Start: 2023-06-12 09:59:33 GMT [testing] Package: paleomix Version: 1.3.7-3 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_1.3.7-3_amd64.deb Size: 983840 MD5sum: c89cd3f74cb0f04cb9c614c8bf2f4147 SHA256: bd93c68aa5250b1c865dea65bb55ead3dd4f4102379066727310729ac515507b [sid] 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 --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/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --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 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt paleomix=1.3.8-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpqepzyjea 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpqepzyjea 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.1s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/proc'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/proc'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/pts'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/pts'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/ptmx'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/ptmx'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/console'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/console'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/shm'] 0m2.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/shm'] 0m2.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.2s DEBUG: Created policy-rc.d and chmodded it. 0m2.2s DEBUG: Created resolv.conf. 0m2.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpqepzyjea/tmp/scripts/ 0m2.2s INFO: Running scripts post_chroot_unpack 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', 'update'] 0m5.1s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [147 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8904 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [6076 kB] Fetched 15.1 MB in 2s (6830 kB/s) Reading package lists... 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', 'update'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', '-yf', 'dist-upgrade'] 0m5.6s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', '-yf', 'dist-upgrade'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.9s DUMP: 3211b9f57c6ab2ee9b513c79c6d73bfa - 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.9s INFO: Running scripts post_setup 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_setup_dummy_users'] 0m6.9s 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 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_setup_dummy_users'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_setup_forbid_home'] 0m6.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_setup_forbid_home'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.0s 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' 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_setup_minimize'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_setup_minimize'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_setup_zz_backports'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_setup_zz_backports'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.0s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3 install ok installed debianutils debianutils 5.7-0.4 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9 install ok installed libc6:amd64 libc6 2.36-9 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6 install ok installed libpam-runtime libpam-runtime 1.5.2-6 install ok installed libpam0g:amd64 libpam0g 1.5.2-6 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.6-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.6-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl perl 5.36.0-7 install ok installed perl-base perl-base 5.36.0-7 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-5 install ok installed usr-is-merged usr-is-merged 35 install ok installed usrmerge usrmerge 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m7.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 0m7.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 0m7.5s INFO: Running scripts is_testable 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/is_testable_uninstallable'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/is_testable_uninstallable'] 0m7.5s INFO: Running scripts pre_test 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_test_exceptions'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_test_exceptions'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_test_root_password'] 0m7.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_test_root_password'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'show', '--no-all-versions', 'paleomix'] 0m7.8s DUMP: Package: paleomix Version: 1.3.7-3 Installed-Size: 2006 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-coloredlogs, python3-configargparse, python3-pysam, python3-ruamel.yaml, python3-setproctitle, python3:any, adapterremoval, bedtools, bowtie2, bwa, bcftools, examl, mafft, mapdamage, phylip, picard-tools, r-base-core, radiant, raxml, samtools Description-en: pipelines and tools for the processing of ancient and modern HTS data The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data: The BAM pipeline processes de-multiplexed reads from one or more samples, through sequence processing and alignment, to generate BAM alignment files useful in downstream analyses; the Phylogenetic pipeline carries out genotyping and phylogenetic inference on BAM alignment files, either produced using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out a suite of analyses on low coverage equine alignments, in order to detect the presence of F1-hybrids in archaeological assemblages. In addition, PALEOMIX aids in metagenomic analysis of the extracts. . The pipelines have been designed with ancient DNA (aDNA) in mind, and includes several features especially useful for the analyses of ancient samples, but can all be for the processing of modern samples, in order to ensure consistent data processing. Description-md5: 7cb3c4aa709e51b480a41a73961d7253 Homepage: https://geogenetics.ku.dk/publications/paleomix Section: science Priority: optional Filename: pool/main/p/paleomix/paleomix_1.3.7-3_amd64.deb Size: 983840 MD5sum: c89cd3f74cb0f04cb9c614c8bf2f4147 SHA256: bd93c68aa5250b1c865dea65bb55ead3dd4f4102379066727310729ac515507b 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'show', '--no-all-versions', 'paleomix'] 0m7.8s INFO: apt-cache knows about the following packages: paleomix 0m7.8s INFO: Running scripts pre_install 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_database-server'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_database-server'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_exceptions'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_exceptions'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_extras'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_extras'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'policy'] 0m7.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.0,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'policy'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'policy', 'paleomix'] 0m7.9s DUMP: paleomix: Installed: (none) Candidate: 1.3.7-3 Version table: 1.3.7-3 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'policy', 'paleomix'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', '-y', 'install', 'paleomix'] 0m51.3s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: adapterremoval 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 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 libcbor0.8 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 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 libllvm15 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 libpicard-java libpixman-1-0 libpmix2 libpng16-16 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 librdmacm1 libreadline8 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsqlite3-0 libssh2-1 libssl3 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3 libtk8.6 libucx0 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 ocl-icd-libopencl1 openjdk-17-jre openjdk-17-jre-headless openmpi-bin openmpi-common openssh-client openssl 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: python3-numpy python3-matplotlib texlive-latex-recommended bowtie2-examples libasound2-plugins alsa-utils libasm-java libxz-java libcommons-io-java-doc libcommons-lang3-java-doc libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java cups-common jython libdom4j-java libjaxen-java libjdom1-java libxalan2-java 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 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-callr r-cran-covr r-cran-crayon r-cran-digest r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-whoami r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-unitizer r-cran-interp r-cran-testthat r-cran-profvis r-cran-rgeos r-cran-dbi r-cran-forcats r-cran-r.utils r-cran-rsqlite r-cran-stringr r-cran-waldo r-cran-magick r-cran-sf r-cran-lintr r-cran-tidyverse r-cran-getopt r-cran-bit64 r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-stringi r-cran-survival r-cran-units r-cran-vdiffr r-cran-fs r-cran-usethis r-cran-dichromat r-cran-bench r-cran-blob r-cran-brio r-cran-evaluate r-cran-hms r-cran-pkgbuild r-cran-pkgload r-cran-purrr r-cran-tidyr r-cran-pkgdown r-cran-zeallot 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 blast2 libwww-perl lynx ruby libatk-wrapper-java-jni fonts-dejavu-extra xauth r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-mockery r-cran-covr r-cran-ragg r-cran-dplyr r-cran-hexbin r-cran-hmisc r-cran-interp r-cran-knitr r-cran-mapproj r-cran-maps r-cran-maptools r-cran-multcomp r-cran-quantreg r-cran-rmarkdown r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 r-cran-crayon r-cran-lubridate r-cran-bit64 r-cran-hms r-cran-stringi r-cran-data.table r-cran-rsqlite r-cran-mockr r-cran-formattable r-cran-generics r-cran-waldo r-cran-dbi libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: adapterremoval 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 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 libcbor0.8 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 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 libllvm15 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 libpicard-java libpixman-1-0 libpmix2 libpng16-16 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 librdmacm1 libreadline8 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsqlite3-0 libssh2-1 libssl3 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3 libtk8.6 libucx0 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 ocl-icd-libopencl1 openjdk-17-jre openjdk-17-jre-headless openmpi-bin openmpi-common openssh-client openssl paleomix 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, 288 newly installed, 0 to remove and 0 not upgraded. Need to get 249 MB of archives. After this operation, 881 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.9-1 [2016 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2 [32.3 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2 [79.0 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:11 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2 [331 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2 [134 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:22 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.9-1 [1416 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libcbor0.8 amd64 0.8.0-2+b1 [27.4 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libfido2-1 amd64 1.12.0-2+b1 [77.2 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 openssh-client amd64 1:9.2p1-2 [988 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 adapterremoval amd64 2.3.3-2 [191 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2 [285 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6 [316 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+b1 [139 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.37-2 [43.3 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10 [381 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 bcftools amd64 1.16-1 [692 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 bedtools amd64 2.30.0+dfsg-3 [665 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 bowtie2 amd64 2.5.0-3+b2 [1409 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 bwa amd64 0.7.17-7+b2 [212 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B] Get:66 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.6-1 [200 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3 [244 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.6+10-1 [43.6 MB] Get:84 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B] Get:85 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230103 [11.4 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-common all 2.24.33-2 [2700 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-0 amd64 2.24.33-2 [1855 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get:117 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get:118 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2 [192 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get:123 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get:126 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:128 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:129 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get:130 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get:133 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get:137 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get:138 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get:140 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get:143 http://deb.debian.org/debian bookworm/main amd64 libgif7 amd64 5.2.1-2.5 [46.9 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:145 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre amd64 17.0.6+10-1 [168 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 default-jre amd64 2:1.17-74 [1056 B] Get:148 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get:150 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get:151 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get:153 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get:154 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:155 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get:156 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get:158 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get:159 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get:160 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get:161 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get:162 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 525.85.05-1 [13.3 kB] Get:163 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get:165 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+b1 [622 kB] Get:166 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get:167 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get:168 http://deb.debian.org/debian bookworm/main amd64 openmpi-common all 4.1.4-3 [167 kB] Get:169 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 examl amd64 3.0.22-3+b2 [951 kB] Get:171 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B] Get:172 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:173 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang3-java all 3.12.0-2 [561 kB] Get:174 http://deb.debian.org/debian bookworm/main amd64 libfreemarker-java all 2.3.31-2 [1528 kB] Get:175 http://deb.debian.org/debian bookworm/main amd64 libgoogle-gson-java all 2.10-1 [261 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 libjoptsimple-java all 5.0.4-4 [73.1 kB] Get:177 http://deb.debian.org/debian bookworm/main amd64 libcommons-codec-java all 1.15-1 [292 kB] Get:178 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get:180 http://deb.debian.org/debian bookworm/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get:182 http://deb.debian.org/debian bookworm/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get:183 http://deb.debian.org/debian bookworm/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 libbarclay-java all 4.1.0+dfsg-1 [103 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 libcommons-compress-java all 1.22-1 [615 kB] Get:188 http://deb.debian.org/debian bookworm/main amd64 libcommons-io-java all 2.11.0-2 [319 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get:190 http://deb.debian.org/debian bookworm/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get:191 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10 [386 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B] Get:193 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:194 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:195 http://deb.debian.org/debian bookworm/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get:196 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get:197 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get:198 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get:199 http://deb.debian.org/debian bookworm/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get:200 http://deb.debian.org/debian bookworm/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2 [1050 kB] Get:201 http://deb.debian.org/debian bookworm/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-5 [153 kB] Get:202 http://deb.debian.org/debian bookworm/main amd64 libngs-jni amd64 3.0.3+dfsg-5 [23.4 kB] Get:203 http://deb.debian.org/debian bookworm/main amd64 libngs-java amd64 3.0.3+dfsg-5 [110 kB] Get:204 http://deb.debian.org/debian bookworm/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get:205 http://deb.debian.org/debian bookworm/main amd64 libsnappy1v5 amd64 1.1.9-3 [26.0 kB] Get:206 http://deb.debian.org/debian bookworm/main amd64 libsnappy-jni amd64 1.1.8.3-1 [7152 B] Get:207 http://deb.debian.org/debian bookworm/main amd64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get:208 http://deb.debian.org/debian bookworm/main amd64 libhtsjdk-java all 3.0.4+dfsg-2 [1813 kB] Get:209 http://deb.debian.org/debian bookworm/main amd64 libgkl-java all 0.8.10+dfsg-3 [25.0 kB] Get:210 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:211 http://deb.debian.org/debian bookworm/main amd64 libgslcblas0 amd64 2.7.1+dfsg-5 [108 kB] Get:212 http://deb.debian.org/debian bookworm/main amd64 libgsl27 amd64 2.7.1+dfsg-5 [941 kB] Get:213 http://deb.debian.org/debian bookworm/main amd64 libgsl-dev amd64 2.7.1+dfsg-5 [1152 kB] Get:214 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:215 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get:216 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:217 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get:218 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get:219 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get:220 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get:221 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:222 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:223 http://deb.debian.org/debian bookworm/main amd64 libpicard-java all 2.27.5+dfsg-2 [1725 kB] Get:224 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:225 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:226 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:227 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:228 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:229 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:230 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get:231 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get:232 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:233 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get:234 http://deb.debian.org/debian bookworm/main amd64 r-cran-littler amd64 0.3.17-1 [96.3 kB] Get:235 http://deb.debian.org/debian bookworm/main amd64 littler all 0.3.17-1 [14.4 kB] Get:236 http://deb.debian.org/debian bookworm/main amd64 mafft amd64 7.505-1 [1078 kB] Get:237 http://deb.debian.org/debian bookworm/main amd64 r-cran-codetools all 0.2-19-1 [90.9 kB] Get:238 http://deb.debian.org/debian bookworm/main amd64 r-cran-iterators all 1.0.14-1 [337 kB] Get:239 http://deb.debian.org/debian bookworm/main amd64 r-cran-foreach all 1.5.2-1 [122 kB] Get:240 http://deb.debian.org/debian bookworm/main amd64 r-cran-gam amd64 1.22-1-1 [308 kB] Get:241 http://deb.debian.org/debian bookworm/main amd64 r-cran-cli amd64 3.6.0-1 [1287 kB] Get:242 http://deb.debian.org/debian bookworm/main amd64 r-cran-glue amd64 1.6.2-1 [152 kB] Get:243 http://deb.debian.org/debian bookworm/main amd64 r-cran-gtable all 0.3.1+dfsg-1 [165 kB] Get:244 http://deb.debian.org/debian bookworm/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:245 http://deb.debian.org/debian bookworm/main amd64 r-cran-rlang amd64 1.0.6-1 [1618 kB] Get:246 http://deb.debian.org/debian bookworm/main amd64 r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB] Get:247 http://deb.debian.org/debian bookworm/main amd64 r-cran-mass amd64 7.3-58.2-1 [1121 kB] Get:248 http://deb.debian.org/debian bookworm/main amd64 r-cran-lattice amd64 0.20-45-3 [1177 kB] Get:249 http://deb.debian.org/debian bookworm/main amd64 r-cran-nlme amd64 3.1.162-1 [2260 kB] Get:250 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrix amd64 1.5-3-1 [3822 kB] Get:251 http://deb.debian.org/debian bookworm/main amd64 r-cran-mgcv amd64 1.8-41-1 [3171 kB] Get:252 http://deb.debian.org/debian bookworm/main amd64 r-cran-farver amd64 2.1.1-1 [1404 kB] Get:253 http://deb.debian.org/debian bookworm/main amd64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get:254 http://deb.debian.org/debian bookworm/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB] Get:255 http://deb.debian.org/debian bookworm/main amd64 r-cran-munsell all 0.5.0-2 [236 kB] Get:256 http://deb.debian.org/debian bookworm/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:257 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:258 http://deb.debian.org/debian bookworm/main amd64 r-cran-viridislite all 0.4.1-1 [1299 kB] Get:259 http://deb.debian.org/debian bookworm/main amd64 r-cran-scales all 1.2.1-1 [614 kB] Get:260 http://deb.debian.org/debian bookworm/main amd64 r-cran-fansi amd64 1.0.4-1 [619 kB] Get:261 http://deb.debian.org/debian bookworm/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:262 http://deb.debian.org/debian bookworm/main amd64 r-cran-utf8 amd64 1.2.3-1 [133 kB] Get:263 http://deb.debian.org/debian bookworm/main amd64 r-cran-vctrs amd64 0.5.2-1 [1371 kB] Get:264 http://deb.debian.org/debian bookworm/main amd64 r-cran-pillar all 1.8.1+dfsg-1 [463 kB] Get:265 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:266 http://deb.debian.org/debian bookworm/main amd64 r-cran-tibble amd64 3.1.8+dfsg-1 [513 kB] Get:267 http://deb.debian.org/debian bookworm/main amd64 r-cran-withr all 2.5.0-1 [236 kB] Get:268 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggplot2 all 3.4.1+dfsg-1 [3333 kB] Get:269 http://deb.debian.org/debian bookworm/main amd64 r-cran-inline all 0.3.19-2 [129 kB] Get:270 http://deb.debian.org/debian bookworm/main amd64 seqtk amd64 1.3-4 [30.6 kB] Get:271 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get:272 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgkitten all 0.2.2-2 [27.0 kB] Get:273 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcpp amd64 1.0.10-1 [2059 kB] Get:274 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcppgsl amd64 0.3.13-1 [203 kB] Get:275 http://deb.debian.org/debian bookworm/main amd64 mapdamage all 2.2.1+dfsg-3 [41.9 kB] Get:276 http://deb.debian.org/debian bookworm/main amd64 python3-monotonic all 1.6-2 [5728 B] Get:277 http://deb.debian.org/debian bookworm/main amd64 python3-humanfriendly all 10.0-3 [85.2 kB] Get:278 http://deb.debian.org/debian bookworm/main amd64 python3-coloredlogs all 15.0.1-1 [47.4 kB] Get:279 http://deb.debian.org/debian bookworm/main amd64 python3-configargparse all 1.5.3-1 [26.1 kB] Get:280 http://deb.debian.org/debian bookworm/main amd64 python3-ruamel.yaml.clib amd64 0.2.7-1+b2 [113 kB] Get:281 http://deb.debian.org/debian bookworm/main amd64 python3-ruamel.yaml all 0.17.21-1 [103 kB] Get:282 http://deb.debian.org/debian bookworm/main amd64 python3-setproctitle amd64 1.3.1-1+b2 [17.9 kB] Get:283 http://deb.debian.org/debian bookworm/main amd64 phylip amd64 1:3.697+dfsg-2 [919 kB] Get:284 http://deb.debian.org/debian bookworm/main amd64 picard-tools all 2.27.5+dfsg-2 [311 kB] Get:285 http://deb.debian.org/debian bookworm/main amd64 radiant all 2.8.1+dfsg-2 [181 kB] Get:286 http://deb.debian.org/debian bookworm/main amd64 raxml amd64 8.2.12+dfsg-8+b2 [1481 kB] Get:287 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Get:288 http://deb.debian.org/debian bookworm/main amd64 paleomix amd64 1.3.7-3 [984 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 249 MB in 2s (125 MB/s) Selecting previously unselected package libssl3:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8141 files and directories currently installed.) Preparing to unpack .../libssl3_3.0.9-1_amd64.deb ... Unpacking libssl3:amd64 (3.0.9-1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. 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Unpacking libncursesw6:amd64 (6.4-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../03-libkrb5support0_1.20.1-2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../04-libk5crypto3_1.20.1-2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../05-libkeyutils1_1.6.3-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-2) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../06-libkrb5-3_1.20.1-2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../07-libgssapi-krb5-2_1.20.1-2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../08-libtirpc-common_1.3.3+ds-1_all.deb ... Unpacking libtirpc-common (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3:amd64. Preparing to unpack .../09-libtirpc3_1.3.3+ds-1_amd64.deb ... Unpacking libtirpc3:amd64 (1.3.3+ds-1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../10-libnsl2_1.3.0-2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../11-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../12-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../13-libsqlite3-0_3.40.1-2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.40.1-2) ... Selecting previously unselected package libpython3.11-stdlib:amd64. 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8976 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.0.9-1_amd64.deb ... Unpacking openssl (3.0.9-1) ... 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Unpacking libhtscodecs2:amd64 (1.3.0-4) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../038-libhts3_1.16+ds-3_amd64.deb ... Unpacking libhts3:amd64 (1.16+ds-3) ... Selecting previously unselected package bcftools. Preparing to unpack .../039-bcftools_1.16-1_amd64.deb ... Unpacking bcftools (1.16-1) ... Selecting previously unselected package bedtools. Preparing to unpack .../040-bedtools_2.30.0+dfsg-3_amd64.deb ... Unpacking bedtools (2.30.0+dfsg-3) ... Selecting previously unselected package bowtie2. Preparing to unpack .../041-bowtie2_2.5.0-3+b2_amd64.deb ... Unpacking bowtie2 (2.5.0-3+b2) ... Selecting previously unselected package bwa. Preparing to unpack .../042-bwa_0.7.17-7+b2_amd64.deb ... Unpacking bwa (0.7.17-7+b2) ... Selecting previously unselected package java-common. Preparing to unpack .../043-java-common_0.74_all.deb ... Unpacking java-common (0.74) ... Selecting previously unselected package libavahi-common-data:amd64. 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Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../050-libfreetype6_2.12.1+dfsg-5_amd64.deb ... Unpacking libfreetype6:amd64 (2.12.1+dfsg-5) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../051-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../052-fontconfig-config_2.14.1-4_amd64.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../053-libfontconfig1_2.14.1-4_amd64.deb ... Unpacking libfontconfig1:amd64 (2.14.1-4) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../054-libnspr4_2%3a4.35-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.35-1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../055-libnss3_2%3a3.87.1-1_amd64.deb ... 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Setting up libsnappy1v5:amd64 (1.1.9-3) ... Setting up libkrb5support0:amd64 (1.20.1-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up libasound2-data (1.2.8-1) ... 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) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libmunge2 (0.5.15-2) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libmbedcrypto7:amd64 (2.28.3-1) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libnspr4:amd64 (2:4.35-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:amd64 (0.8-10) ... Setting up libncurses6:amd64 (6.4-4) ... Setting up libdbus-1-3:amd64 (1.14.6-1) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libhwloc15:amd64 (2.9.0-1) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libatomic1:amd64 (12.2.0-14) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libpcsclite1:amd64 (1.9.9-2) ... Setting up libsensors5:amd64 (1:3.6.0-7.1) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2) ... Setting up libglapi-mesa:amd64 (22.3.6-1+deb12u1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libwebp7:amd64 (1.2.4-0.2) ... Setting up libgif7:amd64 (5.2.1-2.5) ... Setting up libnuma1:amd64 (2.0.16-1) ... Setting up libfreemarker-java (2.3.31-2) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:amd64 (2.3.1-1) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up at-spi2-common (2.46.0-5) ... Setting up libtiff6:amd64 (4.5.0-6) ... Setting up libasound2:amd64 (1.2.8-1+b1) ... Setting up libnl-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up openmpi-common (4.1.4-3) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-1) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up libgtk2.0-common (2.24.33-2) ... Setting up libatk1.0-0:amd64 (2.46.0-5) ... Setting up libkrb5-3:amd64 (1.20.1-2) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.2) ... 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 (1.12.0-2+b1) ... Setting up openssl (3.0.9-1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libsnappy-jni (1.1.8.3-1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... 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 (2.30.0+dfsg-3) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Setting up raxml (8.2.12+dfsg-8+b2) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up libgsl-dev (2.7.1+dfsg-5) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... 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 (2.28.3-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libnss3:amd64 (2:3.87.1-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up shared-mime-info (2.2-1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2) ... Setting up ucf (3.0043+nmu1) ... Setting up libcommons-lang3-java (3.12.0-2) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up libcurl4:amd64 (7.88.1-10) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... 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-5) ... Setting up libtirpc3:amd64 (1.3.3+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 (3.24.37-2) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2) ... Setting up libibverbs1:amd64 (44.0-2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libngs-jni:amd64 (3.0.3+dfsg-5) ... Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libcommons-compress-java (1.22-1) ... Setting up ibverbs-providers:amd64 (44.0-2) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up openssh-client (1:9.2p1-2) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10) ... Setting up libpaper-utils (1.1.29) ... Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libxnvctrl0:amd64 (525.85.05-1) ... Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up adwaita-icon-theme (43-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up 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 (2.4.2-3) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libnsl2:amd64 (1.3.0-2) ... 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-5) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libhtsjdk-java (3.0.4+dfsg-2) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up librdmacm1:amd64 (44.0-2) ... Setting up libucx0:amd64 (1.13.1-1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up bcftools (1.16-1) ... Setting up libhwloc-plugins:amd64 (2.9.0-1) ... Setting up samtools (1.16.1-1) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up r-base-core (4.2.2.20221110-2) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-gtable (0.3.1+dfsg-1) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-lattice (0.20-45-3) ... Setting up r-cran-nlme (3.1.162-1) ... Setting up r-cran-farver (2.1.1-1) ... Setting up r-cran-viridislite (0.4.1-1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.2-2) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up libbarclay-java (4.1.0+dfsg-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up r-cran-littler (0.3.17-1) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up r-cran-rcpp (1.0.10-1) ... Setting up r-cran-codetools (0.2-19-1) ... Setting up python3.11 (3.11.2-6) ... Setting up r-cran-inline (0.3.19-2) ... Setting up r-cran-rlang (1.0.6-1) ... Setting up littler (0.3.17-1) ... Setting up libpmix2:amd64 (4.2.2-1+b1) ... Setting up r-cran-withr (2.5.0-1) ... Setting up libgkl-java (0.8.10+dfsg-3) ... Setting up r-cran-iterators (1.0.14-1) ... Setting up libgtk2.0-0:amd64 (2.24.33-2) ... Setting up libopenmpi3:amd64 (4.1.4-3+b1) ... Setting up r-cran-foreach (1.5.2-1) ... Setting up r-cran-fansi (1.0.4-1) ... Setting up r-cran-mass (7.3-58.2-1) ... Setting up python3 (3.11.2-1+b1) ... Setting up r-cran-glue (1.6.2-1) ... Setting up r-cran-gam (1.22-1-1) ... Setting up r-cran-cli (3.6.0-1) ... Setting up r-cran-lifecycle (1.0.3+dfsg-1) ... Setting up bowtie2 (2.5.0-3+b2) ... Setting up python3-monotonic (1.6-2) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up libpicard-java (2.27.5+dfsg-2) ... Setting up r-cran-utf8 (1.2.3-1) ... 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 python3-setproctitle:amd64 (1.3.1-1+b2) ... Setting up r-cran-matrix (1.5-3-1) ... Setting up r-cran-mgcv (1.8-41-1) ... Setting up python3-coloredlogs (15.0.1-1) ... Setting up r-cran-rcppgsl (0.3.13-1) ... Setting up r-cran-vctrs (0.5.2-1) ... Setting up openmpi-bin (4.1.4-3+b1) ... 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 (1.8.1+dfsg-1) ... Setting up python3-configargparse (1.5.3-1) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up python3-ruamel.yaml.clib:amd64 (0.2.7-1+b2) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-tibble (3.1.8+dfsg-1) ... Setting up examl (3.0.22-3+b2) ... Setting up r-cran-scales (1.2.1-1) ... Setting up python3-ruamel.yaml (0.17.21-1) ... Setting up r-cran-ggplot2 (3.4.1+dfsg-1) ... Setting up mapdamage (2.2.1+dfsg-3) ... Setting up openjdk-17-jre-headless:amd64 (17.0.6+10-1) ... 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 ca-certificates-java (20230103) ... 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:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.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: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:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.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_1.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:SZAFIR_ROOT_CA2.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:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.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 (2:1.17-74) ... Setting up openjdk-17-jre:amd64 (17.0.6+10-1) ... Setting up default-jre (2:1.17-74) ... Setting up picard-tools (2.27.5+dfsg-2) ... Setting up paleomix (1.3.7-3) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for ca-certificates (20230311) ... 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 (20230103) ... done. 0m51.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', '-y', 'install', 'paleomix'] 0m51.3s INFO: Running scripts post_install 0m51.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_install_exceptions'] 0m51.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_install_exceptions'] 0m51.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 0m52.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 0m52.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpqepzyjea to sid 0m52.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m52.7s INFO: Running scripts pre_distupgrade 0m52.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m52.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m52.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_distupgrade_exceptions'] 0m52.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_distupgrade_exceptions'] 0m52.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m52.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m52.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m52.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m52.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m52.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m52.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', 'update'] 0m57.1s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [199 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9451 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6987 kB] Fetched 16.6 MB in 3s (4759 kB/s) Reading package lists... 0m57.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', 'update'] 0m57.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', '-yf', 'dist-upgrade'] 1m10.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libquadmath0 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: gcc-13-base The following packages will be upgraded: at-spi2-common base-files libatk1.0-0 libatomic1 libbsd0 libcommons-compress-java libcrypt1 libcups2 libdbus-1-3 libgcc-s1 libgcrypt20 libgfortran5 libgomp1 libhtscodecs2 libllvm15 libnghttp2-14 libnspr4 libnss3 libopenmpi3 libpcsclite1 libpython3.11-minimal libpython3.11-stdlib libquadmath0 libsasl2-2 libsasl2-modules-db libstdc++6 libsystemd0 libudev1 openjdk-17-jre openjdk-17-jre-headless openmpi-bin openmpi-common paleomix python3.11 python3.11-minimal r-base-core r-cran-mass r-cran-mgcv r-cran-pkgkitten tzdata 40 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 114 MB of archives. After this operation, 2332 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.4-1 [579 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.4-1 [1803 kB] Get:4 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.4-1 [2060 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.4-1 [815 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.35-1 [89.7 kB] Get:7 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.1.0-5 [38.2 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 13.1.0-5 [57.7 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.2-2 [704 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 13.1.0-5 [695 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 252.11-1 [331 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 252.11-1 [107 kB] Get:13 http://deb.debian.org/debian sid/main amd64 tzdata all 2023c-6 [254 kB] Get:14 http://deb.debian.org/debian sid/main amd64 at-spi2-common all 2.48.3-1 [164 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libatk1.0-0 amd64 2.48.3-1 [49.7 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 13.1.0-5 [9300 B] Get:17 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.11.7-4 [115 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libcommons-compress-java all 1.23.0-1 [630 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libcups2 amd64 2.4.2-4 [244 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libdbus-1-3 amd64 1.14.8-1 [200 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 13.1.0-5 [804 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 13.1.0-5 [131 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.5.0-1 [91.2 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libllvm15 amd64 1:15.0.7-4 [23.1 MB] Get:25 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.54.0-1 [73.2 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libnspr4 amd64 2:4.35-1.1 [108 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libnss3 amd64 2:3.89-2 [1331 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libopenmpi3 amd64 4.1.5-2 [2424 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libpcsclite1 amd64 2.0.0-1 [50.0 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 13.1.0-5 [145 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-1 [19.2 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-1 [58.6 kB] Get:33 http://deb.debian.org/debian sid/main amd64 openjdk-17-jre amd64 17.0.7+7-1 [184 kB] Get:34 http://deb.debian.org/debian sid/main amd64 openjdk-17-jre-headless amd64 17.0.7+7-1 [43.7 MB] Get:35 http://deb.debian.org/debian sid/main amd64 openmpi-common all 4.1.5-2 [167 kB] Get:36 http://deb.debian.org/debian sid/main amd64 openmpi-bin amd64 4.1.5-2 [226 kB] Get:37 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.3.0-1 [26.7 MB] Get:38 http://deb.debian.org/debian sid/main amd64 paleomix amd64 1.3.8-1 [984 kB] Get:39 http://deb.debian.org/debian sid/main amd64 r-cran-mass amd64 7.3-58.3-1 [1122 kB] Get:40 http://deb.debian.org/debian sid/main amd64 r-cran-mgcv amd64 1.8-42-1 [3190 kB] Get:41 http://deb.debian.org/debian sid/main amd64 r-cran-pkgkitten all 0.2.3-1 [26.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 114 MB in 2s (68.1 MB/s) (Reading database ... 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Unpacking libllvm15:amd64 (1:15.0.7-4) over (1:15.0.6-4+b1) ... Preparing to unpack .../12-libnghttp2-14_1.54.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.54.0-1) over (1.52.0-1) ... Preparing to unpack .../13-libnspr4_2%3a4.35-1.1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.35-1.1) over (2:4.35-1) ... Preparing to unpack .../14-libnss3_2%3a3.89-2_amd64.deb ... Unpacking libnss3:amd64 (2:3.89-2) over (2:3.87.1-1) ... Preparing to unpack .../15-libopenmpi3_4.1.5-2_amd64.deb ... Unpacking libopenmpi3:amd64 (4.1.5-2) over (4.1.4-3+b1) ... Preparing to unpack .../16-libpcsclite1_2.0.0-1_amd64.deb ... Unpacking libpcsclite1:amd64 (2.0.0-1) over (1.9.9-2) ... Preparing to unpack .../17-libquadmath0_13.1.0-5_amd64.deb ... Unpacking libquadmath0:amd64 (13.1.0-5) over (12.2.0-14) ... Preparing to unpack .../18-libsasl2-modules-db_2.1.28+dfsg1-1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-1) over (2.1.28+dfsg-10) ... Preparing to unpack .../19-libsasl2-2_2.1.28+dfsg1-1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-1) over (2.1.28+dfsg-10) ... Preparing to unpack .../20-openjdk-17-jre_17.0.7+7-1_amd64.deb ... Unpacking openjdk-17-jre:amd64 (17.0.7+7-1) over (17.0.6+10-1) ... Preparing to unpack .../21-openjdk-17-jre-headless_17.0.7+7-1_amd64.deb ... Unpacking openjdk-17-jre-headless:amd64 (17.0.7+7-1) over (17.0.6+10-1) ... Preparing to unpack .../22-openmpi-common_4.1.5-2_all.deb ... Unpacking openmpi-common (4.1.5-2) over (4.1.4-3) ... Preparing to unpack .../23-openmpi-bin_4.1.5-2_amd64.deb ... Unpacking openmpi-bin (4.1.5-2) over (4.1.4-3+b1) ... Preparing to unpack .../24-r-base-core_4.3.0-1_amd64.deb ... Unpacking r-base-core (4.3.0-1) over (4.2.2.20221110-2) ... Preparing to unpack .../25-paleomix_1.3.8-1_amd64.deb ... Unpacking paleomix (1.3.8-1) over (1.3.7-3) ... Preparing to unpack .../26-r-cran-mass_7.3-58.3-1_amd64.deb ... Unpacking r-cran-mass (7.3-58.3-1) over (7.3-58.2-1) ... Preparing to unpack .../27-r-cran-mgcv_1.8-42-1_amd64.deb ... Unpacking r-cran-mgcv (1.8-42-1) over (1.8-41-1) ... Preparing to unpack .../28-r-cran-pkgkitten_0.2.3-1_all.deb ... Unpacking r-cran-pkgkitten (0.2.3-1) over (0.2.2-2) ... Setting up libhtscodecs2:amd64 (1.5.0-1) ... Setting up libcommons-compress-java (1.23.0-1) ... Setting up libopenmpi3:amd64 (4.1.5-2) ... Setting up libnghttp2-14:amd64 (1.54.0-1) ... Setting up libgomp1:amd64 (13.1.0-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-1) ... Setting up tzdata (2023c-6) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jun 12 10:00:42 UTC 2023. Universal Time is now: Mon Jun 12 10:00:42 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libnspr4:amd64 (2:4.35-1.1) ... Setting up libdbus-1-3:amd64 (1.14.8-1) ... Setting up libquadmath0:amd64 (13.1.0-5) ... Setting up r-base-core (4.3.0-1) ... Installing new version of config file /etc/R/Makeconf ... Installing new version of config file /etc/R/repositories ... Setting up libatomic1:amd64 (13.1.0-5) ... Setting up libpcsclite1:amd64 (2.0.0-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-1) ... Setting up libgfortran5:amd64 (13.1.0-5) ... Setting up libcups2:amd64 (2.4.2-4) ... Setting up r-cran-mgcv (1.8-42-1) ... Setting up at-spi2-common (2.48.3-1) ... Setting up libllvm15:amd64 (1:15.0.7-4) ... Setting up openmpi-common (4.1.5-2) ... Setting up libatk1.0-0:amd64 (2.48.3-1) ... Setting up libpython3.11-minimal:amd64 (3.11.4-1) ... Setting up r-cran-pkgkitten (0.2.3-1) ... Setting up paleomix (1.3.8-1) ... Setting up libbsd0:amd64 (0.11.7-4) ... Setting up openmpi-bin (4.1.5-2) ... Setting up python3.11-minimal (3.11.4-1) ... Setting up libpython3.11-stdlib:amd64 (3.11.4-1) ... Setting up r-cran-mass (7.3-58.3-1) ... Setting up libnss3:amd64 (2:3.89-2) ... Setting up openjdk-17-jre-headless:amd64 (17.0.7+7-1) ... Installing new version of config file /etc/java-17-openjdk/jfr/default.jfc ... Installing new version of config file /etc/java-17-openjdk/jfr/profile.jfc ... Installing new version of config file /etc/java-17-openjdk/security/java.security ... Setting up python3.11 (3.11.4-1) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for ca-certificates-java (20230103) ... done. Processing triggers for hicolor-icon-theme (0.17-2) ... Setting up openjdk-17-jre:amd64 (17.0.7+7-1) ... 1m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', '-yf', 'dist-upgrade'] 1m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m11.1s DUMP: 6668516bfae8f1510aa5d18315f5d4b0 - 1m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'show', '--no-all-versions', 'paleomix'] 1m11.4s DUMP: 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-en: pipelines and tools for the processing of ancient and modern HTS data The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data: The BAM pipeline processes de-multiplexed reads from one or more samples, through sequence processing and alignment, to generate BAM alignment files useful in downstream analyses; the Phylogenetic pipeline carries out genotyping and phylogenetic inference on BAM alignment files, either produced using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out a suite of analyses on low coverage equine alignments, in order to detect the presence of F1-hybrids in archaeological assemblages. In addition, PALEOMIX aids in metagenomic analysis of the extracts. . The pipelines have been designed with ancient DNA (aDNA) in mind, and includes several features especially useful for the analyses of ancient samples, but can all be for the processing of modern samples, in order to ensure consistent data processing. Description-md5: 7cb3c4aa709e51b480a41a73961d7253 Homepage: https://geogenetics.ku.dk/publications/paleomix Section: science Priority: optional Filename: pool/main/p/paleomix/paleomix_1.3.8-1_amd64.deb Size: 983864 MD5sum: 5f5fdaf6a3957756e162048d7dfa0362 SHA256: 1962b954a2ab038bd6339542265e1f9720eba2aeaded3066749bda681a7424ba 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'show', '--no-all-versions', 'paleomix'] 1m11.4s INFO: apt-cache knows about the following packages: paleomix 1m11.4s INFO: Running scripts pre_install 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_database-server'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_database-server'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_exceptions'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_exceptions'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_extras'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_extras'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_foreign_architecture'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_foreign_architecture'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'policy'] 1m11.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'policy'] 1m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'policy', 'paleomix'] 1m11.5s DUMP: paleomix: Installed: 1.3.8-1 Candidate: 1.3.8-1 Version table: *** 1.3.8-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'policy', 'paleomix'] 1m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', '-y', 'install', 'paleomix'] 1m12.1s DUMP: Reading package lists... Building dependency tree... Reading state information... paleomix is already the newest version (1.3.8-1). The following package was automatically installed and is no longer required: libquadmath0 Use 'sudo apt autoremove' to remove it. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', '-y', 'install', 'paleomix'] 1m12.1s INFO: Running scripts post_install 1m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_install_exceptions'] 1m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_install_exceptions'] 1m12.1s INFO: Running scripts post_distupgrade 1m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_distupgrade_exceptions'] 1m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_distupgrade_exceptions'] 1m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_distupgrade_zz_backports'] 1m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_distupgrade_zz_backports'] 1m12.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 1m13.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 1m13.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 1m14.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 1m14.0s INFO: Running scripts pre_install 1m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_database-server'] 1m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_database-server'] 1m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_exceptions'] 1m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_exceptions'] 1m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_extras'] 1m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_extras'] 1m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_foreign_architecture'] 1m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_foreign_architecture'] 1m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'policy'] 1m14.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'policy'] 1m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'policy', 'paleomix'] 1m14.1s DUMP: paleomix: Installed: 1.3.8-1 Candidate: 1.3.8-1 Version table: *** 1.3.8-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-cache', 'policy', 'paleomix'] 1m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', '-y', 'install', 'paleomix=1.3.8-1'] 1m14.6s DUMP: Reading package lists... Building dependency tree... Reading state information... paleomix is already the newest version (1.3.8-1). The following package was automatically installed and is no longer required: libquadmath0 Use 'sudo apt autoremove' to remove it. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', '-y', 'install', 'paleomix=1.3.8-1'] 1m14.6s INFO: Running scripts post_install 1m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_install_exceptions'] 1m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_install_exceptions'] 1m14.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 1m15.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 1m16.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', '-ac', '--ignore-obsolete'] 1m20.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', '-ac', '--ignore-obsolete'] 1m20.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m20.7s DUMP: 0.15.6 1m20.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m20.7s INFO: Running adequate version 0.15.6 now. 1m20.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'paleomix'] 1m20.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'paleomix'] 1m20.8s INFO: Running scripts pre_remove 1m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m27.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m27.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_remove_exceptions'] 1m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/pre_remove_exceptions'] 1m27.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m27.8s DUMP: install ok installed adapterremoval adapterremoval 2.3.3-2 install ok installed adduser adduser 3.134 install ok installed adwaita-icon-theme adwaita-icon-theme 43-1 install ok installed apt apt 2.6.1 install ok installed at-spi2-common at-spi2-common 2.48.3-1 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bcftools bcftools 1.16-1 install ok installed bedtools bedtools 2.30.0+dfsg-3 install ok installed bowtie2 bowtie2 2.5.0-3+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed bwa bwa 0.7.17-7+b2 install ok installed ca-certificates ca-certificates 20230311 install ok installed ca-certificates-java ca-certificates-java 20230103 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3 install ok installed debianutils debianutils 5.7-0.4 install ok installed default-jre default-jre 2:1.17-74 install ok installed default-jre-headless default-jre-headless 2:1.17-74 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed examl examl 3.0.22-3+b2 install ok installed findutils findutils 4.9.0-4 install ok installed fontconfig fontconfig 2.14.1-4 install ok installed fontconfig-config fontconfig-config 2.14.1-4 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-6 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gcc-13-base:amd64 gcc-13-base 13.1.0-5 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gtk-update-icon-cache gtk-update-icon-cache 3.24.37-2 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+nmu1 install ok installed ibverbs-providers:amd64 ibverbs-providers 44.0-2 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed java-common java-common 0.74 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapache-pom-java libapache-pom-java 29-2 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libasound2:amd64 libasound2 1.2.8-1+b1 install ok installed libasound2-data libasound2-data 1.2.8-1 install ok installed libatk1.0-0:amd64 libatk1.0-0 2.48.3-1 install ok installed libatomic1:amd64 libatomic1 13.1.0-5 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-10 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-10 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-10 install ok installed libbarclay-java libbarclay-java 4.1.0+dfsg-1 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b6 install ok installed libbsd0:amd64 libbsd0 0.11.7-4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9 install ok installed libc6:amd64 libc6 2.36-9 install ok installed libcairo2:amd64 libcairo2 1.16.0-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcbor0.8:amd64 libcbor0.8 0.8.0-2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcommons-codec-java libcommons-codec-java 1.15-1 install ok installed libcommons-compress-java libcommons-compress-java 1.23.0-1 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 3.12.0-2 install ok installed libcommons-logging-java libcommons-logging-java 1.2-3 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 1:4.4.35-1 install ok installed libcups2:amd64 libcups2 2.4.2-4 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.88.1-10 install ok installed libcurl4:amd64 libcurl4 7.88.1-10 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-2+b1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.14.8-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libdeflate0:amd64 libdeflate0 1.14-1 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.114-1+b1 install ok installed libdrm-common libdrm-common 2.4.114-1 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.114-1+b1 install ok installed libdrm-nouveau2:amd64 libdrm-nouveau2 2.4.114-1+b1 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.114-1+b1 install ok installed libdrm2:amd64 libdrm2 2.4.114-1+b1 install ok installed libedit2:amd64 libedit2 3.1-20221030-2 install ok installed libelf1:amd64 libelf1 0.188-2.1 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 2.5.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libfabric1:amd64 libfabric1 1.17.0-3 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfido2-1:amd64 libfido2-1 1.12.0-2+b1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libfontconfig1:amd64 libfontconfig1 2.14.1-4 install ok installed libfreemarker-java libfreemarker-java 2.3.31-2 install ok installed libfreetype6:amd64 libfreetype6 2.12.1+dfsg-5 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2.1 install ok installed libgatk-native-bindings-java libgatk-native-bindings-java 1.0.0+dfsg-2 install ok installed libgcc-s1:amd64 libgcc-s1 13.1.0-5 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.2-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgdk-pixbuf-2.0-0:amd64 libgdk-pixbuf-2.0-0 2.42.10+dfsg-1+b1 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.42.10+dfsg-1 install ok installed libgfortran5:amd64 libgfortran5 13.1.0-5 install ok installed libgif7:amd64 libgif7 5.2.1-2.5 install ok installed libgkl-java libgkl-java 0.8.10+dfsg-3 install ok installed libgl1:amd64 libgl1 1.6.0-1 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 22.3.6-1+deb12u1 install ok installed libglapi-mesa:amd64 libglapi-mesa 22.3.6-1+deb12u1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.74.6-2 install ok installed libglvnd0:amd64 libglvnd0 1.6.0-1 install ok installed libglx-mesa0:amd64 libglx-mesa0 22.3.6-1+deb12u1 install ok installed libglx0:amd64 libglx0 1.6.0-1 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2 install ok installed libgomp1:amd64 libgomp1 13.1.0-5 install ok installed libgoogle-gson-java libgoogle-gson-java 2.10-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgsl-dev libgsl-dev 2.7.1+dfsg-5 install ok installed libgsl27:amd64 libgsl27 2.7.1+dfsg-5 install ok installed libgslcblas0:amd64 libgslcblas0 2.7.1+dfsg-5 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2 install ok installed libgtk2.0-0:amd64 libgtk2.0-0 2.24.33-2 install ok installed libgtk2.0-common libgtk2.0-common 2.24.33-2 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 6.0.0+dfsg-3 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libhts3:amd64 libhts3 1.16+ds-3 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.5.0-1 install ok installed libhtsjdk-java libhtsjdk-java 3.0.4+dfsg-2 install ok installed libhttpclient-java libhttpclient-java 4.5.14-1 install ok installed libhttpcore-java libhttpcore-java 4.4.16-1 install ok installed libhwloc-plugins:amd64 libhwloc-plugins 2.9.0-1 install ok installed libhwloc15:amd64 libhwloc15 2.9.0-1 install ok installed libibverbs1:amd64 libibverbs1 44.0-2 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu72:amd64 libicu72 72.1-3 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjoptsimple-java libjoptsimple-java 5.0.4-4 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-2 install ok installed liblightcouch-java liblightcouch-java 0.2.0-1 install ok installed libllvm15:amd64 libllvm15 1:15.0.7-4 install ok installed liblog4j2-java liblog4j2-java 2.19.0-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.3-1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.3-1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.3-1 install ok installed libmd0:amd64 libmd0 1.0.4-2 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 2.38.1-5+b1 install ok installed libmunge2 libmunge2 0.5.15-2 install ok installed libncbi-ngs3:amd64 libncbi-ngs3 3.0.3+dfsg-5 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.0.2+dfsg-2 install ok installed libncurses6:amd64 libncurses6 6.4-4 install ok installed libncursesw6:amd64 libncursesw6 6.4-4 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.54.0-1 install ok installed libngs-java:amd64 libngs-java 3.0.3+dfsg-5 install ok installed libngs-jni:amd64 libngs-jni 3.0.3+dfsg-5 install ok installed libnl-3-200:amd64 libnl-3-200 3.7.0-0.2+b1 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.7.0-0.2+b1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libnspr4:amd64 libnspr4 2:4.35-1.1 install ok installed libnss3:amd64 libnss3 2:3.89-2 install ok installed libnuma1:amd64 libnuma1 2.0.16-1 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libopenblas-dev:amd64 libopenblas-dev 0.3.21+ds-4 install ok installed libopenblas-pthread-dev:amd64 libopenblas-pthread-dev 0.3.21+ds-4 install ok installed libopenblas0:amd64 libopenblas0 0.3.21+ds-4 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.21+ds-4 install ok installed libopenmpi3:amd64 libopenmpi3 4.1.5-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6 install ok installed libpam-runtime libpam-runtime 1.5.2-6 install ok installed libpam0g:amd64 libpam0g 1.5.2-6 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.50.12+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.50.12+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.50.12+ds-1 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 0.17-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libpcsclite1:amd64 libpcsclite1 2.0.0-1 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7 install ok installed libpicard-java libpicard-java 2.27.5+dfsg-2 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1 install ok installed libpmix2:amd64 libpmix2 4.2.2-1+b1 install ok installed libpng16-16:amd64 libpng16-16 1.6.39-2 install ok installed libpsl5:amd64 libpsl5 0.21.2-1 install ok installed libpsm-infinipath1 libpsm-infinipath1 3.3+20.604758e7-6.2 install ok installed libpsm2-2 libpsm2-2 11.2.185-2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.2-1+b1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.4-1 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.4-1 install ok installed libquadmath0:amd64 libquadmath0 13.1.0-5 install ok installed librdmacm1:amd64 librdmacm1 44.0-2 install ok installed libreadline8:amd64 libreadline8 8.2-1.3 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+dfsg1-1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsensors-config libsensors-config 1:3.6.0-7.1 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-7.1 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 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 2.38.1-5+b1 install ok installed libsnappy-java libsnappy-java 1.1.8.3-1 install ok installed libsnappy-jni libsnappy-jni 1.1.8.3-1 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.1.9-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.40.1-2 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssh2-1:amd64 libssh2-1 1.10.0-3+b1 install ok installed libssl3:amd64 libssl3 3.0.9-1 install ok installed libstdc++6:amd64 libstdc++6 13.1.0-5 install ok installed libsystemd0:amd64 libsystemd0 252.11-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.13+dfsg-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libthai-data libthai-data 0.1.29-1 install ok installed libthai0:amd64 libthai0 0.1.29-1 install ok installed libtiff6:amd64 libtiff6 4.5.0-6 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.13-2 install ok installed libucx0:amd64 libucx0 1.13.1-1 install ok installed libudev1:amd64 libudev1 252.11-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libwebp7:amd64 libwebp7 1.2.4-0.2 install ok installed libx11-6:amd64 libx11-6 2:1.8.4-2 install ok installed libx11-data libx11-data 2:1.8.4-2 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.8.4-2 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 install ok installed libxi6:amd64 libxi6 2:1.8-1+b1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.2 install ok installed libxnvctrl0:amd64 libxnvctrl0 525.85.05-1 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 0.8.1-1 install ok installed libz3-4:amd64 libz3-4 4.8.12-3.1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed littler littler 0.3.17-1 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mafft mafft 7.505-1 install ok installed mapdamage mapdamage 2.2.1+dfsg-3 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed media-types media-types 10.0.0 install ok installed mount mount 2.38.1-5+b1 install ok installed ncbi-vdb-data ncbi-vdb-data 3.0.2+dfsg-2 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.3.1-1 install ok installed openjdk-17-jre:amd64 openjdk-17-jre 17.0.7+7-1 install ok installed openjdk-17-jre-headless:amd64 openjdk-17-jre-headless 17.0.7+7-1 install ok installed openmpi-bin openmpi-bin 4.1.5-2 install ok installed openmpi-common openmpi-common 4.1.5-2 install ok installed openssh-client openssh-client 1:9.2p1-2 install ok installed openssl openssl 3.0.9-1 install ok installed paleomix paleomix 1.3.8-1 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl perl 5.36.0-7 install ok installed perl-base perl-base 5.36.0-7 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7 install ok installed phylip phylip 1:3.697+dfsg-2 install ok installed picard-tools picard-tools 2.27.5+dfsg-2 install ok installed python3 python3 3.11.2-1+b1 install ok installed python3-coloredlogs python3-coloredlogs 15.0.1-1 install ok installed python3-configargparse python3-configargparse 1.5.3-1 install ok installed python3-humanfriendly python3-humanfriendly 10.0-3 install ok installed python3-minimal python3-minimal 3.11.2-1+b1 install ok installed python3-monotonic python3-monotonic 1.6-2 install ok installed python3-pysam python3-pysam 0.20.0+ds-3+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 0.2.7-1+b2 install ok installed python3-setproctitle:amd64 python3-setproctitle 1.3.1-1+b2 install ok installed python3.11 python3.11 3.11.4-1 install ok installed python3.11-minimal python3.11-minimal 3.11.4-1 install ok installed r-base-core r-base-core 4.3.0-1 install ok installed r-cran-cli r-cran-cli 3.6.0-1 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 1.0.4-1 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 1.22-1-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.4.1+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.6.2-1 install ok installed r-cran-gtable r-cran-gtable 0.3.1+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 0.4.2-1 install ok installed r-cran-lattice r-cran-lattice 0.20-45-3 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.3+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.17-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-mass r-cran-mass 7.3-58.3-1 install ok installed r-cran-matrix r-cran-matrix 1.5-3-1 install ok installed r-cran-mgcv r-cran-mgcv 1.8-42-1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-2 install ok installed r-cran-nlme r-cran-nlme 3.1.162-1 install ok installed r-cran-pillar r-cran-pillar 1.8.1+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.3-1 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 1.0.10-1 install ok installed r-cran-rcppgsl r-cran-rcppgsl 0.3.13-1 install ok installed r-cran-rlang r-cran-rlang 1.0.6-1 install ok installed r-cran-scales r-cran-scales 1.2.1-1 install ok installed r-cran-tibble r-cran-tibble 3.1.8+dfsg-1 install ok installed r-cran-utf8 r-cran-utf8 1.2.3-1 install ok installed r-cran-vctrs r-cran-vctrs 0.5.2-1 install ok installed r-cran-viridislite r-cran-viridislite 0.4.1-1 install ok installed r-cran-withr r-cran-withr 2.5.0-1 install ok installed radiant radiant 2.8.1+dfsg-2 install ok installed raxml raxml 8.2.12+dfsg-8+b2 install ok installed readline-common readline-common 8.2-1.3 install ok installed samtools samtools 1.16.1-1 install ok installed sed sed 4.9-1 install ok installed sensible-utils sensible-utils 0.0.17+nmu1 install ok installed seqtk seqtk 1.3-4 install ok installed shared-mime-info shared-mime-info 2.2-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-6 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 35 install ok installed usrmerge usrmerge 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 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 1:1.2.13.dfsg-1 1m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m27.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', 'remove', 'adapterremoval', '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', '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', 'libcbor0.8: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', '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', 'libllvm15:amd64', 'liblog4j2-java', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmongodb-java', 'libmunge2', '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', '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', 'libquadmath0:amd64', 'librdmacm1:amd64', 'libreadline8:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libucx0: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', 'ocl-icd-libopencl1:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', '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'] 1m32.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adapterremoval 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 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 libcbor0.8 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 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 libllvm15 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 libpicard-java libpixman-1-0 libpmix2 libpng16-16 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 librdmacm1 libreadline8 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsqlite3-0 libssh2-1 libssl3 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3 libtk8.6 libucx0 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 ocl-icd-libopencl1 openjdk-17-jre openjdk-17-jre-headless openmpi-bin openmpi-common openssh-client openssl paleomix 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, 288 to remove and 0 not upgraded. After this operation, 884 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 ... 26160 files and directories currently installed.) Removing paleomix (1.3.8-1) ... Removing adapterremoval (2.3.3-2) ... Removing picard-tools (2.27.5+dfsg-2) ... Removing default-jre (2:1.17-74) ... Removing openjdk-17-jre:amd64 (17.0.7+7-1) ... Removing libgtk2.0-0:amd64 (2.24.33-2) ... Removing adwaita-icon-theme (43-1) ... Removing libatk1.0-0:amd64 (2.48.3-1) ... Removing at-spi2-common (2.48.3-1) ... Removing bcftools (1.16-1) ... Removing bedtools (2.30.0+dfsg-3) ... Removing bowtie2 (2.5.0-3+b2) ... Removing bwa (0.7.17-7+b2) ... Removing mapdamage (2.2.1+dfsg-3) ... Removing r-cran-ggplot2 (3.4.1+dfsg-1) ... Removing r-cran-mgcv (1.8-42-1) ... Removing r-cran-matrix (1.5-3-1) ... Removing r-cran-rcppgsl (0.3.13-1) ... Removing r-cran-rcpp (1.0.10-1) ... Removing r-cran-scales (1.2.1-1) ... Removing r-cran-rcolorbrewer (1.1-3-1) ... Removing r-cran-withr (2.5.0-1) ... Removing default-jre-headless (2:1.17-74) ... Removing examl (3.0.22-3+b2) ... Removing gtk-update-icon-cache (3.24.37-2) ... Removing hicolor-icon-theme (0.17-2) ... Removing openmpi-bin (4.1.5-2) ... Removing libopenmpi3:amd64 (4.1.5-2) ... Removing libucx0:amd64 (1.13.1-1) ... Removing libfabric1:amd64 (1.17.0-3) ... Removing ibverbs-providers:amd64 (44.0-2) ... Removing libpicard-java (2.27.5+dfsg-2) ... Removing libgkl-java (0.8.10+dfsg-3) ... Removing libhtsjdk-java (3.0.4+dfsg-2) ... Removing libcommons-compress-java (1.23.0-1) ... Removing libcommons-jexl2-java (2.1.1-6) ... Removing libatomic1:amd64 (13.1.0-5) ... Removing libbarclay-java (4.1.0+dfsg-1) ... Removing r-cran-gam (1.22-1-1) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing libgl1:amd64 (1.6.0-1) ... Removing libglx0:amd64 (1.6.0-1) ... Removing libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Removing libpmix2:amd64 (4.2.2-1+b1) ... Removing libhwloc-plugins:amd64 (2.9.0-1) ... Removing libxnvctrl0:amd64 (525.85.05-1) ... Removing openssh-client (1:9.2p1-2) ... Removing libfido2-1:amd64 (1.12.0-2+b1) ... Removing libcbor0.8:amd64 (0.8.0-2+b1) ... Removing liblog4j2-java (2.19.0-2) ... Removing liblightcouch-java (0.2.0-1) ... Removing libhttpclient-java (4.5.14-1) ... Removing libcommons-codec-java (1.15-1) ... Removing libcommons-io-java (2.11.0-2) ... Removing libcommons-lang3-java (3.12.0-2) ... Removing libcommons-math3-java (3.6.1-3) ... Removing samtools (1.16.1-1) ... Removing python3-pysam (0.20.0+ds-3+b1) ... Removing libhts3:amd64 (1.16+ds-3) ... Removing libcurl3-gnutls:amd64 (7.88.1-10) ... Removing libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Removing libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Removing libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Removing libdrm-radeon1:amd64 (2.4.114-1+b1) ... Removing libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Removing libdrm-intel1:amd64 (2.4.114-1+b1) ... Removing libllvm15:amd64 (1:15.0.7-4) ... Removing libedit2:amd64 (3.1-20221030-2) ... Removing libelf1:amd64 (0.188-2.1) ... 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 (0.2.7-1+b2) ... Removing python3-setproctitle:amd64 (1.3.1-1+b2) ... 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 libgdk-pixbuf2.0-common (2.42.10+dfsg-1) ... Removing libopenblas-dev:amd64 (0.3.21+ds-4) ... Removing libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... Removing libopenblas0:amd64 (0.3.21+ds-4) ... Removing libgif7:amd64 (5.2.1-2.5) ... Removing libglapi-mesa:amd64 (22.3.6-1+deb12u1) ... Removing shared-mime-info (2.2-1) ... Removing libglvnd0:amd64 (1.6.0-1) ... Removing libgoogle-gson-java (2.10-1) ... Removing libgsl-dev (2.7.1+dfsg-5) ... Removing libgsl27:amd64 (2.7.1+dfsg-5) ... Removing libgslcblas0:amd64 (2.7.1+dfsg-5) ... Removing libgtk2.0-common (2.24.33-2) ... Removing libhtscodecs2:amd64 (1.5.0-1) ... Removing libhttpcore-java (4.4.16-1) ... Removing libhwloc15:amd64 (2.9.0-1) ... Removing librdmacm1:amd64 (44.0-2) ... Removing libibverbs1:amd64 (44.0-2) ... Removing libxml2:amd64 (2.9.14+dfsg-1.2) ... Removing libjoptsimple-java (5.0.4-4) ... Removing libngs-java:amd64 (3.0.3+dfsg-5) ... Removing libngs-jni:amd64 (3.0.3+dfsg-5) ... Removing libncbi-ngs3:amd64 (3.0.3+dfsg-5) ... Removing libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Removing libmbedtls14:amd64 (2.28.3-1) ... Removing libmbedx509-1:amd64 (2.28.3-1) ... Removing libmbedcrypto7:amd64 (2.28.3-1) ... Removing libmjson-java (1.4.0-3) ... Removing libmongodb-java (3.6.3-2) ... Removing libmunge2 (0.5.15-2) ... Removing libncurses6:amd64 (6.4-4) ... Removing libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Removing libnl-3-200:amd64 (3.7.0-0.2+b1) ... Removing libpsm2-2 (11.2.185-2) ... Removing libnuma1:amd64 (2.0.16-1) ... Removing libpciaccess0:amd64 (0.17-2) ... Removing libpsm-infinipath1 (3.3+20.604758e7-6.2) ... 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 libquadmath0:amd64 (13.1.0-5) ... Removing librhino-java (1.7.14-2.1) ... Removing libsensors5:amd64 (1:3.6.0-7.1) ... Removing libsensors-config (1:3.6.0-7.1) ... Removing libslf4j-java (1.7.32-1) ... Removing libsnappy-java (1.1.8.3-1) ... Removing libsnappy-jni (1.1.8.3-1) ... Removing libsnappy1v5:amd64 (1.1.9-3) ... Removing libx11-xcb1:amd64 (2:1.8.4-2) ... 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 libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Removing libxtst6:amd64 (2:1.2.3-1.1) ... Removing libxfixes3:amd64 (1:6.0.0-2) ... Removing libxi6:amd64 (2:1.8-1+b1) ... Removing libxinerama1:amd64 (2:1.1.4-3) ... Removing libxrandr2:amd64 (2:1.5.2-2+b1) ... Removing libxshmfence1:amd64 (1.3-1) ... Removing libz3-4:amd64 (4.8.12-3.1) ... Removing littler (0.3.17-1) ... Removing mafft (7.505-1) ... Removing ncbi-vdb-data (3.0.2+dfsg-2) ... Removing ocl-icd-libopencl1:amd64 (2.3.1-1) ... Removing openmpi-common (4.1.5-2) ... Removing phylip (1:3.697+dfsg-2) ... Removing python3-configargparse (1.5.3-1) ... Removing r-cran-tibble (3.1.8+dfsg-1) ... Removing r-cran-pillar (1.8.1+dfsg-1) ... Removing r-cran-vctrs (0.5.2-1) ... Removing r-cran-lifecycle (1.0.3+dfsg-1) ... Removing r-cran-cli (3.6.0-1) ... 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 (1.0.4-1) ... Removing r-cran-farver (2.1.1-1) ... Removing r-cran-glue (1.6.2-1) ... Removing r-cran-gtable (0.3.1+dfsg-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 (0.4.2-1) ... Removing r-cran-nlme (3.1.162-1) ... Removing r-cran-lattice (0.20-45-3) ... Removing r-cran-littler (0.3.17-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-58.3-1) ... 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 (1.0.6-1) ... Removing r-cran-utf8 (1.2.3-1) ... Removing r-cran-viridislite (0.4.1-1) ... Removing radiant (2.8.1+dfsg-2) ... Removing raxml (8.2.12+dfsg-8+b2) ... Removing seqtk (1.3-4) ... Removing r-base-core (4.3.0-1) ... Removing libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Removing libpango-1.0-0:amd64 (1.50.12+ds-1) ... Removing fontconfig (2.14.1-4) ... Removing libtk8.6:amd64 (8.6.13-2) ... Removing libxft2:amd64 (2.3.6-1) ... Removing libcairo2:amd64 (1.16.0-7) ... Removing libcommons-logging-java (1.2-3) ... Removing libcommons-parent-java (56-1) ... Removing libapache-pom-java (29-2) ... Removing libcurl4:amd64 (7.88.1-10) ... Removing libxt6:amd64 (1:1.2.1-1.1) ... Removing libthai0:amd64 (0.1.29-1) ... Removing libdatrie1:amd64 (0.2.13-2+b1) ... Removing libtiff6:amd64 (4.5.0-6) ... Removing libdeflate0:amd64 (1.14-1) ... Removing libdrm2:amd64 (2.4.114-1+b1) ... Removing libdrm-common (2.4.114-1) ... Removing python3 (3.11.2-1+b1) ... Removing python3.11 (3.11.4-1) ... Removing python3-minimal (3.11.2-1+b1) ... Removing python3.11-minimal (3.11.4-1) ... Removing libfribidi0:amd64 (1.0.8-2.1) ... Removing libopenblas0-pthread:amd64 (0.3.21+ds-4) ... Removing libgfortran5:amd64 (13.1.0-5) ... Removing libgomp1:amd64 (13.1.0-5) ... Removing libpython3-stdlib:amd64 (3.11.2-1+b1) ... Removing libpython3.11-stdlib:amd64 (3.11.4-1) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-2) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libicu72:amd64 (72.1-3) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Removing liblerc4:amd64 (4.0.0+ds-2) ... Removing libncursesw6:amd64 (6.4-4) ... Removing libnghttp2-14:amd64 (1.54.0-1) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libpixman-1-0:amd64 (0.42.2-1) ... Removing libpsl5:amd64 (0.21.2-1) ... Removing libpython3.11-minimal:amd64 (3.11.4-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.2-1.3) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-1) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libssh2-1:amd64 (1.10.0-3+b1) ... Removing libtcl8.6:amd64 (8.6.13+dfsg-2) ... Removing libthai-data (0.1.29-1) ... Removing libtirpc-common (1.3.3+ds-1) ... Removing libwebp7:amd64 (1.2.4-0.2) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing media-types (10.0.0) ... Removing readline-common (8.2-1.3) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.17+nmu1) ... Removing unzip (6.0-28) ... Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-13) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... 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. Removing libx11-6:amd64 (2:1.8.4-2) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.7-4) ... Removing libx11-data (2:1.8.4-2) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing openjdk-17-jre-headless:amd64 (17.0.7+7-1) ... Removing ca-certificates-java (20230103) ... Removing ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libfontconfig1:amd64 (2.14.1-4) ... Removing fontconfig-config (2.14.1-4) ... Removing fonts-dejavu-core (2.37-6) ... Removing java-common (0.74) ... Removing libasound2:amd64 (1.2.8-1+b1) ... Removing libasound2-data (1.2.8-1) ... Removing libcups2:amd64 (2.4.2-4) ... Removing libavahi-client3:amd64 (0.8-10) ... Removing libavahi-common3:amd64 (0.8-10) ... Removing libavahi-common-data:amd64 (0.8-10) ... Removing libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Removing libfreetype6:amd64 (2.12.1+dfsg-5) ... Removing libbrotli1:amd64 (1.0.9-2+b6) ... Removing libdbus-1-3:amd64 (1.14.8-1) ... Removing libexpat1:amd64 (2.5.0-1) ... Removing libglib2.0-0:amd64 (2.74.6-2) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2) ... Removing libkrb5-3:amd64 (1.20.1-2) ... Removing libk5crypto3:amd64 (1.20.1-2) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2) ... Removing liblcms2-2:amd64 (2.14-2) ... Removing libnss3:amd64 (2:3.89-2) ... Removing libnspr4:amd64 (2:4.35-1.1) ... Removing libpcsclite1:amd64 (2.0.0-1) ... Removing libpng16-16:amd64 (1.6.39-2) ... Removing libsqlite3-0:amd64 (3.40.1-2) ... Removing openssl (3.0.9-1) ... Removing libssl3:amd64 (3.0.9-1) ... Processing triggers for libc-bin (2.36-9) ... 1m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', 'remove', 'adapterremoval', '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', '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', 'libcbor0.8: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', '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', 'libllvm15:amd64', 'liblog4j2-java', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmongodb-java', 'libmunge2', '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', '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', 'libquadmath0:amd64', 'librdmacm1:amd64', 'libreadline8:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libucx0: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', 'ocl-icd-libopencl1:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', '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'] 1m32.6s INFO: Running scripts post_remove 1m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_remove_exceptions'] 1m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_remove_exceptions'] 1m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg', '--purge', 'adapterremoval', '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', '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', 'libcbor0.8: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', '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', 'libllvm15:amd64', 'liblog4j2-java', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmongodb-java', 'libmunge2', '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', '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', 'libquadmath0:amd64', 'librdmacm1:amd64', 'libreadline8:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libucx0: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', 'ocl-icd-libopencl1:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', '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'] 1m33.5s DUMP: dpkg: warning: ignoring request to remove adapterremoval which isn't installed (Reading database ... 7591 files and directories currently installed.) Purging configuration files for adwaita-icon-theme (43-1) ... dpkg: warning: ignoring request to remove at-spi2-common which isn't installed dpkg: warning: ignoring request to remove bcftools which isn't installed dpkg: warning: ignoring request to remove bedtools which isn't installed dpkg: warning: ignoring request to remove bowtie2 which isn't installed dpkg: warning: ignoring request to remove bwa which isn't installed Purging configuration files for ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20230103) ... 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 (2.14.1-4) ... Purging configuration files for fontconfig-config (2.14.1-4) ... Purging configuration files for fonts-dejavu-core (2.37-6) ... 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 (44.0-2) ... Purging configuration files for java-common (0.74) ... 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 libcbor0.8 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 Purging configuration files for libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+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 (22.3.6-1+deb12u1) ... dpkg: warning: ignoring request to remove libglapi-mesa which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.74.6-2) ... 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 (1.20.1-2) ... Purging configuration files for libgtk2.0-0:amd64 (2.24.33-2) ... Purging configuration files for libgtk2.0-common (2.24.33-2) ... 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 libllvm15 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 (3.7.0-0.2+b1) ... 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 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+20.604758e7-6.2) ... 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 (3.11.4-1) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 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 (1:3.6.0-7.1) ... dpkg: warning: ignoring request to remove libsensors5 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 libssl3 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 (1.3.3+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 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 (10.0.0) ... dpkg: warning: ignoring request to remove ncbi-vdb-data which isn't installed 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 (17.0.7+7-1) ... Purging configuration files for openmpi-bin (4.1.5-2) ... dpkg: warning: ignoring request to remove openmpi-common which isn't installed Purging configuration files for openssh-client (1:9.2p1-2) ... Purging configuration files for openssl (3.0.9-1) ... 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 (3.11.2-1+b1) ... 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 (3.11.4-1) ... Purging configuration files for r-base-core (4.3.0-1) ... 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 (8.2-1.3) ... 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 (2.2-1) ... 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 1m33.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg', '--purge', 'adapterremoval', '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', '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', 'libcbor0.8: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', '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', 'libllvm15:amd64', 'liblog4j2-java', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmongodb-java', 'libmunge2', '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', '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', 'libquadmath0:amd64', 'librdmacm1:amd64', 'libreadline8:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libucx0: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', 'ocl-icd-libopencl1:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', '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'] 1m33.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg', '--purge', 'paleomix'] 1m33.6s DUMP: dpkg: warning: ignoring request to remove paleomix which isn't installed 1m33.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg', '--purge', 'paleomix'] 1m33.7s INFO: Running scripts post_purge 1m33.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_purge_exceptions'] 1m33.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_purge_exceptions'] 1m33.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg', '--purge', '--pending'] 1m33.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg', '--purge', '--pending'] 1m33.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg', '--remove', '--pending'] 1m33.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg', '--remove', '--pending'] 1m33.7s INFO: Running scripts post_test 1m33.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_test_exceptions'] 1m33.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'tmp/scripts/post_test_exceptions'] 1m33.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 1m34.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 1m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg-divert', '--list'] 1m34.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 1m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'dpkg-divert', '--list'] 1m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', 'clean'] 1m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqepzyjea', 'apt-get', 'clean'] 1m34.2s DEBUG: Recording chroot state 1m35.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/shm'] 1m35.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/shm'] 1m35.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/console'] 1m35.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/console'] 1m35.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/ptmx'] 1m35.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/ptmx'] 1m35.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/pts'] 1m35.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/dev/pts'] 1m35.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/proc'] 1m35.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqepzyjea/proc'] 1m35.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 1m35.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpqepzyjea'] 1m35.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpqepzyjea 1m35.5s INFO: PASS: Upgrading between Debian distributions. 1m35.5s INFO: PASS: All tests. 1m35.5s INFO: piuparts run ends. ret=0 End: 2023-06-12 10:01:09 GMT