1.7.0-1 [51.3 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get:125 http://deb.debian.org/debian sid/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libglapi-mesa amd64 24.0.1-1 [36.1 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libx11-xcb1 amd64 2:1.8.7-1 [232 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get:134 http://deb.debian.org/debian sid/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:136 http://deb.debian.org/debian sid/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libvulkan1 amd64 1.3.275.0-1 [124 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libpciaccess0 amd64 0.17-3 [51.6 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get:143 http://deb.debian.org/debian sid/main amd64 libelf1 amd64 0.190-1+b1 [176 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libllvm17 amd64 1:17.0.6-5 [23.7 MB] Get:146 http://deb.debian.org/debian sid/main amd64 libsensors-config all 1:3.6.0-8 [14.4 kB] Get:147 http://deb.debian.org/debian sid/main amd64 libsensors5 amd64 1:3.6.0-8+b1 [34.7 kB] Get:148 http://deb.debian.org/debian sid/main amd64 libgl1-mesa-dri amd64 24.0.1-1 [8278 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libglx-mesa0 amd64 24.0.1-1 [151 kB] Get:150 http://deb.debian.org/debian sid/main amd64 libglx0 amd64 1.7.0-1 [34.7 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libgl1 amd64 1.7.0-1 [89.7 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libgif7 amd64 5.2.1-2.5+b1 [43.1 kB] Get:153 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23 [252 kB] Get:154 http://deb.debian.org/debian sid/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get:155 http://deb.debian.org/debian sid/main amd64 openjdk-17-jre amd64 17.0.10+7-1 [184 kB] Get:156 http://deb.debian.org/debian sid/main amd64 default-jre amd64 2:1.17-75 [1056 B] Get:157 http://deb.debian.org/debian sid/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get:158 http://deb.debian.org/debian sid/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get:159 http://deb.debian.org/debian sid/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libibverbs1 amd64 48.0-1.1 [61.2 kB] Get:162 http://deb.debian.org/debian sid/main amd64 ibverbs-providers amd64 48.0-1.1 [340 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14-20240201-3 [9292 B] Get:164 http://deb.debian.org/debian sid/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get:165 http://deb.debian.org/debian sid/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get:166 http://deb.debian.org/debian sid/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get:167 http://deb.debian.org/debian sid/main amd64 librdmacm1 amd64 48.0-1.1 [69.5 kB] Get:168 http://deb.debian.org/debian sid/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get:169 http://deb.debian.org/debian sid/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get:170 http://deb.debian.org/debian sid/main amd64 libmunge2 amd64 0.5.15-3+b1 [20.0 kB] Get:171 http://deb.debian.org/debian sid/main amd64 libxnvctrl0 amd64 525.147.05-1 [13.5 kB] Get:172 http://deb.debian.org/debian sid/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1 [39.7 kB] Get:173 http://deb.debian.org/debian sid/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB] Get:174 http://deb.debian.org/debian sid/main amd64 libpmix2 amd64 5.0.1-4+b1 [645 kB] Get:175 http://deb.debian.org/debian sid/main amd64 libucx0 amd64 1.16.0+ds-1 [968 kB] Get:176 http://deb.debian.org/debian sid/main amd64 libopenmpi3 amd64 4.1.6-5 [2427 kB] Get:177 http://deb.debian.org/debian sid/main amd64 openmpi-common all 4.1.6-5 [168 kB] Get:178 http://deb.debian.org/debian sid/main amd64 openmpi-bin amd64 4.1.6-5 [226 kB] Get:179 http://deb.debian.org/debian sid/main amd64 examl amd64 3.0.22-4 [954 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libapache-pom-java all 29-2 [5276 B] Get:181 http://deb.debian.org/debian sid/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:182 http://deb.debian.org/debian sid/main amd64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get:183 http://deb.debian.org/debian sid/main amd64 libfreemarker-java all 2.3.31-2 [1528 kB] Get:184 http://deb.debian.org/debian sid/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get:185 http://deb.debian.org/debian sid/main amd64 libjoptsimple-java all 5.0.4-4 [73.1 kB] Get:186 http://deb.debian.org/debian sid/main amd64 libcommons-codec-java all 1.16.0-1 [297 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get:188 http://deb.debian.org/debian sid/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get:189 http://deb.debian.org/debian sid/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get:190 http://deb.debian.org/debian sid/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get:191 http://deb.debian.org/debian sid/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get:192 http://deb.debian.org/debian sid/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get:193 http://deb.debian.org/debian sid/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get:194 http://deb.debian.org/debian sid/main amd64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] Get:195 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:196 http://deb.debian.org/debian sid/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB] Get:197 http://deb.debian.org/debian sid/main amd64 libcommons-io-java all 2.11.0-2 [319 kB] Get:198 http://deb.debian.org/debian sid/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get:199 http://deb.debian.org/debian sid/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get:200 http://deb.debian.org/debian sid/main amd64 libcurl4 amd64 8.6.0-3 [430 kB] Get:201 http://deb.debian.org/debian sid/main amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B] Get:202 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240201-3 [836 kB] Get:203 http://deb.debian.org/debian sid/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get:204 http://deb.debian.org/debian sid/main amd64 libmbedcrypto7 amd64 2.28.7-1 [280 kB] Get:205 http://deb.debian.org/debian sid/main amd64 libmbedx509-1 amd64 2.28.7-1 [130 kB] Get:206 http://deb.debian.org/debian sid/main amd64 libmbedtls14 amd64 2.28.7-1 [165 kB] Get:207 http://deb.debian.org/debian sid/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get:208 http://deb.debian.org/debian sid/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2 [1050 kB] Get:209 http://deb.debian.org/debian sid/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-6 [154 kB] Get:210 http://deb.debian.org/debian sid/main amd64 libngs-jni amd64 3.0.3+dfsg-6 [23.4 kB] Get:211 http://deb.debian.org/debian sid/main amd64 libngs-java amd64 3.0.3+dfsg-6 [110 kB] Get:212 http://deb.debian.org/debian sid/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get:213 http://deb.debian.org/debian sid/main amd64 libsnappy1v5 amd64 1.1.10-1+b1 [27.6 kB] Get:214 http://deb.debian.org/debian sid/main amd64 libsnappy-jni amd64 1.1.10.5-1 [6360 B] Get:215 http://deb.debian.org/debian sid/main amd64 libsnappy-java all 1.1.10.5-1 [87.4 kB] Get:216 http://deb.debian.org/debian sid/main amd64 libhtsjdk-java all 4.1.0+dfsg-1 [1833 kB] Get:217 http://deb.debian.org/debian sid/main amd64 libgkl-java all 0.8.11+dfsg-2 [24.7 kB] Get:218 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240201-3 [136 kB] Get:219 http://deb.debian.org/debian sid/main amd64 libgslcblas0 amd64 2.7.1+dfsg-6+b1 [107 kB] Get:220 http://deb.debian.org/debian sid/main amd64 libgsl27 amd64 2.7.1+dfsg-6+b1 [934 kB] Get:221 http://deb.debian.org/debian sid/main amd64 libgsl-dev amd64 2.7.1+dfsg-6+b1 [1146 kB] Get:222 http://deb.debian.org/debian sid/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:223 http://deb.debian.org/debian sid/main amd64 libopenblas0-pthread amd64 0.3.26+ds-1 [6807 kB] Get:224 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:225 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.4+20240113-1 [104 kB] Get:226 http://deb.debian.org/debian sid/main amd64 libopenblas0 amd64 0.3.26+ds-1 [37.5 kB] Get:227 http://deb.debian.org/debian sid/main amd64 libopenblas-pthread-dev amd64 0.3.26+ds-1 [4780 kB] Get:228 http://deb.debian.org/debian sid/main amd64 libopenblas-dev amd64 0.3.26+ds-1 [50.5 kB] Get:229 http://deb.debian.org/debian sid/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:230 http://deb.debian.org/debian sid/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:231 http://deb.debian.org/debian sid/main amd64 libpicard-java all 3.1.1+dfsg-1 [1743 kB] Get:232 http://deb.debian.org/debian sid/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:233 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2+b1 [1033 kB] Get:234 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:235 http://deb.debian.org/debian sid/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:236 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.13-2+b1 [783 kB] Get:237 http://deb.debian.org/debian sid/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:238 http://deb.debian.org/debian sid/main amd64 zip amd64 3.0-13 [230 kB] Get:239 http://deb.debian.org/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:240 http://deb.debian.org/debian sid/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:241 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.3.2-1 [26.8 MB] Get:242 http://deb.debian.org/debian sid/main amd64 r-cran-littler amd64 0.3.19-1 [99.8 kB] Get:243 http://deb.debian.org/debian sid/main amd64 littler all 0.3.19-1 [15.4 kB] Get:244 http://deb.debian.org/debian sid/main amd64 mafft amd64 7.505-1 [1078 kB] Get:245 http://deb.debian.org/debian sid/main amd64 r-cran-codetools all 0.2-19-1 [90.9 kB] Get:246 http://deb.debian.org/debian sid/main amd64 r-cran-iterators all 1.0.14-1 [337 kB] Get:247 http://deb.debian.org/debian sid/main amd64 r-cran-foreach all 1.5.2-1 [122 kB] Get:248 http://deb.debian.org/debian sid/main amd64 r-cran-gam amd64 1.22-3-1 [390 kB] Get:249 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.2-1 [1325 kB] Get:250 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:251 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.3-1 [1669 kB] Get:252 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:253 http://deb.debian.org/debian sid/main amd64 r-cran-gtable all 0.3.4+dfsg-1 [221 kB] Get:254 http://deb.debian.org/debian sid/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:255 http://deb.debian.org/debian sid/main amd64 r-cran-mass amd64 7.3-60.0.1-1 [1118 kB] Get:256 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-5-1 [1394 kB] Get:257 http://deb.debian.org/debian sid/main amd64 r-cran-nlme amd64 3.1.164-1 [2280 kB] Get:258 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.6-5-1 [3789 kB] Get:259 http://deb.debian.org/debian sid/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get:260 http://deb.debian.org/debian sid/main amd64 r-cran-farver amd64 2.1.1-1 [1404 kB] Get:261 http://deb.debian.org/debian sid/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:262 http://deb.debian.org/debian sid/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB] Get:263 http://deb.debian.org/debian sid/main amd64 r-cran-munsell all 0.5.0-2 [236 kB] Get:264 http://deb.debian.org/debian sid/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:265 http://deb.debian.org/debian sid/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:266 http://deb.debian.org/debian sid/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:267 http://deb.debian.org/debian sid/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:268 http://deb.debian.org/debian sid/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:269 http://deb.debian.org/debian sid/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:270 http://deb.debian.org/debian sid/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:271 http://deb.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:272 http://deb.debian.org/debian sid/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:273 http://deb.debian.org/debian sid/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:274 http://deb.debian.org/debian sid/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:275 http://deb.debian.org/debian sid/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get:276 http://deb.debian.org/debian sid/main amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3405 kB] Get:277 http://deb.debian.org/debian sid/main amd64 r-cran-inline all 0.3.19-2 [129 kB] Get:278 http://deb.debian.org/debian sid/main amd64 seqtk amd64 1.4-2 [34.6 kB] Get:279 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.22.0+ds-1+b1 [4110 kB] Get:280 http://deb.debian.org/debian sid/main amd64 r-cran-pkgkitten all 0.2.3-1 [26.7 kB] Get:281 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.12-1 [2071 kB] Get:282 http://deb.debian.org/debian sid/main amd64 r-cran-rcppgsl amd64 0.3.13-1 [203 kB] Get:283 http://deb.debian.org/debian sid/main amd64 mapdamage all 2.2.1+dfsg-3 [41.9 kB] Get:284 http://deb.debian.org/debian sid/main amd64 python3-monotonic all 1.6-2 [5728 B] Get:285 http://deb.debian.org/debian sid/main amd64 python3-humanfriendly all 10.0-3 [85.2 kB] Get:286 http://deb.debian.org/debian sid/main amd64 python3-coloredlogs all 15.0.1-1 [47.4 kB] Get:287 http://deb.debian.org/debian sid/main amd64 python3-configargparse all 1.7-1 [31.3 kB] Get:288 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml.clib amd64 0.2.8-1 [186 kB] Get:289 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml all 0.17.21-1 [103 kB] Get:290 http://deb.debian.org/debian sid/main amd64 python3-setproctitle amd64 1.3.3-1+b1 [19.5 kB] Get:291 http://deb.debian.org/debian sid/main amd64 phylip amd64 1:3.697+dfsg-3 [957 kB] Get:292 http://deb.debian.org/debian sid/main amd64 picard-tools all 3.1.1+dfsg-1 [311 kB] Get:293 http://deb.debian.org/debian sid/main amd64 radiant all 2.8.1+dfsg-2 [181 kB] Get:294 http://deb.debian.org/debian sid/main amd64 raxml amd64 8.2.13+dfsg-1 [1480 kB] Get:295 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.19.2-1 [645 kB] Get:296 http://deb.debian.org/debian sid/main amd64 paleomix amd64 1.3.8-1 [984 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 257 MB in 2s (136 MB/s) Selecting previously unselected package perl-modules-5.38. 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Setting up libicu72:amd64 (72.1-4+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up seqtk (1.4-2) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up libgatk-native-bindings-java (1.0.0+dfsg-2) ... Setting up java-common (0.75) ... Setting up libdatrie1:amd64 (0.2.13-3) ... Setting up libgslcblas0:amd64 (2.7.1+dfsg-6+b1) ... Setting up libcbor0.10:amd64 (0.10.2-1.2) ... Setting up libglib2.0-0:amd64 (2.78.4-1) ... No schema files found: doing nothing. Setting up bwa (0.7.17-7+b3) ... Setting up libglvnd0:amd64 (1.7.0-1) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up radiant (2.8.1+dfsg-2) ... Setting up libtirpc-common (1.3.4+ds-1) ... Setting up libmjson-java (1.4.0-3) ... Setting up unzip (6.0-28) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libsqlite3-0:amd64 (3.45.1-1) ... Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Setting up phylip (1:3.697+dfsg-3) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libsensors-config (1:3.6.0-8) ... Setting up libnghttp2-14:amd64 (1.59.0-1) ... Setting up libdeflate0:amd64 (1.19-1) ... Setting up libgsl27:amd64 (2.7.1+dfsg-6+b1) ... Setting up libgomp1:amd64 (14-20240201-3) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libsnappy1v5:amd64 (1.1.10-1+b1) ... Setting up libkrb5support0:amd64 (1.20.1-5+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Setting up libasound2-data (1.2.10-3) ... Setting up zip (3.0-13) ... Setting up librhino-java (1.7.14-2.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libmunge2:amd64 (0.5.15-3+b1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Setting up libmbedcrypto7:amd64 (2.28.7-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:amd64 (0.8-13+b1) ... Setting up libncurses6:amd64 (6.4+20240113-1) ... Setting up libdbus-1-3:amd64 (1.14.10-4) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up perl-modules-5.38 (5.38.2-3) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16:amd64 (1.6.42-1) ... Setting up libhwloc15:amd64 (2.10.0-1+b1) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libatomic1:amd64 (14-20240201-3) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2+b1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:amd64 (2.0.1-1+b1) ... Setting up libsensors5:amd64 (1:3.6.0-8+b1) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libncursesw6:amd64 (6.4+20240113-1) ... Setting up libk5crypto3:amd64 (1.20.1-5+b1) ... Setting up libglapi-mesa:amd64 (24.0.1-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Setting up libgfortran5:amd64 (14-20240201-3) ... Setting up libvulkan1:amd64 (1.3.275.0-1) ... Setting up libwebp7:amd64 (1.3.2-0.4) ... Setting up libgif7:amd64 (5.2.1-2.5+b1) ... Setting up libnuma1:amd64 (2.0.18-1) ... Setting up libfreemarker-java (2.3.31-2) ... Setting up sensible-utils (0.0.22) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up at-spi2-common (2.50.0-1) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libasound2:amd64 (1.2.10-3) ... Setting up libnl-3-200:amd64 (3.7.0-0.3) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up openmpi-common (4.1.6-5) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up libssh2-1:amd64 (1.11.0-4) ... Setting up netbase (6.4) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up libgtk2.0-common (2.24.33-3) ... Setting up libatk1.0-0:amd64 (2.50.0-1+b1) ... Setting up libkrb5-3:amd64 (1.20.1-5+b1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libhttpcore-java (4.4.16-1) ... Setting up libjoptsimple-java (5.0.4-4) ... Setting up libfido2-1:amd64 (1.14.0-1) ... Setting up openssl (3.1.5-1) ... Setting up libbsd0:amd64 (0.11.8-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libelf1:amd64 (0.190-1+b1) ... Setting up libsnappy-jni (1.1.10.5-1) ... Setting up readline-common (8.2-3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Setting up xdg-utils (1.1.3-4.1) ... 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 libgdbm6:amd64 (1.23-5+b1) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Setting up raxml (8.2.13+dfsg-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.12.0-3) ... 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 libxcb1:amd64 (1.15-1) ... Setting up libgsl-dev (2.7.1+dfsg-6+b1) ... Setting up libopenblas0-pthread:amd64 (0.3.26+ds-1) ... 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 libxcb-xfixes0:amd64 (1.15-1) ... Setting up libmbedx509-1:amd64 (2.28.7-1) ... Setting up libmbedtls14:amd64 (2.28.7-1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.15.0-1) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libedit2:amd64 (3.1-20230828-1) ... Setting up libreadline8:amd64 (8.2-3+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-13+b1) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libnss3:amd64 (2:3.98-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up shared-mime-info (2.4-1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5+b1) ... Setting up libgdbm-compat4:amd64 (1.23-5+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up libopenblas0:amd64 (0.3.26+ds-1) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libcurl4:amd64 (8.6.0-3) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b1) ... Setting up libsnappy-java (1.1.10.5-1) ... Setting up libfontconfig1:amd64 (2.15.0-1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-codec-java (1.16.0-1) ... Setting up libllvm17:amd64 (1:17.0.6-5) ... Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libavahi-client3:amd64 (0.8-13+b1) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libopenblas-pthread-dev:amd64 (0.3.26+ds-1) ... 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 libncbi-ngs3:amd64 (3.0.3+dfsg-6) ... Setting up libtirpc3:amd64 (1.3.4+ds-1) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libpaper1:amd64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up gtk-update-icon-cache (3.24.41-1) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1) ... Setting up libibverbs1:amd64 (48.0-1.1) ... Setting up fontconfig (2.15.0-1) ... Regenerating fonts cache... done. Setting up libngs-jni:amd64 (3.0.3+dfsg-6) ... Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up ibverbs-providers:amd64 (48.0-1.1) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up openssh-client (1:9.6p1-3) ... Setting up libpango-1.0-0:amd64 (1.51.0+ds-4) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (24.0.1-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libperl5.38:amd64 (5.38.2-3) ... Setting up libcurl3-gnutls:amd64 (8.6.0-3) ... Setting up libpaper-utils (1.1.29) ... Setting up libcairo2:amd64 (1.18.0-1+b1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libxnvctrl0:amd64 (525.147.05-1) ... Setting up libopenblas-dev:amd64 (0.3.26+ds-1) ... Setting up perl (5.38.2-3) ... Setting up adwaita-icon-theme (46~beta-4) ... 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 libxfixes3:amd64 (1:6.0.0-2) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ... Setting up libxt6:amd64 (1:1.2.1-1.1) ... Setting up libcups2:amd64 (2.4.7-1+b1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libngs-java:amd64 (3.0.3+dfsg-6) ... Setting up libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... Setting up libhtsjdk-java (4.1.0+dfsg-1) ... Setting up libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... Setting up librdmacm1:amd64 (48.0-1.1) ... Setting up libucx0:amd64 (1.16.0+ds-1) ... Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libhts3:amd64 (1.19+ds-1) ... Setting up libglx-mesa0:amd64 (24.0.1-1) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up libglx0:amd64 (1.7.0-1) ... Setting up mafft (7.505-1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.8-1) ... Setting up libtk8.6:amd64 (8.6.13-2+b1) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up bcftools (1.19-1) ... Setting up libhwloc-plugins:amd64 (2.10.0-1+b1) ... Setting up samtools (1.19.2-1) ... Setting up libgl1:amd64 (1.7.0-1) ... Setting up r-base-core (4.3.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-5-1) ... Setting up r-cran-nlme (3.1.164-1) ... Setting up r-cran-farver (2.1.1-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up r-cran-viridislite (0.4.2-2) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.3-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up libbarclay-java (5.0.0+dfsg-1) ... Setting up libpython3-stdlib:amd64 (3.11.6-1) ... Setting up r-cran-littler (0.3.19-1) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up r-cran-rcpp (1.0.12-1) ... Setting up r-cran-codetools (0.2-19-1) ... Setting up python3.11 (3.11.8-1) ... Setting up r-cran-inline (0.3.19-2) ... Setting up r-cran-rlang (1.1.3-1) ... Setting up littler (0.3.19-1) ... Setting up libpmix2:amd64 (5.0.1-4+b1) ... Setting up r-cran-withr (3.0.0+dfsg-1) ... Setting up libgkl-java (0.8.11+dfsg-2) ... Setting up r-cran-iterators (1.0.14-1) ... Setting up libgtk2.0-0:amd64 (2.24.33-3) ... Setting up libopenmpi3:amd64 (4.1.6-5) ... Setting up r-cran-foreach (1.5.2-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-mass (7.3-60.0.1-1) ... Setting up python3 (3.11.6-1) ... Setting up r-cran-glue (1.7.0-1) ... Setting up r-cran-gam (1.22-3-1) ... Setting up r-cran-cli (3.6.2-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up bowtie2 (2.5.2-1) ... Setting up python3-monotonic (1.6-2) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up libpicard-java (3.1.1+dfsg-1) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-colorspace (2.1-0+dfsg-1) ... Setting up python3-humanfriendly (10.0-3) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-gtable (0.3.4+dfsg-1) ... Setting up python3-setproctitle:amd64 (1.3.3-1+b1) ... Setting up r-cran-matrix (1.6-5-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up python3-coloredlogs (15.0.1-1) ... Setting up r-cran-rcppgsl (0.3.13-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up openmpi-bin (4.1.6-5) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up python3-configargparse (1.7-1) ... Setting up python3-pysam (0.22.0+ds-1+b1) ... Setting up python3-ruamel.yaml.clib:amd64 (0.2.8-1) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up examl (3.0.22-4) ... Setting up r-cran-scales (1.3.0-1) ... Setting up python3-ruamel.yaml (0.17.21-1) ... Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... Setting up mapdamage (2.2.1+dfsg-3) ... Processing triggers for libc-bin (2.37-15) ... 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: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: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:Security_Communication_Root_CA.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_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.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 default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:amd64 (17.0.10+7-1) ... Setting up default-jre (2:1.17-75) ... Setting up picard-tools (3.1.1+dfsg-1) ... Setting up paleomix (1.3.8-1) ... Processing triggers for ca-certificates (20240203) ... 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. 0m59.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-get', '-y', 'install', 'paleomix=1.3.8-1'] 0m59.7s INFO: Running scripts post_install 0m59.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_install_exceptions'] 0m59.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_install_exceptions'] 0m59.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_install_log_alternatives'] 0m59.7s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=python3: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --auto /usr/bin/python3 LOG-ALTERNATIVES: dpkg=libblas3: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 LOG-ALTERNATIVES: dpkg=libpsm-infinipath1: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 libpsm_infinipath.so.1 /usr/lib/libpsm1/libpsm_infinipath.so.1.16 40 LOG-ALTERNATIVES: dpkg=xdg-utils: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/bin/open open /usr/bin/xdg-open 50 --slave /usr/share/man/man1/open.1.gz open.1.gz /usr/share/man/man1/xdg-open.1.gz LOG-ALTERNATIVES: dpkg=liblapack3: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 LOG-ALTERNATIVES: dpkg=libopenblas0-pthread: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 100 LOG-ALTERNATIVES: dpkg=libopenblas0-pthread: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 100 LOG-ALTERNATIVES: dpkg=libopenblas0-pthread: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libopenblas.so.0 libopenblas.so.0-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 100 LOG-ALTERNATIVES: dpkg=libopenblas-pthread-dev: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so libblas.so-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so 100 --slave /usr/lib/x86_64-linux-gnu/libblas.a libblas.a-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.a --slave /usr/include/x86_64-linux-gnu/cblas.h cblas.h-x86_64-linux-gnu /usr/include/x86_64-linux-gnu/openblas-pthread/cblas.h --slave /usr/lib/x86_64-linux-gnu/pkgconfig/blas.pc blas.pc-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/pkgconfig/blas-openblas.pc LOG-ALTERNATIVES: dpkg=libopenblas-pthread-dev: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so liblapack.so-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so 100 --slave /usr/lib/x86_64-linux-gnu/liblapack.a liblapack.a-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.a --slave /usr/lib/x86_64-linux-gnu/pkgconfig/lapack.pc lapack.pc-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/pkgconfig/lapack-openblas.pc LOG-ALTERNATIVES: dpkg=libopenblas-pthread-dev: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libopenblas.so libopenblas.so-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so 100 --slave /usr/lib/x86_64-linux-gnu/libopenblas.a libopenblas.a-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.a --slave /usr/include/x86_64-linux-gnu/cblas-openblas.h cblas-openblas.h-x86_64-linux-gnu /usr/include/x86_64-linux-gnu/openblas-pthread/cblas.h --slave /usr/include/x86_64-linux-gnu/f77blas.h f77blas.h-x86_64-linux-gnu /usr/include/x86_64-linux-gnu/openblas-pthread/f77blas.h --slave /usr/include/x86_64-linux-gnu/openblas_config.h openblas_config.h-x86_64-linux-gnu /usr/include/x86_64-linux-gnu/openblas-pthread/openblas_config.h --slave /usr/lib/x86_64-linux-gnu/pkgconfig/openblas.pc openblas.pc-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/pkgconfig/openblas.pc --slave /usr/lib/x86_64-linux-gnu/cmake/openblas/OpenBLASConfig.cmake OpenBLASConfig.cmake-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/cmake/openblas/OpenBLASConfig.cmake --slave /usr/lib/x86_64-linux-gnu/cmake/openblas/OpenBLASConfigVersion.cmake OpenBLASConfigVersion.cmake-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/cmake/openblas/OpenBLASConfigVersion.cmake LOG-ALTERNATIVES: dpkg=perl: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --remove rename /usr/bin/prename LOG-ALTERNATIVES: dpkg=adwaita-icon-theme: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/share/icons/default/index.theme x-cursor-theme /usr/share/icons/Adwaita/cursor.theme 90 LOG-ALTERNATIVES: dpkg=openjdk-17-jre-headless: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/bin/java java /usr/lib/jvm/java-17-openjdk-amd64/bin/java 1711 --slave /usr/share/man/man1/java.1.gz java.1.gz /usr/lib/jvm/java-17-openjdk-amd64/man/man1/java.1.gz LOG-ALTERNATIVES: dpkg=openjdk-17-jre-headless: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/bin/jpackage jpackage /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage 1711 --slave /usr/share/man/man1/jpackage.1.gz jpackage.1.gz /usr/lib/jvm/java-17-openjdk-amd64/man/man1/jpackage.1.gz LOG-ALTERNATIVES: dpkg=openjdk-17-jre-headless: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/bin/keytool keytool /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool 1711 --slave /usr/share/man/man1/keytool.1.gz keytool.1.gz /usr/lib/jvm/java-17-openjdk-amd64/man/man1/keytool.1.gz LOG-ALTERNATIVES: dpkg=openjdk-17-jre-headless: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/bin/rmiregistry rmiregistry /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry 1711 --slave /usr/share/man/man1/rmiregistry.1.gz rmiregistry.1.gz /usr/lib/jvm/java-17-openjdk-amd64/man/man1/rmiregistry.1.gz LOG-ALTERNATIVES: dpkg=openjdk-17-jre-headless: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/bin/jexec jexec /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec 1711 --slave /usr/share/binfmts/jar jexec-binfmt /usr/lib/jvm/java-17-openjdk-amd64/lib/jar.binfmt LOG-ALTERNATIVES: dpkg=openmpi-bin: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/bin/mpirun mpirun /usr/bin/mpirun.openmpi 50 --slave /usr/share/man/man1/mpirun.1.gz mpirun.1.gz /usr/share/man/man1/mpirun.openmpi.1.gz --slave /usr/bin/mpiexec mpiexec /usr/bin/mpiexec.openmpi --slave /usr/share/man/man1/mpiexec.1.gz mpiexec.1.gz /usr/share/man/man1/mpiexec.openmpi.1.gz LOG-ALTERNATIVES: dpkg=openmpi-bin: piuparts=paleomix=1.3.8-1: /usr/bin/update-alternatives --install /usr/bin/mpicc mpi /usr/bin/mpicc.openmpi 50 --slave /usr/bin/mpic++ mpic++ /usr/bin/mpic++.openmpi --slave /usr/bin/mpicxx mpicxx /usr/bin/mpic++.openmpi --slave /usr/bin/mpiCC mpiCC /usr/bin/mpic++.openmpi --slave /usr/bin/mpif77 mpif77 /usr/bin/mpif77.openmpi --slave /usr/bin/mpif90 mpif90 /usr/bin/mpif90.openmpi --slave /usr/bin/mpifort mpifort /usr/bin/mpifort.openmpi --slave /usr/share/man/man1/mpicc.1.gz mpicc.1.gz /usr/share/man/man1/mpicc.openmpi.1.gz --slave /usr/share/man/man1/mpic++.1.gz mpic++.1.gz /usr/share/man/man1/mpic++.openmpi.1.gz --slave /usr/share/man/man1/mpicxx.1.gz mpicxx.1.gz /usr/share/man/man1/mpicxx.openmpi.1.gz --slave /usr/share/man/man1/mpiCC.1.gz mpiCC.1.gz /usr/share/man/man1/mpiCC.openmpi.1.gz --slave /usr/share/man/man1/mpif77.1.gz mpif77.1.gz /usr/share/man/man1/mpif77.openmpi.1.gz --slave /usr/share/man/man1/mpif90.1.gz mpif90.1.gz /usr/share/man/man1/mpif90.openmpi.1.gz --slave /usr/share/man/man1/mpifort.1.gz mpifort.1.gz /usr/share/man/man1/mpifort.openmpi.1.gz 0m59.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_install_log_alternatives'] 0m59.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n'] 1m1.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n'] 1m3.6s ERROR: WARN: Broken symlinks: /usr/lib/jvm/java-17-openjdk-amd64/lib/libatk-wrapper.so -> ../../../x86_64-linux-gnu/jni/libatk-wrapper.so (openjdk-17-jre:amd64) 1m3.7s INFO: /bin converted to /usr/bin by /usr merge 1m3.7s INFO: /lib converted to /usr/lib by /usr merge 1m3.7s INFO: /lib/init converted to /usr/lib/init by /usr merge 1m3.7s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 1m3.7s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 1m3.7s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 1m3.7s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 1m3.7s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 1m3.7s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 1m3.7s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 1m3.7s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 1m3.7s INFO: /lib64 converted to /usr/lib64 by /usr merge 1m3.7s INFO: /sbin converted to /usr/sbin by /usr merge 1m4.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', '-ac', '--ignore-obsolete'] 1m9.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', '-ac', '--ignore-obsolete'] 1m9.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m9.6s DUMP: 0.15.6 1m9.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m9.6s INFO: Running adequate version 0.15.6 now. 1m9.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'paleomix'] 1m9.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'paleomix'] 1m9.7s INFO: Running scripts pre_remove 1m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m17.0s DUMP: UNOWNED SYMLINK /usr/lib/x86_64-linux-gnu/libmpi_usempi_ignore_tkr-gfortranso.40 -> libmpi_usempi_ignore_tkr-gfortran.so.40.30.0 1m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_remove_exceptions'] 1m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/pre_remove_exceptions'] 1m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m17.3s DUMP: install ok installed adapterremoval adapterremoval 2.3.3-2 install ok installed adduser adduser 3.137 install ok installed adwaita-icon-theme adwaita-icon-theme 46~beta-4 install ok installed apt apt 2.7.12 install ok installed at-spi2-common at-spi2-common 2.50.0-1 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bcftools bcftools 1.19-1 install ok installed bedtools bedtools 2.31.1+dfsg-2 install ok installed bowtie2 bowtie2 2.5.2-1 install ok installed bsdutils bsdutils 1:2.39.3-6 install ok installed bwa bwa 0.7.17-7+b3 install ok installed ca-certificates ca-certificates 20240203 install ok installed ca-certificates-java ca-certificates-java 20240118 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.16 install ok installed default-jre default-jre 2:1.17-75 install ok installed default-jre-headless default-jre-headless 2:1.17-75 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.4 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed examl examl 3.0.22-4 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig fontconfig 2.15.0-1 install ok installed fontconfig-config fontconfig-config 2.15.0-1 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 14-20240201-3 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gtk-update-icon-cache gtk-update-icon-cache 3.24.41-1 install ok installed gzip gzip 1.12-1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.17-2 install ok installed hostname hostname 3.23+nmu2 install ok installed ibverbs-providers:amd64 ibverbs-providers 48.0-1.1 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed java-common java-common 0.75 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapache-pom-java libapache-pom-java 29-2 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.12 install ok installed libasound2:amd64 libasound2 1.2.10-3 install ok installed libasound2-data libasound2-data 1.2.10-3 install ok installed libatk1.0-0:amd64 libatk1.0-0 2.50.0-1+b1 install ok installed libatomic1:amd64 libatomic1 14-20240201-3 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-13+b1 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-13+b1 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-13+b1 install ok installed libbarclay-java libbarclay-java 5.0.0+dfsg-1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.39.3-6 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.11.8-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-15 install ok installed libc6:amd64 libc6 2.37-15 install ok installed libcairo2:amd64 libcairo2 1.18.0-1+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcbor0.10:amd64 libcbor0.10 0.10.2-1.2 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcommons-codec-java libcommons-codec-java 1.16.0-1 install ok installed libcommons-compress-java libcommons-compress-java 1.25.0-1 install ok installed libcommons-io-java libcommons-io-java 2.11.0-2 install ok installed libcommons-jexl2-java libcommons-jexl2-java 2.1.1-6 install ok installed libcommons-lang3-java libcommons-lang3-java 3.14.0-1 install ok installed libcommons-logging-java libcommons-logging-java 1.3.0-1 install ok installed libcommons-math3-java libcommons-math3-java 3.6.1-3 install ok installed libcommons-parent-java libcommons-parent-java 56-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcups2:amd64 libcups2 2.4.7-1+b1 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 8.6.0-3 install ok installed libcurl4:amd64 libcurl4 8.6.0-3 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4+b1 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.14.10-4 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b1 install ok installed libdeflate0:amd64 libdeflate0 1.19-1 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.120-2 install ok installed libdrm-common libdrm-common 2.4.120-2 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.120-2 install ok installed libdrm-nouveau2:amd64 libdrm-nouveau2 2.4.120-2 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.120-2 install ok installed libdrm2:amd64 libdrm2 2.4.120-2 install ok installed libedit2:amd64 libedit2 3.1-20230828-1 install ok installed libelf1:amd64 libelf1 0.190-1+b1 install ok installed libevent-core-2.1-7:amd64 libevent-core-2.1-7 2.1.12-stable-8 install ok installed libevent-pthreads-2.1-7:amd64 libevent-pthreads-2.1-7 2.1.12-stable-8 install ok installed libexpat1:amd64 libexpat1 2.6.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libfabric1:amd64 libfabric1 1.17.0-3 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfido2-1:amd64 libfido2-1 1.14.0-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1 install ok installed libfreemarker-java libfreemarker-java 2.3.31-2 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b1 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libgatk-native-bindings-java libgatk-native-bindings-java 1.0.0+dfsg-2 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240201-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-5+b1 install ok installed libgdbm6:amd64 libgdbm6 1.23-5+b1 install ok installed libgdk-pixbuf-2.0-0:amd64 libgdk-pixbuf-2.0-0 2.42.10+dfsg-3+b1 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.42.10+dfsg-3 install ok installed libgfortran5:amd64 libgfortran5 14-20240201-3 install ok installed libgif7:amd64 libgif7 5.2.1-2.5+b1 install ok installed libgkl-java libgkl-java 0.8.11+dfsg-2 install ok installed libgl1:amd64 libgl1 1.7.0-1 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 24.0.1-1 install ok installed libglapi-mesa:amd64 libglapi-mesa 24.0.1-1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.78.4-1 install ok installed libglvnd0:amd64 libglvnd0 1.7.0-1 install ok installed libglx-mesa0:amd64 libglx-mesa0 24.0.1-1 install ok installed libglx0:amd64 libglx0 1.7.0-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30:amd64 libgnutls30 3.8.3-1 install ok installed libgomp1:amd64 libgomp1 14-20240201-3 install ok installed libgoogle-gson-java libgoogle-gson-java 2.10.1-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgsl-dev libgsl-dev 2.7.1+dfsg-6+b1 install ok installed libgsl27:amd64 libgsl27 2.7.1+dfsg-6+b1 install ok installed libgslcblas0:amd64 libgslcblas0 2.7.1+dfsg-6+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5+b1 install ok installed libgtk2.0-0:amd64 libgtk2.0-0 2.24.33-3 install ok installed libgtk2.0-common libgtk2.0-common 2.24.33-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2+b1 install ok installed libhts3:amd64 libhts3 1.19+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.0-1+b1 install ok installed libhtsjdk-java libhtsjdk-java 4.1.0+dfsg-1 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 2.10.0-1+b1 install ok installed libhwloc15:amd64 libhwloc15 2.10.0-1+b1 install ok installed libibverbs1:amd64 libibverbs1 48.0-1.1 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu72:amd64 libicu72 72.1-4+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjoptsimple-java libjoptsimple-java 5.0.4-4 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-5+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-5+b1 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2+b1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5+b3 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed liblightcouch-java liblightcouch-java 0.2.0-1 install ok installed libllvm17:amd64 libllvm17 1:17.0.6-5 install ok installed liblog4j2-java liblog4j2-java 2.19.0-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.4.5-0.3 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.7-1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.7-1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.7-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmjson-java libmjson-java 1.4.0-3 install ok installed libmongodb-java libmongodb-java 3.6.3-2 install ok installed libmount1:amd64 libmount1 2.39.3-6 install ok installed libmunge2:amd64 libmunge2 0.5.15-3+b1 install ok installed libncbi-ngs3:amd64 libncbi-ngs3 3.0.3+dfsg-6 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.0.2+dfsg-2 install ok installed libncurses6:amd64 libncurses6 6.4+20240113-1 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.59.0-1 install ok installed libngs-java:amd64 libngs-java 3.0.3+dfsg-6 install ok installed libngs-jni:amd64 libngs-jni 3.0.3+dfsg-6 install ok installed libnl-3-200:amd64 libnl-3-200 3.7.0-0.3 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.7.0-0.3 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libnspr4:amd64 libnspr4 2:4.35-1.1+b1 install ok installed libnss3:amd64 libnss3 2:3.98-1 install ok installed libnuma1:amd64 libnuma1 2.0.18-1 install ok installed libopenblas-dev:amd64 libopenblas-dev 0.3.26+ds-1 install ok installed libopenblas-pthread-dev:amd64 libopenblas-pthread-dev 0.3.26+ds-1 install ok installed libopenblas0:amd64 libopenblas0 0.3.26+ds-1 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.26+ds-1 install ok installed libopenmpi3:amd64 libopenmpi3 4.1.6-5 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1+b1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1+b1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.51.0+ds-4 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.51.0+ds-4 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.51.0+ds-4 install ok installed libpaper-utils libpaper-utils 1.1.29 install ok installed libpaper1:amd64 libpaper1 1.1.29 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpcsclite1:amd64 libpcsclite1 2.0.1-1+b1 install ok installed libperl5.38:amd64 libperl5.38 5.38.2-3 install ok installed libpicard-java libpicard-java 3.1.1+dfsg-1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpmix2:amd64 libpmix2 5.0.1-4+b1 install ok installed libpng16-16:amd64 libpng16-16 1.6.42-1 install ok installed libpsl5:amd64 libpsl5 0.21.2-1+b1 install ok installed libpsm-infinipath1 libpsm-infinipath1 3.3+20.604758e7-6.3 install ok installed libpsm2-2 libpsm2-2 11.2.185-2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.6-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.8-1 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.8-1 install ok installed librdmacm1:amd64 librdmacm1 48.0-1.1 install ok installed libreadline8:amd64 libreadline8 8.2-3+b1 install ok installed librhino-java librhino-java 1.7.14-2.1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-4+b1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsensors-config libsensors-config 1:3.6.0-8 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-8+b1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.4 install ok installed libslf4j-java libslf4j-java 1.7.32-1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-6 install ok installed libsnappy-java libsnappy-java 1.1.10.5-1 install ok installed libsnappy-jni libsnappy-jni 1.1.10.5-1 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.1.10-1+b1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.1-1 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssh2-1:amd64 libssh2-1 1.11.0-4 install ok installed libssl3:amd64 libssl3 3.1.5-1 install ok installed libstdc++6:amd64 libstdc++6 14-20240201-3 install ok installed libsystemd0:amd64 libsystemd0 255.3-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.13+dfsg-2+b1 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.4+ds-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.13-2+b1 install ok installed libucx0:amd64 libucx0 1.16.0+ds-1 install ok installed libudev1:amd64 libudev1 255.3-2 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-6 install ok installed libvulkan1:amd64 libvulkan1 1.3.275.0-1 install ok installed libwebp7:amd64 libwebp7 1.3.2-0.4 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-dri2-0:amd64 libxcb-dri2-0 1.15-1 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.15-1 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.15-1 install ok installed libxcb-present0:amd64 libxcb-present0 1.15-1 install ok installed libxcb-randr0:amd64 libxcb-randr0 1.15-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb-sync1:amd64 libxcb-sync1 1.15-1 install ok installed libxcb-xfixes0:amd64 libxcb-xfixes0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxcomposite1:amd64 libxcomposite1 1:0.4.5-1 install ok installed libxcursor1:amd64 libxcursor1 1:1.2.1-1 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.6-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxfixes3:amd64 libxfixes3 1:6.0.0-2 install ok installed libxft2:amd64 libxft2 2.3.6-1+b1 install ok installed libxi6:amd64 libxi6 2:1.8.1-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3+b2 install ok installed libxnvctrl0:amd64 libxnvctrl0 525.147.05-1 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.2-2+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxshmfence1:amd64 libxshmfence1 1.3-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6:amd64 libxt6 1:1.2.1-1.1 install ok installed libxtst6:amd64 libxtst6 2:1.2.3-1.1 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libz3-4:amd64 libz3-4 4.8.12-3.1+b2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed littler littler 0.3.19-1 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2+b1 install ok installed mafft mafft 7.505-1 install ok installed mapdamage mapdamage 2.2.1+dfsg-3 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.39.3-6 install ok installed ncbi-vdb-data ncbi-vdb-data 3.0.2+dfsg-2 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.3.2-1 install ok installed openjdk-17-jre:amd64 openjdk-17-jre 17.0.10+7-1 install ok installed openjdk-17-jre-headless:amd64 openjdk-17-jre-headless 17.0.10+7-1 install ok installed openmpi-bin openmpi-bin 4.1.6-5 install ok installed openmpi-common openmpi-common 4.1.6-5 install ok installed openssh-client openssh-client 1:9.6p1-3 install ok installed openssl openssl 3.1.5-1 install ok installed paleomix paleomix 1.3.8-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl perl 5.38.2-3 install ok installed perl-base perl-base 5.38.2-3 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3 install ok installed phylip phylip 1:3.697+dfsg-3 install ok installed picard-tools picard-tools 3.1.1+dfsg-1 install ok installed python3 python3 3.11.6-1 install ok installed python3-coloredlogs python3-coloredlogs 15.0.1-1 install ok installed python3-configargparse python3-configargparse 1.7-1 install ok installed python3-humanfriendly python3-humanfriendly 10.0-3 install ok installed python3-minimal python3-minimal 3.11.6-1 install ok installed python3-monotonic python3-monotonic 1.6-2 install ok installed python3-pysam python3-pysam 0.22.0+ds-1+b1 install ok installed python3-ruamel.yaml python3-ruamel.yaml 0.17.21-1 install ok installed python3-ruamel.yaml.clib:amd64 python3-ruamel.yaml.clib 0.2.8-1 install ok installed python3-setproctitle:amd64 python3-setproctitle 1.3.3-1+b1 install ok installed python3.11 python3.11 3.11.8-1 install ok installed python3.11-minimal python3.11-minimal 3.11.8-1 install ok installed r-base-core r-base-core 4.3.2-1 install ok installed r-cran-cli r-cran-cli 3.6.2-1 install ok installed r-cran-codetools r-cran-codetools 0.2-19-1 install ok installed r-cran-colorspace r-cran-colorspace 2.1-0+dfsg-1 install ok installed r-cran-fansi r-cran-fansi 1.0.5-1 install ok installed r-cran-farver r-cran-farver 2.1.1-1 install ok installed r-cran-foreach r-cran-foreach 1.5.2-1 install ok installed r-cran-gam r-cran-gam 1.22-3-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.4.4+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.7.0-1 install ok installed r-cran-gtable r-cran-gtable 0.3.4+dfsg-1 install ok installed r-cran-inline r-cran-inline 0.3.19-2 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 0.22-5-1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.19-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-mass r-cran-mass 7.3-60.0.1-1 install ok installed r-cran-matrix r-cran-matrix 1.6-5-1 install ok installed r-cran-mgcv r-cran-mgcv 1.9-1-1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-2 install ok installed r-cran-nlme r-cran-nlme 3.1.164-1 install ok installed r-cran-pillar r-cran-pillar 1.9.0+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.3-1 install ok installed r-cran-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-3-1 install ok installed r-cran-rcpp r-cran-rcpp 1.0.12-1 install ok installed r-cran-rcppgsl r-cran-rcppgsl 0.3.13-1 install ok installed r-cran-rlang r-cran-rlang 1.1.3-1 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-2 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 3.0.0+dfsg-1 install ok installed radiant radiant 2.8.1+dfsg-2 install ok installed raxml raxml 8.2.13+dfsg-1 install ok installed readline-common readline-common 8.2-3 install ok installed samtools samtools 1.19.2-1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.22 install ok installed seqtk seqtk 1.4-2 install ok installed shared-mime-info shared-mime-info 2.4-1 install ok installed sysvinit-utils sysvinit-utils 3.08-6 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-1 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.39.3-6 install ok installed x11-common x11-common 1:7.7+23 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3+b1 1m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-get', 'remove', 'adapterremoval', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'bcftools', 'bedtools', 'bowtie2', 'bwa', 'ca-certificates', 'ca-certificates-java', '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', 'libapache-pom-java', 'libasound2:amd64', 'libasound2-data', 'libatk1.0-0:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcbor0.10:amd64', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libfontconfig1:amd64', 'libfreemarker-java', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgatk-native-bindings-java', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgkl-java', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjoptsimple-java', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblightcouch-java', 'libllvm17:amd64', 'liblog4j2-java', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmongodb-java', 'libmunge2:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenmpi3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.38:amd64', 'libpicard-java', 'libpixman-1-0:amd64', 'libpmix2:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'librdmacm1:amd64', 'libreadline8: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', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libucx0:amd64', 'libvulkan1:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0: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', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'ncbi-vdb-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'perl', 'perl-modules-5.38', 'phylip', 'picard-tools', 'python3', 'python3-coloredlogs', 'python3-configargparse', 'python3-humanfriendly', 'python3-minimal', 'python3-monotonic', 'python3-pysam', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib:amd64', 'python3-setproctitle:amd64', 'python3.11', 'python3.11-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', 'sensible-utils', 'seqtk', 'shared-mime-info', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'paleomix'] 1m21.7s 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 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 libapache-pom-java libasound2 libasound2-data libatk1.0-0 libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libbrotli1 libbsd0 libcairo2 libcbor0.10 libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfido2-1 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libgatk-native-bindings-java libgdbm-compat4 libgdbm6 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgkl-java libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgoogle-gson-java libgraphite2-3 libgsl-dev libgsl27 libgslcblas0 libgssapi-krb5-2 libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhts3 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibverbs1 libice6 libicu72 libjbig0 libjoptsimple-java libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 liblightcouch-java libllvm17 liblog4j2-java libmbedcrypto7 libmbedtls14 libmbedx509-1 libmjson-java libmongodb-java libmunge2 libncbi-ngs3 libncbi-vdb3 libncurses6 libncursesw6 libnghttp2-14 libngs-java libngs-jni libnl-3-200 libnl-route-3-200 libnsl2 libnspr4 libnss3 libnuma1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenmpi3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.38 libpicard-java libpixman-1-0 libpmix2 libpng16-16 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librdmacm1 libreadline8 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsqlite3-0 libssh2-1 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3 libtk8.6 libucx0 libvulkan1 libwebp7 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml2 libxnvctrl0 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxxf86vm1 libz3-4 littler mafft mapdamage media-types ncbi-vdb-data netbase ocl-icd-libopencl1 openjdk-17-jre openjdk-17-jre-headless openmpi-bin openmpi-common openssh-client openssl paleomix perl perl-modules-5.38 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 python3.11 python3.11-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 sensible-utils seqtk shared-mime-info ucf unzip x11-common xdg-utils zip 0 upgraded, 0 newly installed, 296 to remove and 0 not upgraded. After this operation, 976 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 ... 21474 files and directories currently installed.) Removing paleomix (1.3.8-1) ... Removing adapterremoval (2.3.3-2) ... Removing examl (3.0.22-4) ... Removing openmpi-bin (4.1.6-5) ... Removing libopenmpi3:amd64 (4.1.6-5) ... Removing libucx0:amd64 (1.16.0+ds-1) ... Removing libfabric1:amd64 (1.17.0-3) ... Removing librdmacm1:amd64 (48.0-1.1) ... Removing openssh-client (1:9.6p1-3) ... Removing picard-tools (3.1.1+dfsg-1) ... Removing default-jre (2:1.17-75) ... Removing openjdk-17-jre:amd64 (17.0.10+7-1) ... Removing libgtk2.0-0:amd64 (2.24.33-3) ... Removing adwaita-icon-theme (46~beta-4) ... Removing libatk1.0-0:amd64 (2.50.0-1+b1) ... Removing at-spi2-common (2.50.0-1) ... Removing bcftools (1.19-1) ... Removing bedtools (2.31.1+dfsg-2) ... Removing bowtie2 (2.5.2-1) ... Removing bwa (0.7.17-7+b3) ... Removing mapdamage (2.2.1+dfsg-3) ... Removing r-cran-ggplot2 (3.4.4+dfsg-1) ... Removing r-cran-scales (1.3.0-1) ... Removing r-cran-rcolorbrewer (1.1-3-1) ... Removing r-cran-mgcv (1.9-1-1) ... Removing r-cran-matrix (1.6-5-1) ... Removing r-cran-viridislite (0.4.2-2) ... Removing r-cran-rcppgsl (0.3.13-1) ... Removing r-cran-rcpp (1.0.12-1) ... Removing default-jre-headless (2:1.17-75) ... Removing openjdk-17-jre-headless:amd64 (17.0.10+7-1) ... Removing ca-certificates-java (20240118) ... Removing gtk-update-icon-cache (3.24.41-1) ... Removing hicolor-icon-theme (0.17-2) ... Removing ibverbs-providers:amd64 (48.0-1.1) ... Removing java-common (0.75) ... Removing libpicard-java (3.1.1+dfsg-1) ... Removing libgkl-java (0.8.11+dfsg-2) ... Removing libhtsjdk-java (4.1.0+dfsg-1) ... Removing libcommons-jexl2-java (2.1.1-6) ... Removing libbarclay-java (5.0.0+dfsg-1) ... Removing liblog4j2-java (2.19.0-2) ... Removing liblightcouch-java (0.2.0-1) ... Removing libhttpclient-java (4.5.14-1) ... Removing libcommons-logging-java (1.3.0-1) ... Removing libcommons-lang3-java (3.14.0-1) ... Removing libasound2:amd64 (1.2.10-3) ... Removing libasound2-data (1.2.10-3) ... Removing libatomic1:amd64 (14-20240201-3) ... Removing libcups2:amd64 (2.4.7-1+b1) ... Removing libavahi-client3:amd64 (0.8-13+b1) ... Removing libavahi-common3:amd64 (0.8-13+b1) ... Removing libavahi-common-data:amd64 (0.8-13+b1) ... Removing r-cran-gam (1.22-3-1) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing libgl1:amd64 (1.7.0-1) ... Removing libglx0:amd64 (1.7.0-1) ... Removing libglx-mesa0:amd64 (24.0.1-1) ... Removing libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Removing libfido2-1:amd64 (1.14.0-1) ... Removing libcbor0.10:amd64 (0.10.2-1.2) ... Removing libcommons-codec-java (1.16.0-1) ... Removing libcommons-compress-java (1.25.0-1) ... Removing libcommons-io-java (2.11.0-2) ... Removing libcommons-math3-java (3.6.1-3) ... Removing samtools (1.19.2-1) ... Removing python3-pysam (0.22.0+ds-1+b1) ... Removing libhts3:amd64 (1.19+ds-1) ... Removing libcurl3-gnutls:amd64 (8.6.0-3) ... Removing libdbus-1-3:amd64 (1.14.10-4) ... Removing libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b1) ... Removing libgl1-mesa-dri:amd64 (24.0.1-1) ... Removing libdrm-amdgpu1:amd64 (2.4.120-2) ... Removing libdrm-radeon1:amd64 (2.4.120-2) ... Removing libdrm-nouveau2:amd64 (2.4.120-2) ... Removing libdrm-intel1:amd64 (2.4.120-2) ... Removing libllvm17:amd64 (1:17.0.6-5) ... Removing libedit2:amd64 (3.1-20230828-1) ... Removing libelf1:amd64 (0.190-1+b1) ... Removing libpmix2:amd64 (5.0.1-4+b1) ... Removing libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Removing libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Removing python3-ruamel.yaml (0.17.21-1) ... Removing python3-ruamel.yaml.clib:amd64 (0.2.8-1) ... Removing python3-setproctitle:amd64 (1.3.3-1+b1) ... Removing python3-coloredlogs (15.0.1-1) ... Removing python3-humanfriendly (10.0-3) ... Removing python3-monotonic (1.6-2) ... Removing libfreemarker-java (2.3.31-2) ... Removing libgatk-native-bindings-java (1.0.0+dfsg-2) ... Removing mafft (7.505-1) ... Removing perl (5.38.2-3) ... Removing libperl5.38:amd64 (5.38.2-3) ... Removing libgdbm-compat4:amd64 (1.23-5+b1) ... Removing libgdbm6:amd64 (1.23-5+b1) ... Removing libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Removing libopenblas-dev:amd64 (0.3.26+ds-1) ... Removing libopenblas-pthread-dev:amd64 (0.3.26+ds-1) ... Removing libopenblas0:amd64 (0.3.26+ds-1) ... Removing libgif7:amd64 (5.2.1-2.5+b1) ... Removing libglapi-mesa:amd64 (24.0.1-1) ... Removing shared-mime-info (2.4-1) ... Removing libglvnd0:amd64 (1.7.0-1) ... Removing libgoogle-gson-java (2.10.1-1) ... Removing libgsl-dev (2.7.1+dfsg-6+b1) ... Removing libgsl27:amd64 (2.7.1+dfsg-6+b1) ... Removing libgslcblas0:amd64 (2.7.1+dfsg-6+b1) ... Removing libgtk2.0-common (2.24.33-3) ... Removing libhtscodecs2:amd64 (1.6.0-1+b1) ... Removing libhttpcore-java (4.4.16-1) ... Removing libhwloc-plugins:amd64 (2.10.0-1+b1) ... Removing libhwloc15:amd64 (2.10.0-1+b1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Removing libjoptsimple-java (5.0.4-4) ... Removing liblcms2-2:amd64 (2.14-2+b1) ... Removing libngs-java:amd64 (3.0.3+dfsg-6) ... Removing libngs-jni:amd64 (3.0.3+dfsg-6) ... Removing libncbi-ngs3:amd64 (3.0.3+dfsg-6) ... Removing libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Removing libmbedtls14:amd64 (2.28.7-1) ... Removing libmbedx509-1:amd64 (2.28.7-1) ... Removing libmbedcrypto7:amd64 (2.28.7-1) ... Removing libmjson-java (1.4.0-3) ... Removing libmongodb-java (3.6.3-2) ... Removing libmunge2:amd64 (0.5.15-3+b1) ... Removing libncurses6:amd64 (6.4+20240113-1) ... Removing libnss3:amd64 (2:3.98-1) ... Removing libnspr4:amd64 (2:4.35-1.1+b1) ... Removing libpsm2-2 (11.2.185-2) ... Removing libnuma1:amd64 (2.0.18-1) ... Removing libpciaccess0:amd64 (0.17-3) ... Removing libpcsclite1:amd64 (2.0.1-1+b1) ... Removing libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: warning: alternative /usr/lib/libpsm1/libpsm_infinipath.so.1.16 (part of link group libpsm_infinipath.so.1) doesn't exist; removing from list of alternatives update-alternatives: warning: /etc/alternatives/libpsm_infinipath.so.1 is dangling; it will be updated with best choice Removing librhino-java (1.7.14-2.1) ... Removing libsensors5:amd64 (1:3.6.0-8+b1) ... Removing libsensors-config (1:3.6.0-8) ... Removing libslf4j-java (1.7.32-1) ... Removing libsnappy-java (1.1.10.5-1) ... Removing libsnappy-jni (1.1.10.5-1) ... Removing libsnappy1v5:amd64 (1.1.10-1+b1) ... Removing libvulkan1:amd64 (1.3.275.0-1) ... Removing libx11-xcb1:amd64 (2:1.8.7-1) ... Removing libxcb-dri2-0:amd64 (1.15-1) ... Removing libxcb-dri3-0:amd64 (1.15-1) ... Removing libxcb-glx0:amd64 (1.15-1) ... Removing libxcb-present0:amd64 (1.15-1) ... Removing libxcb-randr0:amd64 (1.15-1) ... Removing libxcb-sync1:amd64 (1.15-1) ... Removing libxcb-xfixes0:amd64 (1.15-1) ... Removing libxcomposite1:amd64 (1:0.4.5-1) ... Removing libxcursor1:amd64 (1:1.2.1-1) ... Removing libxdamage1:amd64 (1:1.1.6-1) ... Removing libxtst6:amd64 (2:1.2.3-1.1) ... Removing libxfixes3:amd64 (1:6.0.0-2) ... Removing libxi6:amd64 (2:1.8.1-1) ... Removing libxinerama1:amd64 (2:1.1.4-3) ... Removing libxnvctrl0:amd64 (525.147.05-1) ... Removing libxrandr2:amd64 (2:1.5.2-2+b1) ... Removing libxshmfence1:amd64 (1.3-1) ... Removing libz3-4:amd64 (4.8.12-3.1+b2) ... Removing littler (0.3.19-1) ... Removing ncbi-vdb-data (3.0.2+dfsg-2) ... Removing ocl-icd-libopencl1:amd64 (2.3.2-1) ... Removing openmpi-common (4.1.6-5) ... Removing perl-modules-5.38 (5.38.2-3) ... Removing phylip (1:3.697+dfsg-3) ... Removing python3-configargparse (1.7-1) ... Removing r-cran-tibble (3.2.1+dfsg-2) ... Removing r-cran-pillar (1.9.0+dfsg-1) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-gtable (0.3.4+dfsg-1) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-cli (3.6.2-1) ... Removing r-cran-foreach (1.5.2-1) ... Removing r-cran-codetools (0.2-19-1) ... Removing r-cran-munsell (0.5.0-2) ... Removing r-cran-colorspace (2.1-0+dfsg-1) ... Removing r-cran-fansi (1.0.5-1) ... Removing r-cran-farver (2.1.1-1) ... Removing r-cran-glue (1.7.0-1) ... Removing r-cran-inline (0.3.19-2) ... 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 (3.1.164-1) ... Removing r-cran-lattice (0.22-5-1) ... Removing r-cran-littler (0.3.19-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-60.0.1-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-pkgkitten (0.2.3-1) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rlang (1.1.3-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing r-cran-withr (3.0.0+dfsg-1) ... Removing radiant (2.8.1+dfsg-2) ... Removing raxml (8.2.13+dfsg-1) ... Removing seqtk (1.4-2) ... Removing libibverbs1:amd64 (48.0-1.1) ... Removing adduser (3.137) ... Removing r-base-core (4.3.2-1) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... Removing libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... Removing libpango-1.0-0:amd64 (1.51.0+ds-4) ... Removing fontconfig (2.15.0-1) ... Removing libtk8.6:amd64 (8.6.13-2+b1) ... Removing libxft2:amd64 (2.3.6-1+b1) ... Removing libcairo2:amd64 (1.18.0-1+b1) ... Removing libfontconfig1:amd64 (2.15.0-1) ... Removing fontconfig-config (2.15.0-1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libcommons-parent-java (56-1) ... Removing libapache-pom-java (29-2) ... Removing libharfbuzz0b:amd64 (8.3.0-2) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Removing libcurl4:amd64 (8.6.0-3) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libxt6:amd64 (1:1.2.1-1.1) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.19-1) ... Removing libdrm2:amd64 (2.4.120-2) ... Removing libdrm-common (2.4.120-2) ... Removing python3 (3.11.6-1) ... Removing python3.11 (3.11.8-1) ... Removing python3-minimal (3.11.6-1) ... Removing python3.11-minimal (3.11.8-1) ... Removing libexpat1:amd64 (2.6.0-1) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing libopenblas0-pthread:amd64 (0.3.26+ds-1) ... Removing libgfortran5:amd64 (14-20240201-3) ... Removing libglib2.0-0:amd64 (2.78.4-1) ... Removing libgomp1:amd64 (14-20240201-3) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libpython3-stdlib:amd64 (3.11.6-1) ... Removing libpython3.11-stdlib:amd64 (3.11.8-1) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3) ... Removing libtirpc3:amd64 (1.3.4+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-5+b1) ... Removing libicu72:amd64 (72.1-4+b1) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing libkrb5-3:amd64 (1.20.1-5+b1) ... Removing libk5crypto3:amd64 (1.20.1-5+b1) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.20.1-5+b1) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing libnghttp2-14:amd64 (1.59.0-1) ... Removing libnl-route-3-200:amd64 (3.7.0-0.3) ... Removing libnl-3-200:amd64 (3.7.0-0.3) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libpng16-16:amd64 (1.6.42-1) ... Removing libpsl5:amd64 (0.21.2-1+b1) ... Removing libpython3.11-minimal:amd64 (3.11.8-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.2-3+b1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Removing libwebp7:amd64 (1.3.2-0.4) ... Removing libsharpyuv0:amd64 (1.3.2-0.4) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libsqlite3-0:amd64 (3.45.1-1) ... Removing libssh2-1:amd64 (1.11.0-4) ... Removing libtcl8.6:amd64 (8.6.13+dfsg-2+b1) ... Removing libthai-data (0.1.29-2) ... Removing libtirpc-common (1.3.4+ds-1) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing openssl (3.1.5-1) ... Removing readline-common (8.2-3) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.22) ... Removing unzip (6.0-28) ... Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-13) ... Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libbsd0:amd64 (0.11.8-1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Processing triggers for libc-bin (2.37-15) ... 1m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-get', 'remove', 'adapterremoval', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'bcftools', 'bedtools', 'bowtie2', 'bwa', 'ca-certificates', 'ca-certificates-java', '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', 'libapache-pom-java', 'libasound2:amd64', 'libasound2-data', 'libatk1.0-0:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcbor0.10:amd64', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libfontconfig1:amd64', 'libfreemarker-java', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgatk-native-bindings-java', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgkl-java', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjoptsimple-java', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblightcouch-java', 'libllvm17:amd64', 'liblog4j2-java', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmongodb-java', 'libmunge2:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenmpi3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.38:amd64', 'libpicard-java', 'libpixman-1-0:amd64', 'libpmix2:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'librdmacm1:amd64', 'libreadline8: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', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libucx0:amd64', 'libvulkan1:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0: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', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'ncbi-vdb-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'perl', 'perl-modules-5.38', 'phylip', 'picard-tools', 'python3', 'python3-coloredlogs', 'python3-configargparse', 'python3-humanfriendly', 'python3-minimal', 'python3-monotonic', 'python3-pysam', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib:amd64', 'python3-setproctitle:amd64', 'python3.11', 'python3.11-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', 'sensible-utils', 'seqtk', 'shared-mime-info', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'paleomix'] 1m21.7s INFO: Running scripts post_remove 1m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_remove_exceptions'] 1m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_remove_exceptions'] 1m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg', '--purge', 'adapterremoval', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'bcftools', 'bedtools', 'bowtie2', 'bwa', 'ca-certificates', 'ca-certificates-java', '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', 'libapache-pom-java', 'libasound2:amd64', 'libasound2-data', 'libatk1.0-0:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcbor0.10:amd64', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libfontconfig1:amd64', 'libfreemarker-java', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgatk-native-bindings-java', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgkl-java', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjoptsimple-java', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblightcouch-java', 'libllvm17:amd64', 'liblog4j2-java', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmongodb-java', 'libmunge2:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenmpi3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.38:amd64', 'libpicard-java', 'libpixman-1-0:amd64', 'libpmix2:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'librdmacm1:amd64', 'libreadline8: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', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libucx0:amd64', 'libvulkan1:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0: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', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'ncbi-vdb-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'perl', 'perl-modules-5.38', 'phylip', 'picard-tools', 'python3', 'python3-coloredlogs', 'python3-configargparse', 'python3-humanfriendly', 'python3-minimal', 'python3-monotonic', 'python3-pysam', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib:amd64', 'python3-setproctitle:amd64', 'python3.11', 'python3.11-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', 'sensible-utils', 'seqtk', 'shared-mime-info', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip'] 1m22.5s DUMP: dpkg: warning: ignoring request to remove adapterremoval which isn't installed (Reading database ... 5362 files and directories currently installed.) Purging configuration files for adduser (3.137) ... Purging configuration files for adwaita-icon-theme (46~beta-4) ... 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 (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20240118) ... 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 (2.15.0-1) ... Purging configuration files for fontconfig-config (2.15.0-1) ... Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: ignoring request to remove gtk-update-icon-cache which isn't installed dpkg: warning: ignoring request to remove hicolor-icon-theme which isn't installed Purging configuration files for ibverbs-providers:amd64 (48.0-1.1) ... Purging configuration files for java-common (0.75) ... dpkg: warning: ignoring request to remove libapache-pom-java which isn't installed dpkg: warning: ignoring request to remove libasound2 which isn't installed dpkg: warning: ignoring request to remove libasound2-data which isn't installed dpkg: warning: ignoring request to remove libatk1.0-0 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libavahi-client3 which isn't installed dpkg: warning: ignoring request to remove libavahi-common-data which isn't installed dpkg: warning: ignoring request to remove libavahi-common3 which isn't installed dpkg: warning: ignoring request to remove libbarclay-java which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcbor0.10 which isn't installed dpkg: warning: ignoring request to remove libcommons-codec-java which isn't installed dpkg: warning: ignoring request to remove libcommons-compress-java which isn't installed dpkg: warning: ignoring request to remove libcommons-io-java which isn't installed dpkg: warning: ignoring request to remove libcommons-jexl2-java which isn't installed dpkg: warning: ignoring request to remove libcommons-lang3-java which isn't installed dpkg: warning: ignoring request to remove libcommons-logging-java which isn't installed dpkg: warning: ignoring request to remove libcommons-math3-java which isn't installed dpkg: warning: ignoring request to remove libcommons-parent-java which isn't installed dpkg: warning: ignoring request to remove libcups2 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdbus-1-3 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdrm-amdgpu1 which isn't installed dpkg: warning: ignoring request to remove libdrm-common which isn't installed dpkg: warning: ignoring request to remove libdrm-intel1 which isn't installed dpkg: warning: ignoring request to remove libdrm-nouveau2 which isn't installed dpkg: warning: ignoring request to remove libdrm-radeon1 which isn't installed dpkg: warning: ignoring request to remove libdrm2 which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libelf1 which isn't installed dpkg: warning: ignoring request to remove libevent-core-2.1-7 which isn't installed dpkg: warning: ignoring request to remove libevent-pthreads-2.1-7 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfabric1 which isn't installed dpkg: warning: ignoring request to remove libfido2-1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreemarker-java which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgatk-native-bindings-java which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed Purging configuration files for libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b1) ... 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 (24.0.1-1) ... dpkg: warning: ignoring request to remove libglapi-mesa which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.78.4-1) ... dpkg: warning: ignoring request to remove libglvnd0 which isn't installed dpkg: warning: ignoring request to remove libglx-mesa0 which isn't installed dpkg: warning: ignoring request to remove libglx0 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgoogle-gson-java which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libgsl-dev which isn't installed dpkg: warning: ignoring request to remove libgsl27 which isn't installed dpkg: warning: ignoring request to remove libgslcblas0 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-5+b1) ... Purging configuration files for libgtk2.0-0:amd64 (2.24.33-3) ... Purging configuration files for libgtk2.0-common (2.24.33-3) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libhtsjdk-java which isn't installed dpkg: warning: ignoring request to remove libhttpclient-java which isn't installed dpkg: warning: ignoring request to remove libhttpcore-java which isn't installed dpkg: warning: ignoring request to remove libhwloc-plugins which isn't installed dpkg: warning: ignoring request to remove libhwloc15 which isn't installed dpkg: warning: ignoring request to remove libibverbs1 which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjoptsimple-java which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove liblightcouch-java which isn't installed dpkg: warning: ignoring request to remove libllvm17 which isn't installed dpkg: warning: ignoring request to remove liblog4j2-java which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1 which isn't installed dpkg: warning: ignoring request to remove libmjson-java which isn't installed dpkg: warning: ignoring request to remove libmongodb-java which isn't installed dpkg: warning: ignoring request to remove libmunge2 which isn't installed dpkg: warning: ignoring request to remove libncbi-ngs3 which isn't installed dpkg: warning: ignoring request to remove libncbi-vdb3 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libngs-java which isn't installed dpkg: warning: ignoring request to remove libngs-jni which isn't installed Purging configuration files for libnl-3-200:amd64 (3.7.0-0.3) ... dpkg: warning: ignoring request to remove libnl-route-3-200 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libnspr4 which isn't installed dpkg: warning: ignoring request to remove libnss3 which isn't installed dpkg: warning: ignoring request to remove libnuma1 which isn't installed dpkg: warning: ignoring request to remove libopenblas-dev which isn't installed dpkg: warning: ignoring request to remove libopenblas-pthread-dev which isn't installed dpkg: warning: ignoring request to remove libopenblas0 which isn't installed dpkg: warning: ignoring request to remove libopenblas0-pthread which isn't installed dpkg: warning: ignoring request to remove libopenmpi3 which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.29) ... 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 libperl5.38 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 libpmix2 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed Purging configuration files for libpsm-infinipath1 (3.3+20.604758e7-6.3) ... 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 libpython3.11-minimal:amd64 (3.11.8-1) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove librdmacm1 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed 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 (1:3.6.0-8) ... 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 libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 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 (1.3.4+ds-1) ... dpkg: warning: ignoring request to remove libtirpc3 which isn't installed 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 libvulkan1 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-dri2-0 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 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 libxml2 which isn't installed dpkg: warning: ignoring request to remove libxnvctrl0 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 libxt6 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 (10.1.0) ... dpkg: warning: ignoring request to remove ncbi-vdb-data which isn't installed Purging configuration files for netbase (6.4) ... dpkg: warning: ignoring request to remove ocl-icd-libopencl1 which isn't installed dpkg: warning: ignoring request to remove openjdk-17-jre which isn't installed Purging configuration files for openjdk-17-jre-headless:amd64 (17.0.10+7-1) ... Purging configuration files for openmpi-bin (4.1.6-5) ... dpkg: warning: ignoring request to remove openmpi-common which isn't installed Purging configuration files for openssh-client (1:9.6p1-3) ... Purging configuration files for openssl (3.1.5-1) ... Purging configuration files for perl (5.38.2-3) ... dpkg: warning: ignoring request to remove perl-modules-5.38 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 (3.11.6-1) ... 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 python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.8-1) ... Purging configuration files for r-base-core (4.3.2-1) ... 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 (8.2-3) ... dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed dpkg: warning: ignoring request to remove seqtk which isn't installed Purging configuration files for shared-mime-info (2.4-1) ... Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 1m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg', '--purge', 'adapterremoval', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'bcftools', 'bedtools', 'bowtie2', 'bwa', 'ca-certificates', 'ca-certificates-java', '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', 'libapache-pom-java', 'libasound2:amd64', 'libasound2-data', 'libatk1.0-0:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcbor0.10:amd64', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libfontconfig1:amd64', 'libfreemarker-java', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgatk-native-bindings-java', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgkl-java', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjoptsimple-java', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblightcouch-java', 'libllvm17:amd64', 'liblog4j2-java', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmongodb-java', 'libmunge2:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenmpi3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.38:amd64', 'libpicard-java', 'libpixman-1-0:amd64', 'libpmix2:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'librdmacm1:amd64', 'libreadline8: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', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libucx0:amd64', 'libvulkan1:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0: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', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'ncbi-vdb-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'perl', 'perl-modules-5.38', 'phylip', 'picard-tools', 'python3', 'python3-coloredlogs', 'python3-configargparse', 'python3-humanfriendly', 'python3-minimal', 'python3-monotonic', 'python3-pysam', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib:amd64', 'python3-setproctitle:amd64', 'python3.11', 'python3.11-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', 'sensible-utils', 'seqtk', 'shared-mime-info', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip'] 1m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg', '--purge', 'paleomix'] 1m22.5s DUMP: dpkg: warning: ignoring request to remove paleomix which isn't installed 1m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg', '--purge', 'paleomix'] 1m22.5s INFO: Running scripts post_purge 1m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_purge_exceptions'] 1m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_purge_exceptions'] 1m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg', '--purge', '--pending'] 1m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg', '--purge', '--pending'] 1m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg', '--remove', '--pending'] 1m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg', '--remove', '--pending'] 1m22.5s INFO: Running scripts post_test 1m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_test_exceptions'] 1m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'tmp/scripts/post_test_exceptions'] 1m22.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n'] 1m23.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n'] 1m23.7s ERROR: WARN: Broken symlinks: /usr/lib/x86_64-linux-gnu/libmpi_usempi_ignore_tkr-gfortranso.40 -> libmpi_usempi_ignore_tkr-gfortran.so.40.30.0 1m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg-divert', '--list'] 1m23.8s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 1m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'dpkg-divert', '--list'] 1m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-get', 'clean'] 1m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n', 'apt-get', 'clean'] 1m23.8s DEBUG: Recording chroot state 1m24.6s INFO: Warning: Package purging left files on system: /usr/lib/x86_64-linux-gnu/libmpi_usempi_ignore_tkr-gfortranso.40 -> libmpi_usempi_ignore_tkr-gfortran.so.40.30.0 not owned 1m24.6s INFO: PASS: Installation and purging test. 1m25.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/shm'] 1m25.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/shm'] 1m25.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/console'] 1m25.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/console'] 1m25.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/ptmx'] 1m25.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/ptmx'] 1m25.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/pts'] 1m25.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/dev/pts'] 1m25.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/proc'] 1m25.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n/proc'] 1m25.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n'] 1m25.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp8pqt8b8n'] 1m25.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp8pqt8b8n 1m25.2s INFO: PASS: All tests. 1m25.2s INFO: piuparts run ends. ret=0 End: 2024-02-25 06:43:04 GMT