Start: 2024-04-14 15:42:13 GMT [stable] Package: paleomix Version: 1.3.2-1 Installed-Size: 2003 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_1.3.2-1_amd64.deb Size: 982544 MD5sum: ca18db651a0e38c1395bb087fb9a4605 SHA256: 327426e5107ea733fc3fee711b5b48bebde3547a95b3ec30471b65853bd712b4 [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/bullseye-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/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 1.4.1~202403190841~1.4-4-g85045c69 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/bullseye-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt paleomix=1.3.8-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpuarkol71 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpuarkol71 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpuarkol71', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpuarkol71', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpuarkol71/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpuarkol71/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpuarkol71/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', 'update'] 0m1.5s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', 'update'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', '-yf', 'dist-upgrade'] 0m1.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', '-yf', 'dist-upgrade'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.4s DUMP: 29fcf27583012b383113cec2bf757015 - 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.4s INFO: Running scripts post_setup 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_setup_dummy_users'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_setup_dummy_users'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_setup_forbid_home'] 0m3.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_setup_forbid_home'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.4s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_setup_zz_backports'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_setup_zz_backports'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.4s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat 0m3.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 0m3.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 0m3.9s INFO: Running scripts is_testable 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/is_testable_uninstallable'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/is_testable_uninstallable'] 0m3.9s INFO: Running scripts pre_test 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_test_exceptions'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_test_exceptions'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_test_root_password'] 0m4.0s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_test_root_password'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'show', '--no-all-versions', 'paleomix'] 0m4.3s DUMP: Package: paleomix Version: 1.3.2-1 Installed-Size: 2003 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_1.3.2-1_amd64.deb Size: 982544 MD5sum: ca18db651a0e38c1395bb087fb9a4605 SHA256: 327426e5107ea733fc3fee711b5b48bebde3547a95b3ec30471b65853bd712b4 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'show', '--no-all-versions', 'paleomix'] 0m4.3s INFO: apt-cache knows about the following packages: paleomix 0m4.3s INFO: Running scripts pre_install 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_database-server'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_database-server'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_exceptions'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_exceptions'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_extras'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_extras'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'policy'] 0m4.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'policy'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'policy', 'paleomix'] 0m4.4s DUMP: paleomix: Installed: (none) Candidate: 1.3.2-1 Version table: 1.3.2-1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'policy', 'paleomix'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', '-y', 'install', 'paleomix'] 0m58.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: adapterremoval ant ant-optional bcftools bedtools bowtie2 bwa ca-certificates ca-certificates-java default-jre default-jre-headless examl fontconfig fontconfig-config fonts-dejavu-core ibverbs-providers java-common libactivation-java libaopalliance-java libapache-pom-java libargs4j-java libasound2 libasound2-data libatinject-jsr330-api-java libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libbrotli1 libbsd0 libcairo2 libcbor0 libcdi-api-java libcodemodel-java libcommons-cli-java 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 libdom4j-java libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdtd-parser-java libedit2 libelf1 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfastinfoset-java libfido2-1 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libgatk-native-bindings-java libgdbm-compat4 libgdbm6 libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java 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 libgsl25 libgslcblas0 libguava-java libguice-java libharfbuzz0b libhts3 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibverbs1 libice6 libicu67 libistack-commons-java libjaxb-api-java libjaxb-java libjaxen-java libjbig0 libjoptsimple-java libjpeg62-turbo libjsoup-java libjsr305-java liblapack3 liblcms2-2 libldap-2.4-2 liblightcouch-java libllvm11 liblog4j2-java libmaven-file-management-java libmaven-parent-java libmaven-resolver-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libmd0 libmongodb-java libmpdec3 libncurses6 libncursesw6 libnghttp2-14 libngs-java libngs-sdk-dev libngs-sdk2 libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenmpi3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.32 libpicard-java libpixman-1-0 libplexus-archiver-java libplexus-cipher-java libplexus-classworlds-java libplexus-component-annotations-java libplexus-interpolation-java libplexus-io-java libplexus-sec-dispatcher-java libplexus-utils2-java libpmix2 libpng16-16 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 librdmacm1 libreadline8 librelaxng-datatype-java librngom-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsisu-inject-java libsisu-plexus-java libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsqlite3-0 libssh2-1 libstax-ex-java libstreambuffer-java libtbb2 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtxw2-java libucx0 libvulkan1 libwagon-http-java libwagon-provider-api-java libwebp6 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxml-commons-resolver1.1-java libxml2 libxnvctrl0 libxrender1 libxshmfence1 libxsom-java libxss1 libxt6 libxtst6 libxxf86vm1 libxz-java libz3-4 littler mafft mapdamage media-types ocl-icd-libopencl1 openjdk-11-jre openjdk-11-jre-headless openmpi-bin openmpi-common openssh-client openssl perl perl-modules-5.32 phylip picard-tools python3 python3-coloredlogs python3-configargparse python3-humanfriendly python3-minimal python3-pysam python3-ruamel.yaml python3-ruamel.yaml.clib python3-setproctitle python3.9 python3.9-minimal r-base-core r-cran-assertthat r-cran-brio r-cran-callr r-cran-cli r-cran-codetools r-cran-colorspace r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest r-cran-ellipsis r-cran-evaluate 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-jsonlite 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-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppgsl r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr radiant raxml readline-common samtools sensible-utils seqtk ucf unzip x11-common xdg-utils zip Suggested packages: ant-doc default-jdk | java-compiler | java-sdk antlr javacc junit junit4 jython libbcel-java libbsf-java libcommons-net-java libmail-java libjaxp1.3-java libjdepend-java libjsch-java liblog4j1.2-java liboro-java libregexp-java libxalan2-java python3-numpy python3-matplotlib texlive-latex-recommended bowtie2-examples libaopalliance-java-doc libasound2-plugins alsa-utils libatinject-jsr330-api-java-doc libel-api-java libcommons-io-java-doc libcommons-lang3-java-doc libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java cups-common libdom4j-java-doc libmsv-java libxpp2-java libxpp3-java libjdom1-java librhino-java gdbm-l10n libgoogle-gson-java-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libasm-java libcglib-java libhwloc-contrib-plugins libxom-java libjoptsimple-java-doc libjsoup-java-doc libjsr305-java-doc liblcms2-utils 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 libwoodstox-java libmaven-file-management-java-doc libmaven-shared-io-java-doc libmaven-shared-utils-java-doc liblogback-java pciutils pcscd libplexus-classworlds-java-doc libplexus-sec-dispatcher-java-doc libplexus-utils2-java-doc lm-sensors testng tcl8.6 tk8.6 libxml-commons-resolver1.1-java-doc opencl-icd libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl phylip-doc python3-doc python3-tk python3-venv python3.9-venv python3.9-doc binutils binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-covr r-cran-htmlwidgets r-cran-knitr r-cran-rmarkdown r-cran-prettycode 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-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-rpart r-cran-sf r-cran-svglite r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats r-cran-stringr r-cran-magick r-cran-httr r-cran-curl r-cran-plyr r-cran-getopt r-cran-bit64 r-cran-cpp11 r-cran-bitops r-cran-dichromat r-cran-mockery r-cran-usethis r-cran-bench r-cran-blob r-cran-formattable r-cran-hms r-cran-htmltools r-cran-purrr r-cran-tidyr r-cran-zeallot readline-doc cwltool Recommended packages: alsa-ucm-conf alsa-topology-conf dbus libgkl-jni libglib2.0-data shared-mime-info xdg-user-dirs libldap-common libjansi-java libgpm2 publicsuffix libsasl2-modules mesa-vulkan-drivers | vulkan-icd blast2 libwww-perl lynx ruby libatk-wrapper-java-jni fonts-dejavu-extra xauth netbase r-recommended r-base-dev r-doc-html r-cran-cliapp r-cran-mockery r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-vdiffr r-cran-quantreg r-cran-xml2 r-cran-lubridate r-cran-curl r-cran-rmarkdown r-cran-mockr r-cran-bit64 r-cran-hms r-cran-data.table r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-generics 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 ant ant-optional bcftools bedtools bowtie2 bwa ca-certificates ca-certificates-java default-jre default-jre-headless examl fontconfig fontconfig-config fonts-dejavu-core ibverbs-providers java-common libactivation-java libaopalliance-java libapache-pom-java libargs4j-java libasound2 libasound2-data libatinject-jsr330-api-java libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libbrotli1 libbsd0 libcairo2 libcbor0 libcdi-api-java libcodemodel-java libcommons-cli-java 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 libdom4j-java libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdtd-parser-java libedit2 libelf1 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfastinfoset-java libfido2-1 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libgatk-native-bindings-java libgdbm-compat4 libgdbm6 libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java 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 libgsl25 libgslcblas0 libguava-java libguice-java libharfbuzz0b libhts3 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibverbs1 libice6 libicu67 libistack-commons-java libjaxb-api-java libjaxb-java libjaxen-java libjbig0 libjoptsimple-java libjpeg62-turbo libjsoup-java libjsr305-java liblapack3 liblcms2-2 libldap-2.4-2 liblightcouch-java libllvm11 liblog4j2-java libmaven-file-management-java libmaven-parent-java libmaven-resolver-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libmd0 libmongodb-java libmpdec3 libncurses6 libncursesw6 libnghttp2-14 libngs-java libngs-sdk-dev libngs-sdk2 libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenmpi3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.32 libpicard-java libpixman-1-0 libplexus-archiver-java libplexus-cipher-java libplexus-classworlds-java libplexus-component-annotations-java libplexus-interpolation-java libplexus-io-java libplexus-sec-dispatcher-java libplexus-utils2-java libpmix2 libpng16-16 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 librdmacm1 libreadline8 librelaxng-datatype-java librngom-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsisu-inject-java libsisu-plexus-java libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsqlite3-0 libssh2-1 libstax-ex-java libstreambuffer-java libtbb2 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtxw2-java libucx0 libvulkan1 libwagon-http-java libwagon-provider-api-java libwebp6 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxml-commons-resolver1.1-java libxml2 libxnvctrl0 libxrender1 libxshmfence1 libxsom-java libxss1 libxt6 libxtst6 libxxf86vm1 libxz-java libz3-4 littler mafft mapdamage media-types ocl-icd-libopencl1 openjdk-11-jre openjdk-11-jre-headless openmpi-bin openmpi-common openssh-client openssl paleomix perl perl-modules-5.32 phylip picard-tools python3 python3-coloredlogs python3-configargparse python3-humanfriendly python3-minimal python3-pysam python3-ruamel.yaml python3-ruamel.yaml.clib python3-setproctitle python3.9 python3.9-minimal r-base-core r-cran-assertthat r-cran-brio r-cran-callr r-cran-cli r-cran-codetools r-cran-colorspace r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest r-cran-ellipsis r-cran-evaluate 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-jsonlite 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-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppgsl r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr radiant raxml readline-common samtools sensible-utils seqtk ucf unzip x11-common xdg-utils zip 0 upgraded, 330 newly installed, 0 to remove and 0 not upgraded. Need to get 243 MB of archives. After this operation, 826 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 perl-modules-5.32 all 5.32.1-4+deb11u3 [2823 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.19-2 [64.9 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.19-2 [44.7 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libperl5.32 amd64 5.32.1-4+deb11u3 [4121 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.32.1-4+deb11u3 [293 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2+deb11u2 [132 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 libcbor0 amd64 0.5.0+dfsg-2 [24.0 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 libfido2-1 amd64 1.6.0-2 [53.3 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 openssh-client amd64 1:8.4p1-5+deb11u3 [932 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 adapterremoval amd64 2.3.1-3 [194 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 libnspr4 amd64 2:4.29-1 [112 kB] Get:32 http://deb.debian.org/debian bullseye/main amd64 libnss3 amd64 2:3.61-1+deb11u3 [1305 kB] Get:33 http://deb.debian.org/debian bullseye/main amd64 ca-certificates-java all 20190909+deb11u1 [15.9 kB] Get:34 http://deb.debian.org/debian bullseye/main amd64 java-common all 0.72 [14.5 kB] Get:35 http://deb.debian.org/debian bullseye/main amd64 libavahi-common-data amd64 0.8-5+deb11u2 [124 kB] Get:36 http://deb.debian.org/debian bullseye/main amd64 libavahi-common3 amd64 0.8-5+deb11u2 [58.7 kB] Get:37 http://deb.debian.org/debian bullseye/main amd64 libdbus-1-3 amd64 1.12.28-0+deb11u1 [223 kB] Get:38 http://deb.debian.org/debian bullseye/main amd64 libavahi-client3 amd64 0.8-5+deb11u2 [62.6 kB] Get:39 http://deb.debian.org/debian bullseye/main amd64 libcups2 amd64 2.3.3op2-3+deb11u6 [351 kB] Get:40 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get:41 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get:42 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:43 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:44 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get:45 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:46 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:47 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:48 http://deb.debian.org/debian bullseye/main amd64 libasound2-data all 1.2.4-1.1 [38.2 kB] Get:49 http://deb.debian.org/debian bullseye/main amd64 libasound2 amd64 1.2.4-1.1 [356 kB] Get:50 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1+deb11u1 [1374 kB] Get:51 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:52 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get:53 http://deb.debian.org/debian bullseye/main amd64 libpcsclite1 amd64 1.9.1-1 [60.2 kB] Get:54 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre-headless amd64 11.0.22+7-1~deb11u1 [38.2 MB] Get:55 http://deb.debian.org/debian bullseye/main amd64 default-jre-headless amd64 2:1.11-72 [10.9 kB] Get:56 http://deb.debian.org/debian bullseye/main amd64 ant all 1.10.9-4 [2118 kB] Get:57 http://deb.debian.org/debian bullseye/main amd64 ant-optional all 1.10.9-4 [381 kB] Get:58 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get:59 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get:60 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get:61 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u1 [77.2 kB] Get:62 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:63 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:64 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get:65 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u11 [344 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 bcftools amd64 1.11-1 [617 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 bedtools amd64 2.30.0+dfsg-1 [663 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 libtbb2 amd64 2020.3-1 [161 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 bowtie2 amd64 2.4.2-2+b3 [1342 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 bwa amd64 0.7.17-6+b1 [212 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 libglvnd0 amd64 1.3.2-1 [53.6 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:75 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u2 [311 kB] Get:78 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u2 [772 kB] Get:79 http://deb.debian.org/debian bullseye/main amd64 libdrm-common all 2.4.104-1 [14.9 kB] Get:80 http://deb.debian.org/debian bullseye/main amd64 libdrm2 amd64 2.4.104-1 [41.5 kB] Get:81 http://deb.debian.org/debian bullseye/main amd64 libglapi-mesa amd64 20.3.5-1 [71.7 kB] Get:82 http://deb.debian.org/debian bullseye/main amd64 libx11-xcb1 amd64 2:1.7.2-1+deb11u2 [204 kB] Get:83 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri2-0 amd64 1.14-3 [103 kB] Get:84 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri3-0 amd64 1.14-3 [102 kB] Get:85 http://deb.debian.org/debian bullseye/main amd64 libxcb-glx0 amd64 1.14-3 [118 kB] Get:86 http://deb.debian.org/debian bullseye/main amd64 libxcb-present0 amd64 1.14-3 [101 kB] Get:87 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get:88 http://deb.debian.org/debian bullseye/main amd64 libxcb-sync1 amd64 1.14-3 [105 kB] Get:89 http://deb.debian.org/debian bullseye/main amd64 libxcb-xfixes0 amd64 1.14-3 [105 kB] Get:90 http://deb.debian.org/debian bullseye/main amd64 libxdamage1 amd64 1:1.1.5-2 [15.7 kB] Get:91 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get:92 http://deb.debian.org/debian bullseye/main amd64 libxfixes3 amd64 1:5.0.3-2 [22.1 kB] Get:93 http://deb.debian.org/debian bullseye/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:94 http://deb.debian.org/debian bullseye/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:95 http://deb.debian.org/debian bullseye/main amd64 libdrm-amdgpu1 amd64 2.4.104-1 [28.5 kB] Get:96 http://deb.debian.org/debian bullseye/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get:97 http://deb.debian.org/debian bullseye/main amd64 libdrm-intel1 amd64 2.4.104-1 [71.8 kB] Get:98 http://deb.debian.org/debian bullseye/main amd64 libdrm-nouveau2 amd64 2.4.104-1 [26.8 kB] Get:99 http://deb.debian.org/debian bullseye/main amd64 libdrm-radeon1 amd64 2.4.104-1 [30.2 kB] Get:100 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get:101 http://deb.debian.org/debian bullseye/main amd64 libz3-4 amd64 4.8.10-1 [6949 kB] Get:102 http://deb.debian.org/debian bullseye/main amd64 libllvm11 amd64 1:11.0.1-2 [17.9 MB] Get:103 http://deb.debian.org/debian bullseye/main amd64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get:104 http://deb.debian.org/debian bullseye/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get:105 http://deb.debian.org/debian bullseye/main amd64 libvulkan1 amd64 1.2.162.0-1 [103 kB] Get:106 http://deb.debian.org/debian bullseye/main amd64 libgl1-mesa-dri amd64 20.3.5-1 [9633 kB] Get:107 http://deb.debian.org/debian bullseye/main amd64 libglx-mesa0 amd64 20.3.5-1 [186 kB] Get:108 http://deb.debian.org/debian bullseye/main amd64 libglx0 amd64 1.3.2-1 [35.7 kB] Get:109 http://deb.debian.org/debian bullseye/main amd64 libgl1 amd64 1.3.2-1 [89.5 kB] Get:110 http://deb.debian.org/debian bullseye/main amd64 libgif7 amd64 5.1.9-2 [45.1 kB] Get:111 http://deb.debian.org/debian bullseye/main amd64 libxi6 amd64 2:1.7.10-1 [83.4 kB] Get:112 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:113 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get:114 http://deb.debian.org/debian bullseye/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get:115 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre amd64 11.0.22+7-1~deb11u1 [194 kB] Get:116 http://deb.debian.org/debian bullseye/main amd64 default-jre amd64 2:1.11-72 [1044 B] Get:117 http://deb.debian.org/debian bullseye/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-1 [139 kB] Get:118 http://deb.debian.org/debian bullseye/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-1 [57.1 kB] Get:119 http://deb.debian.org/debian bullseye/main amd64 libnl-3-200 amd64 3.4.0-1+b1 [63.6 kB] Get:120 http://deb.debian.org/debian bullseye/main amd64 libnl-route-3-200 amd64 3.4.0-1+b1 [161 kB] Get:121 http://deb.debian.org/debian bullseye/main amd64 libibverbs1 amd64 33.2-1 [59.4 kB] Get:122 http://deb.debian.org/debian bullseye/main amd64 ibverbs-providers amd64 33.2-1 [253 kB] Get:123 http://deb.debian.org/debian bullseye/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.1 [169 kB] Get:124 http://deb.debian.org/debian bullseye/main amd64 libnuma1 amd64 2.0.12-1+b1 [26.3 kB] Get:125 http://deb.debian.org/debian bullseye/main amd64 libpsm2-2 amd64 11.2.185-1 [181 kB] Get:126 http://deb.debian.org/debian bullseye/main amd64 librdmacm1 amd64 33.2-1 [68.9 kB] Get:127 http://deb.debian.org/debian bullseye/main amd64 libfabric1 amd64 1.11.0-2 [521 kB] Get:128 http://deb.debian.org/debian bullseye/main amd64 libhwloc15 amd64 2.4.1+dfsg-1 [150 kB] Get:129 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:130 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get:131 http://deb.debian.org/debian bullseye/main amd64 libxnvctrl0 amd64 470.141.03-1~deb11u1 [27.5 kB] Get:132 http://deb.debian.org/debian bullseye/main amd64 ocl-icd-libopencl1 amd64 2.2.14-2 [42.5 kB] Get:133 http://deb.debian.org/debian bullseye/main amd64 libhwloc-plugins amd64 2.4.1+dfsg-1 [21.4 kB] Get:134 http://deb.debian.org/debian bullseye/main amd64 libpmix2 amd64 4.0.0-4.1+deb11u1 [553 kB] Get:135 http://deb.debian.org/debian bullseye/main amd64 libucx0 amd64 1.10.1~rc1+really.1.10.0-1 [649 kB] Get:136 http://deb.debian.org/debian bullseye/main amd64 libopenmpi3 amd64 4.1.0-10 [2370 kB] Get:137 http://deb.debian.org/debian bullseye/main amd64 openmpi-common all 4.1.0-10 [179 kB] Get:138 http://deb.debian.org/debian bullseye/main amd64 openmpi-bin amd64 4.1.0-10 [238 kB] Get:139 http://deb.debian.org/debian bullseye/main amd64 examl amd64 3.0.22-1+b4 [927 kB] Get:140 http://deb.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get:141 http://deb.debian.org/debian bullseye/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get:142 http://deb.debian.org/debian bullseye/main amd64 libaopalliance-java all 20070526-6 [9048 B] Get:143 http://deb.debian.org/debian bullseye/main amd64 libapache-pom-java all 18-1 [4676 B] Get:144 http://deb.debian.org/debian bullseye/main amd64 libargs4j-java all 2.33-1.1 [137 kB] Get:145 http://deb.debian.org/debian bullseye/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get:146 http://deb.debian.org/debian bullseye/main amd64 libfreemarker-java all 2.3.23-11 [1221 kB] Get:147 http://deb.debian.org/debian bullseye/main amd64 libjoptsimple-java all 5.0.4-4 [73.1 kB] Get:148 http://deb.debian.org/debian bullseye/main amd64 libgoogle-gson-java all 2.8.6-1+deb11u1 [225 kB] Get:149 http://deb.debian.org/debian bullseye/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get:150 http://deb.debian.org/debian bullseye/main amd64 libcommons-codec-java all 1.15-1 [292 kB] Get:151 http://deb.debian.org/debian bullseye/main amd64 libcommons-logging-java all 1.2-2 [62.2 kB] Get:152 http://deb.debian.org/debian bullseye/main amd64 libhttpcore-java all 4.4.14-1 [631 kB] Get:153 http://deb.debian.org/debian bullseye/main amd64 libhttpclient-java all 4.5.13-2 [1233 kB] Get:154 http://deb.debian.org/debian bullseye/main amd64 liblightcouch-java all 0.0.6-1.1 [65.2 kB] Get:155 http://deb.debian.org/debian bullseye/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get:156 http://deb.debian.org/debian bullseye/main amd64 libslf4j-java all 1.7.30-1 [144 kB] Get:157 http://deb.debian.org/debian bullseye/main amd64 liblog4j2-java all 2.17.1-1~deb11u1 [2081 kB] Get:158 http://deb.debian.org/debian bullseye/main amd64 libbarclay-java all 2.1.0-3.1 [116 kB] Get:159 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get:160 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1.1~deb11u1 [543 kB] Get:161 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get:162 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get:163 http://deb.debian.org/debian bullseye/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get:164 http://deb.debian.org/debian bullseye/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get:165 http://deb.debian.org/debian bullseye/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get:166 http://deb.debian.org/debian bullseye/main amd64 libdom4j-java all 2.1.3-1 [310 kB] Get:167 http://deb.debian.org/debian bullseye/main amd64 libcommons-io-java all 2.8.0-1 [279 kB] Get:168 http://deb.debian.org/debian bullseye/main amd64 libmaven-shared-utils-java all 3.3.0-1+deb11u1 [149 kB] Get:169 http://deb.debian.org/debian bullseye/main amd64 libcommons-cli-java all 1.4-2 [57.3 kB] Get:170 http://deb.debian.org/debian bullseye/main amd64 libcommons-lang3-java all 3.11-1 [550 kB] Get:171 http://deb.debian.org/debian bullseye/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get:172 http://deb.debian.org/debian bullseye/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get:173 http://deb.debian.org/debian bullseye/main amd64 libguava-java all 29.0-6 [2419 kB] Get:174 http://deb.debian.org/debian bullseye/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get:175 http://deb.debian.org/debian bullseye/main amd64 libmaven-parent-java all 31-2 [5100 B] Get:176 http://deb.debian.org/debian bullseye/main amd64 libplexus-utils2-java all 3.3.0-1 [250 kB] Get:177 http://deb.debian.org/debian bullseye/main amd64 libwagon-provider-api-java all 3.3.4-1 [50.2 kB] Get:178 http://deb.debian.org/debian bullseye/main amd64 libmaven-resolver-java all 1.4.2-3 [556 kB] Get:179 http://deb.debian.org/debian bullseye/main amd64 libplexus-cipher-java all 1.8-2 [15.0 kB] Get:180 http://deb.debian.org/debian bullseye/main amd64 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get:181 http://deb.debian.org/debian bullseye/main amd64 libplexus-component-annotations-java all 2.1.0-1 [7620 B] Get:182 http://deb.debian.org/debian bullseye/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get:183 http://deb.debian.org/debian bullseye/main amd64 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get:184 http://deb.debian.org/debian bullseye/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get:185 http://deb.debian.org/debian bullseye/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get:186 http://deb.debian.org/debian bullseye/main amd64 libmaven3-core-java all 3.6.3-5 [1538 kB] Get:187 http://deb.debian.org/debian bullseye/main amd64 libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get:188 http://deb.debian.org/debian bullseye/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get:189 http://deb.debian.org/debian bullseye/main amd64 libcommons-compress-java all 1.20-1 [574 kB] Get:190 http://deb.debian.org/debian bullseye/main amd64 libplexus-io-java all 3.2.0-1.1 [65.0 kB] Get:191 http://deb.debian.org/debian bullseye/main amd64 libsnappy1v5 amd64 1.1.8-1 [17.9 kB] Get:192 http://deb.debian.org/debian bullseye/main amd64 libsnappy-jni amd64 1.1.8.3-1 [7152 B] Get:193 http://deb.debian.org/debian bullseye/main amd64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get:194 http://deb.debian.org/debian bullseye/main amd64 libxz-java all 1.8-2 [141 kB] Get:195 http://deb.debian.org/debian bullseye/main amd64 libplexus-archiver-java all 3.6.0-2 [171 kB] Get:196 http://deb.debian.org/debian bullseye/main amd64 libjsoup-java all 1.10.2-2 [350 kB] Get:197 http://deb.debian.org/debian bullseye/main amd64 libwagon-http-java all 3.3.4-1 [53.9 kB] Get:198 http://deb.debian.org/debian bullseye/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get:199 http://deb.debian.org/debian bullseye/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-10 [163 kB] Get:200 http://deb.debian.org/debian bullseye/main amd64 libcommons-jexl2-java all 2.1.1-5 [256 kB] Get:201 http://deb.debian.org/debian bullseye/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get:202 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u11 [347 kB] Get:203 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get:204 http://deb.debian.org/debian bullseye/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get:205 http://deb.debian.org/debian bullseye/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get:206 http://deb.debian.org/debian bullseye/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get:207 http://deb.debian.org/debian bullseye/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get:208 http://deb.debian.org/debian bullseye/main amd64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get:209 http://deb.debian.org/debian bullseye/main amd64 libxsom-java all 2.3.0.1-10 [396 kB] Get:210 http://deb.debian.org/debian bullseye/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get:211 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2+deb11u1 [64.9 kB] Get:212 http://deb.debian.org/debian bullseye/main amd64 libgatk-native-bindings-java all 1.0.0-2.1 [7344 B] Get:213 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB] Get:214 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:215 http://deb.debian.org/debian bullseye/main amd64 libgkl-java all 0.8.7+dfsg-1 [998 kB] Get:216 http://deb.debian.org/debian bullseye/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB] Get:217 http://deb.debian.org/debian bullseye/main amd64 libgslcblas0 amd64 2.6+dfsg-2 [102 kB] Get:218 http://deb.debian.org/debian bullseye/main amd64 libgsl25 amd64 2.6+dfsg-2 [934 kB] Get:219 http://deb.debian.org/debian bullseye/main amd64 libgsl-dev amd64 2.6+dfsg-2 [1123 kB] Get:220 http://deb.debian.org/debian bullseye/main amd64 librngom-java all 2.3.0.1-10 [288 kB] Get:221 http://deb.debian.org/debian bullseye/main amd64 libtxw2-java all 2.3.0.1-10 [134 kB] Get:222 http://deb.debian.org/debian bullseye/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get:223 http://deb.debian.org/debian bullseye/main amd64 libjaxb-java all 2.3.0.1-10 [1954 kB] Get:224 http://deb.debian.org/debian bullseye/main amd64 libngs-sdk2 amd64 2.10.9-1 [59.2 kB] Get:225 http://deb.debian.org/debian bullseye/main amd64 libngs-sdk-dev amd64 2.10.9-1 [104 kB] Get:226 http://deb.debian.org/debian bullseye/main amd64 libngs-java amd64 2.10.9-1 [80.4 kB] Get:227 http://deb.debian.org/debian bullseye/main amd64 libhtsjdk-java all 2.23.0+dfsg-2 [1607 kB] Get:228 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:229 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:230 http://deb.debian.org/debian bullseye/main amd64 libopenblas0-pthread amd64 0.3.13+ds-3+deb11u1 [6016 kB] Get:231 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get:232 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u2 [102 kB] Get:233 http://deb.debian.org/debian bullseye/main amd64 libopenblas0 amd64 0.3.13+ds-3+deb11u1 [32.9 kB] Get:234 http://deb.debian.org/debian bullseye/main amd64 libopenblas-pthread-dev amd64 0.3.13+ds-3+deb11u1 [4450 kB] Get:235 http://deb.debian.org/debian bullseye/main amd64 libopenblas-dev amd64 0.3.13+ds-3+deb11u1 [44.2 kB] Get:236 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get:237 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get:238 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get:239 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get:240 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get:241 http://deb.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get:242 http://deb.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get:243 http://deb.debian.org/debian bullseye/main amd64 libpicard-java all 2.24.1+dfsg-1 [1617 kB] Get:244 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:245 http://deb.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.11+dfsg-1 [1018 kB] Get:246 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get:247 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u5 [290 kB] Get:248 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:249 http://deb.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:250 http://deb.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.11-2 [780 kB] Get:251 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get:252 http://deb.debian.org/debian bullseye/main amd64 zip amd64 3.0-12 [232 kB] Get:253 http://deb.debian.org/debian bullseye/main amd64 unzip amd64 6.0-26+deb11u1 [172 kB] Get:254 http://deb.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:255 http://deb.debian.org/debian bullseye/main amd64 r-base-core amd64 4.0.4-1 [25.1 MB] Get:256 http://deb.debian.org/debian bullseye/main amd64 r-cran-littler amd64 0.3.12-1 [95.9 kB] Get:257 http://deb.debian.org/debian bullseye/main amd64 littler all 0.3.12-1 [15.6 kB] Get:258 http://deb.debian.org/debian bullseye/main amd64 mafft amd64 7.475-1 [1051 kB] Get:259 http://deb.debian.org/debian bullseye/main amd64 r-cran-codetools all 0.2-18-1 [91.8 kB] Get:260 http://deb.debian.org/debian bullseye/main amd64 r-cran-iterators all 1.0.13-1 [329 kB] Get:261 http://deb.debian.org/debian bullseye/main amd64 r-cran-foreach all 1.5.1-1 [120 kB] Get:262 http://deb.debian.org/debian bullseye/main amd64 r-cran-gam amd64 1.20-1 [302 kB] Get:263 http://deb.debian.org/debian bullseye/main amd64 r-cran-digest amd64 0.6.27-1 [192 kB] Get:264 http://deb.debian.org/debian bullseye/main amd64 r-cran-glue amd64 1.4.2-1 [138 kB] Get:265 http://deb.debian.org/debian bullseye/main amd64 r-cran-gtable all 0.3.0+dfsg-2 [163 kB] Get:266 http://deb.debian.org/debian bullseye/main amd64 r-cran-brio amd64 1.1.1-1 [31.7 kB] Get:267 http://deb.debian.org/debian bullseye/main amd64 r-cran-ps amd64 1.5.0-1 [277 kB] Get:268 http://deb.debian.org/debian bullseye/main amd64 r-cran-r6 all 2.5.0-1 [104 kB] Get:269 http://deb.debian.org/debian bullseye/main amd64 r-cran-processx amd64 3.4.5-1 [295 kB] Get:270 http://deb.debian.org/debian bullseye/main amd64 r-cran-callr all 3.5.1-1 [386 kB] Get:271 http://deb.debian.org/debian bullseye/main amd64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get:272 http://deb.debian.org/debian bullseye/main amd64 r-cran-cli all 2.3.0-1 [480 kB] Get:273 http://deb.debian.org/debian bullseye/main amd64 r-cran-crayon all 1.4.0-1 [143 kB] Get:274 http://deb.debian.org/debian bullseye/main amd64 r-cran-rprojroot all 2.0.2-1 [114 kB] Get:275 http://deb.debian.org/debian bullseye/main amd64 r-cran-desc all 1.2.0-3 [301 kB] Get:276 http://deb.debian.org/debian bullseye/main amd64 r-cran-rlang amd64 0.4.10-1 [1176 kB] Get:277 http://deb.debian.org/debian bullseye/main amd64 r-cran-ellipsis amd64 0.3.1-1 [31.7 kB] Get:278 http://deb.debian.org/debian bullseye/main amd64 r-cran-evaluate all 0.14-2 [81.1 kB] Get:279 http://deb.debian.org/debian bullseye/main amd64 r-cran-jsonlite amd64 1.7.2+dfsg-1 [447 kB] Get:280 http://deb.debian.org/debian bullseye/main amd64 r-cran-lifecycle all 0.2.0-2 [93.2 kB] Get:281 http://deb.debian.org/debian bullseye/main amd64 r-cran-magrittr amd64 2.0.1-1 [198 kB] Get:282 http://deb.debian.org/debian bullseye/main amd64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get:283 http://deb.debian.org/debian bullseye/main amd64 r-cran-withr all 2.4.1-1 [210 kB] Get:284 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgbuild all 1.2.0-1 [146 kB] Get:285 http://deb.debian.org/debian bullseye/main amd64 r-cran-rstudioapi all 0.13-1 [262 kB] Get:286 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgload amd64 1.1.0-1 [168 kB] Get:287 http://deb.debian.org/debian bullseye/main amd64 r-cran-praise all 1.0.0-4 [20.1 kB] Get:288 http://deb.debian.org/debian bullseye/main amd64 r-cran-diffobj amd64 0.3.2-1 [1069 kB] Get:289 http://deb.debian.org/debian bullseye/main amd64 r-cran-fansi amd64 0.4.2-1 [345 kB] Get:290 http://deb.debian.org/debian bullseye/main amd64 r-cran-utf8 amd64 1.1.4-2 [131 kB] Get:291 http://deb.debian.org/debian bullseye/main amd64 r-cran-vctrs amd64 0.3.6-1 [1107 kB] Get:292 http://deb.debian.org/debian bullseye/main amd64 r-cran-pillar all 1.4.7-1 [227 kB] Get:293 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:294 http://deb.debian.org/debian bullseye/main amd64 r-cran-tibble amd64 3.0.6+dfsg-1 [416 kB] Get:295 http://deb.debian.org/debian bullseye/main amd64 r-cran-rematch2 all 2.1.2-2 [46.3 kB] Get:296 http://deb.debian.org/debian bullseye/main amd64 r-cran-waldo all 0.2.3-2 [79.3 kB] Get:297 http://deb.debian.org/debian bullseye/main amd64 r-cran-testthat amd64 3.0.1-1 [1451 kB] Get:298 http://deb.debian.org/debian bullseye/main amd64 r-cran-isoband amd64 0.2.3-2 [2085 kB] Get:299 http://deb.debian.org/debian bullseye/main amd64 r-cran-mass amd64 7.3-53.1-1 [1115 kB] Get:300 http://deb.debian.org/debian bullseye/main amd64 r-cran-lattice amd64 0.20-41-1+b1 [1164 kB] Get:301 http://deb.debian.org/debian bullseye/main amd64 r-cran-nlme amd64 3.1.152-1 [2241 kB] Get:302 http://deb.debian.org/debian bullseye/main amd64 r-cran-matrix amd64 1.3-2-1 [3604 kB] Get:303 http://deb.debian.org/debian bullseye/main amd64 r-cran-mgcv amd64 1.8-34-1 [2998 kB] Get:304 http://deb.debian.org/debian bullseye/main amd64 r-cran-farver amd64 2.0.3-1+b1 [1393 kB] Get:305 http://deb.debian.org/debian bullseye/main amd64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get:306 http://deb.debian.org/debian bullseye/main amd64 r-cran-colorspace amd64 2.0-0+dfsg-1 [1684 kB] Get:307 http://deb.debian.org/debian bullseye/main amd64 r-cran-munsell all 0.5.0-2 [236 kB] Get:308 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcolorbrewer all 1.1-2-3 [54.4 kB] Get:309 http://deb.debian.org/debian bullseye/main amd64 r-cran-viridislite all 0.3.0-4 [59.2 kB] Get:310 http://deb.debian.org/debian bullseye/main amd64 r-cran-scales all 1.1.1-1 [557 kB] Get:311 http://deb.debian.org/debian bullseye/main amd64 r-cran-ggplot2 all 3.3.3+dfsg-1 [3158 kB] Get:312 http://deb.debian.org/debian bullseye/main amd64 r-cran-inline all 0.3.17-1 [128 kB] Get:313 http://deb.debian.org/debian bullseye/main amd64 seqtk amd64 1.3-2 [29.7 kB] Get:314 http://deb.debian.org/debian bullseye/main amd64 python3-pysam amd64 0.15.4+ds-3+b2 [1536 kB] Get:315 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgkitten all 0.2.1-1 [26.5 kB] Get:316 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcpp amd64 1.0.6-1 [2035 kB] Get:317 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcppgsl amd64 0.3.8-1 [363 kB] Get:318 http://deb.debian.org/debian bullseye/main amd64 mapdamage all 2.2.1+dfsg-1 [42.5 kB] Get:319 http://deb.debian.org/debian bullseye/main amd64 python3-humanfriendly all 9.1-1 [84.6 kB] Get:320 http://deb.debian.org/debian bullseye/main amd64 python3-coloredlogs all 7.3-2 [28.0 kB] Get:321 http://deb.debian.org/debian bullseye/main amd64 python3-configargparse all 1.2.3-1 [25.2 kB] Get:322 http://deb.debian.org/debian bullseye/main amd64 python3-ruamel.yaml.clib amd64 0.2.2-1+b2 [132 kB] Get:323 http://deb.debian.org/debian bullseye/main amd64 python3-ruamel.yaml all 0.16.12-2 [110 kB] Get:324 http://deb.debian.org/debian bullseye/main amd64 python3-setproctitle amd64 1.2.1-1+b1 [16.8 kB] Get:325 http://deb.debian.org/debian bullseye/main amd64 phylip amd64 1:3.697+dfsg-2 [919 kB] Get:326 http://deb.debian.org/debian bullseye/main amd64 picard-tools all 2.24.1+dfsg-1 [313 kB] Get:327 http://deb.debian.org/debian bullseye/main amd64 radiant all 2.7.1+dfsg-4 [180 kB] Get:328 http://deb.debian.org/debian bullseye/main amd64 raxml amd64 8.2.12+dfsg-6+b4 [1434 kB] Get:329 http://deb.debian.org/debian bullseye/main amd64 samtools amd64 1.11-1 [545 kB] Get:330 http://deb.debian.org/debian bullseye/main amd64 paleomix amd64 1.3.2-1 [983 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 243 MB in 3s (87.5 MB/s) Selecting previously unselected package perl-modules-5.32. (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 ... 6674 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.32_5.32.1-4+deb11u3_all.deb ... Unpacking perl-modules-5.32 (5.32.1-4+deb11u3) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.19-2_amd64.deb ... Unpacking libgdbm6:amd64 (1.19-2) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.19-2_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.19-2) ... Selecting previously unselected package libperl5.32:amd64. Preparing to unpack .../3-libperl5.32_5.32.1-4+deb11u3_amd64.deb ... Unpacking libperl5.32:amd64 (5.32.1-4+deb11u3) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.32.1-4+deb11u3_amd64.deb ... Unpacking perl (5.32.1-4+deb11u3) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.2.10-2+deb11u5_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2+deb11u5) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_amd64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (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 ... 8939 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../3-libncursesw6_6.2+20201114-2+deb11u2_amd64.deb ... Unpacking libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../5-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../6-libsqlite3-0_3.34.1-3_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.34.1-3) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../7-libpython3.9-stdlib_3.9.2-1_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../8-python3.9_3.9.2-1_amd64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.9.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (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 ... 9377 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_1.1.1w-0+deb11u1_amd64.deb ... Unpacking openssl (1.1.1w-0+deb11u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmd0:amd64. Preparing to unpack .../004-libmd0_1.0.3-3_amd64.deb ... Unpacking libmd0:amd64 (1.0.3-3) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../005-libbsd0_0.11.3-1+deb11u1_amd64.deb ... Unpacking libbsd0:amd64 (0.11.3-1+deb11u1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../006-libedit2_3.1-20191231-2+b1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20191231-2+b1) ... Selecting previously unselected package libcbor0:amd64. Preparing to unpack .../007-libcbor0_0.5.0+dfsg-2_amd64.deb ... Unpacking libcbor0:amd64 (0.5.0+dfsg-2) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../008-libfido2-1_1.6.0-2_amd64.deb ... Unpacking libfido2-1:amd64 (1.6.0-2) ... 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Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-1) ... Setting up libxz-java (1.8-2) ... Setting up libtcl8.6:amd64 (8.6.11+dfsg-1) ... Setting up libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libngs-sdk-dev:amd64 (2.10.9-1) ... Setting up libpcsclite1:amd64 (1.9.1-1) ... Setting up libsensors5:amd64 (1:3.6.0-7) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libactivation-java (1.2.0-2) ... Setting up libglapi-mesa:amd64 (20.3.5-1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libvulkan1:amd64 (1.2.162.0-1) ... Setting up libgif7:amd64 (5.1.9-2) ... Setting up libnuma1:amd64 (2.0.12-1+b1) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up libfreemarker-java (2.3.23-11) ... Setting up sensible-utils (0.0.14) ... Setting up ocl-icd-libopencl1:amd64 (2.2.14-2) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up libjsoup-java (1.10.2-2) ... Setting up libasound2:amd64 (1.2.4-1.1) ... Setting up libnl-3-200:amd64 (3.4.0-1+b1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libpsm2-2 (11.2.185-1) ... Setting up openmpi-common (4.1.0-10) ... Setting up libplexus-sec-dispatcher-java (1.4-4) ... Setting up libthai-data (0.1.28-3) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u5) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.1) ... 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 (4.4.14-1) ... Setting up libjoptsimple-java (5.0.4-4) ... Setting up libngs-java:amd64 (2.10.9-1) ... Setting up libfido2-1:amd64 (1.6.0-2) ... Setting up librelaxng-datatype-java (1.0+ds1-3.1) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libbsd0:amd64 (0.11.3-1+deb11u1) ... Setting up libdrm-common (2.4.104-1) ... Setting up libcdi-api-java (1.2-3) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libsnappy-jni (1.1.8.3-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... 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-1) ... Setting up libargs4j-java (2.33-1.1) ... Setting up libgdbm6:amd64 (1.19-2) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-1) ... Setting up raxml (8.2.12+dfsg-6+b4) ... Setting up libdom4j-java (2.1.3-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libwagon-provider-api-java (3.3.4-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3+deb11u1) ... 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 (1.14-3) ... Setting up libgsl-dev (2.6+dfsg-2) ... Setting up libopenblas0-pthread:amd64 (0.3.13+ds-3+deb11u1) ... 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 (1.14-3) ... Setting up libxcb-render0:amd64 (1.14-3) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libxcb-glx0:amd64 (1.14-3) ... Setting up libmaven-parent-java (31-2) ... Setting up libedit2:amd64 (3.1-20191231-2+b1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libcommons-parent-java (43-1) ... Setting up libavahi-common3:amd64 (0.8-5+deb11u2) ... Setting up libcommons-logging-java (1.2-2) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u11) ... Setting up libnss3:amd64 (2:3.61-1+deb11u3) ... Setting up libxcb-shm0:amd64 (1.14-3) ... Setting up libnl-route-3-200:amd64 (3.4.0-1+b1) ... Setting up libxcb-present0:amd64 (1.14-3) ... Setting up libcommons-jexl2-java (2.1.1-5) ... Setting up libthai0:amd64 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libmaven-resolver-java (1.4.2-3) ... Setting up libllvm11:amd64 (1:11.0.1-2) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libguava-java (29.0-6) ... Setting up libxcb-sync1:amd64 (1.14-3) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libgdbm-compat4:amd64 (1.19-2) ... Setting up ucf (3.0043) ... Setting up libperl5.32:amd64 (5.32.1-4+deb11u3) ... Setting up libcommons-lang3-java (3.11-1) ... Setting up libxcb-dri2-0:amd64 (1.14-3) ... Setting up librngom-java (2.3.0.1-10) ... Setting up libdrm2:amd64 (2.4.104-1) ... Setting up libopenblas0:amd64 (0.3.13+ds-3+deb11u1) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u11) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u2) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libxsom-java (2.3.0.1-10) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libavahi-client3:amd64 (0.8-5+deb11u2) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libdrm-amdgpu1:amd64 (2.4.104-1) ... Setting up libopenblas-pthread-dev:amd64 (0.3.13+ds-3+deb11u1) ... 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 libxcb-dri3-0:amd64 (1.14-3) ... Setting up libpaper1:amd64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libx11-xcb1:amd64 (2:1.7.2-1+deb11u2) ... Setting up libibverbs1:amd64 (33.2-1) ... Setting up libhts3:amd64 (1.11-4) ... Setting up libdrm-nouveau2:amd64 (2.4.104-1) ... Setting up libxdamage1:amd64 (1:1.1.5-2) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libcommons-compress-java (1.20-1) ... Setting up ibverbs-providers:amd64 (33.2-1) ... Setting up libcommons-io-java (2.8.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.104-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up openssh-client (1:8.4p1-5+deb11u3) ... Setting up libdrm-intel1:amd64 (2.4.104-1) ... Setting up libgl1-mesa-dri:amd64 (20.3.5-1) ... Setting up bcftools (1.11-1) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up libguice-java (4.2.3-2) ... Setting up samtools (1.11-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libxnvctrl0:amd64 (470.141.03-1~deb11u1) ... Setting up libopenblas-dev:amd64 (0.3.13+ds-3+deb11u1) ... Setting up perl (5.32.1-4+deb11u3) ... Setting up libxfixes3:amd64 (1:5.0.3-2) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up libcups2:amd64 (2.3.3op2-3+deb11u6) ... Setting up libhttpclient-java (4.5.13-2) ... Setting up liblightcouch-java (0.0.6-1.1) ... Setting up libwagon-http-java (3.3.4-1) ... Setting up libmaven-shared-utils-java (3.3.0-1+deb11u1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up python3.9 (3.9.2-1) ... Setting up librdmacm1:amd64 (33.2-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libucx0:amd64 (1.10.1~rc1+really.1.10.0-1) ... Setting up libxft2:amd64 (2.3.2-2) ... Setting up libplexus-io-java (3.2.0-1.1) ... Setting up libglx-mesa0:amd64 (20.3.5-1) ... Setting up libxi6:amd64 (2:1.7.10-1) ... Setting up libglx0:amd64 (1.3.2-1) ... Setting up libmaven3-core-java (3.6.3-5) ... Setting up mafft (7.475-1) ... Setting up libmaven-shared-io-java (3.0.0-3) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up liblog4j2-java (2.17.1-1~deb11u1) ... Setting up libtk8.6:amd64 (8.6.11-2) ... Setting up libpango-1.0-0:amd64 (1.46.2-3) ... Setting up python3 (3.9.2-3) ... Setting up libhwloc-plugins:amd64 (2.4.1+dfsg-1) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up bowtie2 (2.4.2-2+b3) ... Setting up libgl1:amd64 (1.3.2-1) ... Setting up python3-humanfriendly (9.1-1) ... Setting up python3-setproctitle:amd64 (1.2.1-1+b1) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libplexus-archiver-java (3.6.0-2) ... Setting up libpangoft2-1.0-0:amd64 (1.46.2-3) ... Setting up python3-coloredlogs (7.3-2) ... Setting up libbarclay-java (2.1.0-3.1) ... Setting up libpangocairo-1.0-0:amd64 (1.46.2-3) ... Setting up python3-configargparse (1.2.3-1) ... Setting up libfabric1 (1.11.0-2) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up libpmix2:amd64 (4.0.0-4.1+deb11u1) ... Setting up libopenmpi3:amd64 (4.1.0-10) ... Setting up python3-ruamel.yaml.clib:amd64 (0.2.2-1+b2) ... Setting up r-base-core (4.0.4-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.4.0-1) ... Setting up r-cran-gtable (0.3.0+dfsg-2) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-lattice (0.20-41-1+b1) ... Setting up r-cran-ps (1.5.0-1) ... Setting up r-cran-nlme (3.1.152-1) ... Setting up r-cran-farver (2.0.3-1+b1) ... Setting up python3-ruamel.yaml (0.16.12-2) ... Setting up r-cran-viridislite (0.3.0-4) ... Setting up r-cran-r6 (2.5.0-1) ... Setting up r-cran-pkgkitten (0.2.1-1) ... Setting up r-cran-magrittr (2.0.1-1) ... Setting up openmpi-bin (4.1.0-10) ... 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-littler (0.3.12-1) ... Setting up r-cran-rcpp (1.0.6-1) ... Setting up r-cran-codetools (0.2-18-1) ... Setting up r-cran-brio (1.1.1-1) ... Setting up r-cran-inline (0.3.17-1) ... Setting up r-cran-diffobj (0.3.2-1) ... Setting up r-cran-rlang (0.4.10-1) ... Setting up r-cran-assertthat (0.2.1-2) ... Setting up littler (0.3.12-1) ... Setting up r-cran-withr (2.4.1-1) ... Setting up r-cran-processx (3.4.5-1) ... Setting up r-cran-praise (1.0.0-4) ... Setting up r-cran-iterators (1.0.13-1) ... Setting up r-cran-digest (0.6.27-1) ... Setting up r-cran-evaluate (0.14-2) ... Setting up r-cran-foreach (1.5.1-1) ... Setting up r-cran-prettyunits (1.1.1-2) ... Setting up r-cran-fansi (0.4.2-1) ... Setting up r-cran-mass (7.3-53.1-1) ... Setting up r-cran-glue (1.4.2-1) ... Setting up r-cran-gam (1.20-1) ... Setting up r-cran-cli (2.3.0-1) ... Setting up r-cran-lifecycle (0.2.0-2) ... Setting up r-cran-rprojroot (2.0.2-1) ... Setting up r-cran-jsonlite (1.7.2+dfsg-1) ... Setting up r-cran-rstudioapi (0.13-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.1.4-2) ... Setting up r-cran-colorspace (2.0-0+dfsg-1) ... Setting up examl (3.0.22-1+b4) ... Setting up r-cran-rcolorbrewer (1.1-2-3) ... Setting up r-cran-matrix (1.3-2-1) ... Setting up r-cran-mgcv (1.8-34-1) ... Setting up r-cran-rcppgsl (0.3.8-1) ... Setting up r-cran-ellipsis (0.3.1-1) ... Setting up r-cran-callr (3.5.1-1) ... Setting up r-cran-desc (1.2.0-3) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-scales (1.1.1-1) ... Setting up r-cran-pkgbuild (1.2.0-1) ... Setting up r-cran-vctrs (0.3.6-1) ... Setting up r-cran-pillar (1.4.7-1) ... Setting up r-cran-pkgload (1.1.0-1) ... Setting up r-cran-tibble (3.0.6+dfsg-1) ... Setting up r-cran-rematch2 (2.1.2-2) ... Setting up r-cran-waldo (0.2.3-2) ... Setting up r-cran-testthat (3.0.1-1) ... Setting up r-cran-isoband (0.2.3-2) ... Setting up r-cran-ggplot2 (3.3.3+dfsg-1) ... Setting up mapdamage (2.2.1+dfsg-1) ... Setting up default-jre-headless (2:1.11-72) ... Setting up openjdk-11-jre-headless:amd64 (11.0.22+7-1~deb11u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jre:amd64 (11.0.22+7-1~deb11u1) ... Setting up default-jre (2:1.11-72) ... Setting up ant (1.10.9-4) ... Setting up ca-certificates-java (20190909+deb11u1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Setting up ant-optional (1.10.9-4) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10) ... Setting up libtxw2-java (2.3.0.1-10) ... Setting up libjaxb-java (2.3.0.1-10) ... Setting up libhtsjdk-java (2.23.0+dfsg-2) ... Setting up libpicard-java (2.24.1+dfsg-1) ... Setting up picard-tools (2.24.1+dfsg-1) ... Setting up paleomix (1.3.2-1) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. 0m58.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', '-y', 'install', 'paleomix'] 0m58.7s INFO: Running scripts post_install 0m58.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_install_exceptions'] 0m58.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_install_exceptions'] 0m58.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 1m0.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 1m0.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpuarkol71 to sid 1m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 1m0.2s INFO: Running scripts pre_distupgrade 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_distupgrade_exceptions'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_distupgrade_exceptions'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', 'update'] 1m4.5s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9899 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7191 kB] Fetched 17.3 MB in 3s (5638 kB/s) Reading package lists... 1m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', 'update'] 1m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', '-yf', 'dist-upgrade'] 2m29.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: ant ant-optional libaopalliance-java libargs4j-java libatinject-jsr330-api-java libcbor0 libcdi-api-java libcodemodel-java libcommons-cli-java libdtd-parser-java liberror-prone-java libfastinfoset-java libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libglib2.0-0 libguava-java libguice-java libicu67 libistack-commons-java libjaxb-api-java libjaxb-java libjsoup-java libjsr305-java libldap-2.4-2 libllvm11 libmaven-file-management-java libmaven-parent-java libmaven-resolver-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libmpdec3 libngs-sdk-dev libngs-sdk2 libperl5.32 libplexus-archiver-java libplexus-cipher-java libplexus-classworlds-java libplexus-component-annotations-java libplexus-interpolation-java libplexus-io-java libplexus-sec-dispatcher-java libplexus-utils2-java libpython3.9-minimal libpython3.9-stdlib libquadmath0 librelaxng-datatype-java librngom-java libsisu-inject-java libsisu-plexus-java libstax-ex-java libstreambuffer-java libtbb2 libtiff5 libtxw2-java libwagon-http-java libwagon-provider-api-java libwebp6 libxml-commons-resolver1.1-java libxsom-java perl-modules-5.32 python3.9 python3.9-minimal r-cran-assertthat r-cran-ellipsis r-cran-prettyunits Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libasound2 libcups2 libcurl3-gnutls libcurl4 libdb5.3 libelf1 libevent-core-2.1-7 libevent-pthreads-2.1-7 libext2fs2 libgdbm-compat4 libgdbm6 libgnutls30 libgsl25 libhogweed6 libhts3 libnettle8 libopenmpi3 libpmix2 libpng16-16 libpsl5 librdmacm1 libreadline8 libsemanage1 libssh2-1 libtirpc3 libxt6 The following NEW packages will be installed: adwaita-icon-theme at-spi2-common fonts-dejavu-mono gcc-14-base gtk-update-icon-cache hicolor-icon-theme libamd-comgr2 libamdhip64-5 libapt-pkg6.0t64 libasound2t64 libatk1.0-0t64 libatomic1 libcap2 libcbor0.10 libcups2t64 libcurl3t64-gnutls libcurl4t64 libdb5.3t64 libelf1t64 liberror-prone-java libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libext2fs2t64 libffi8 libfile-find-rule-perl libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libglib2.0-0t64 libgnutls30t64 libgsl27 libgtk2.0-0t64 libgtk2.0-common libhogweed6t64 libhsa-runtime64-1 libhsakmt1 libhts3t64 libhtscodecs2 libicu72 libldap-2.5-0 liblerc4 libllvm17t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmjson-java libmunge2 libncbi-ngs3 libncbi-vdb3 libnettle8t64 libngs-jni libnumber-compare-perl libopenmpi3t64 libperl5.38t64 libpmix2t64 libpng16-16t64 libpsl5t64 libpython3.11-minimal libpython3.11-stdlib librdmacm1t64 libreadline8t64 librhino-java libsemanage2 libsepol2 libsharpyuv0 libssh2-1t64 libssl3t64 libtext-glob-perl libtiff6 libtirpc3t64 libunistring5 libuv1t64 libwebp7 libxcb-randr0 libxcomposite1 libxcursor1 libxinerama1 libxrandr2 libxt6t64 ncbi-vdb-data netbase openjdk-17-jre openjdk-17-jre-headless perl-modules-5.38 python3.11 python3.11-minimal r-cran-fs shared-mime-info usrmerge The following packages will be upgraded: adapterremoval adduser ant ant-optional apt base-files base-passwd bash bcftools bedtools bowtie2 bsdutils bwa ca-certificates ca-certificates-java coreutils dash debconf debian-archive-keyring debianutils default-jre default-jre-headless diffutils dpkg e2fsprogs examl findutils fontconfig fontconfig-config fonts-dejavu-core gcc-10-base gcc-9-base gpgv grep gzip hostname ibverbs-providers init-system-helpers java-common libacl1 libaopalliance-java libapache-pom-java libargs4j-java libasound2-data libattr1 libaudit-common libaudit1 libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libblkid1 libbrotli1 libbsd0 libbz2-1.0 libc-bin libc6 libcairo2 libcap-ng0 libcodemodel-java libcom-err2 libcommons-cli-java libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-parent-java libcrypt1 libdatrie1 libdbus-1-3 libdebconfclient0 libdeflate0 libdom4j-java libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libexpat1 libfabric1 libfido2-1 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libgatk-native-bindings-java libgcc-s1 libgcrypt20 libgfortran5 libgif7 libgkl-java libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgmp10 libgomp1 libgoogle-gson-java libgpg-error0 libgraphite2-3 libgsl-dev libgslcblas0 libgssapi-krb5-2 libguava-java libharfbuzz0b libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibverbs1 libidn2-0 libjaxb-java libjbig0 libjpeg62-turbo libjsoup-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblightcouch-java liblog4j2-java liblz4-1 liblzma5 libmaven-parent-java libmaven-resolver-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libmd0 libmount1 libncurses6 libncursesw6 libnghttp2-14 libngs-java libnl-3-200 libnl-route-3-200 libnsl2 libnspr4 libnss3 libnuma1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcre2-8-0 libpcre3 libpcsclite1 libpicard-java libpixman-1-0 libplexus-archiver-java libplexus-cipher-java libplexus-classworlds-java libplexus-component-annotations-java libplexus-io-java libplexus-sec-dispatcher-java libplexus-utils2-java libpsm-infinipath1 libpsm2-2 libpython3-stdlib libquadmath0 librngom-java librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsensors-config libsensors5 libslf4j-java libsmartcols1 libsnappy-java libsnappy-jni libsnappy1v5 libsqlite3-0 libss2 libstdc++6 libsystemd0 libtasn1-6 libtcl8.6 libthai-data libthai0 libtinfo6 libtirpc-common libtk8.6 libtxw2-java libucx0 libudev1 libuuid1 libvulkan1 libwagon-http-java libwagon-provider-api-java libx11-6 libx11-data libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxdamage1 libxext6 libxfixes3 libxft2 libxi6 libxml2 libxnvctrl0 libxrender1 libxsom-java libxtst6 libxxhash0 libxz-java libz3-4 libzstd1 littler login logsave lsb-base mafft mapdamage mawk media-types mount ncurses-base ncurses-bin ocl-icd-libopencl1 openjdk-11-jre openjdk-11-jre-headless openmpi-bin openmpi-common openssh-client openssl paleomix passwd perl perl-base phylip picard-tools python3 python3-coloredlogs python3-configargparse python3-humanfriendly python3-minimal python3-pysam python3-ruamel.yaml python3-ruamel.yaml.clib python3-setproctitle r-base-core r-cran-brio r-cran-callr r-cran-cli r-cran-codetools r-cran-colorspace r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest r-cran-ellipsis r-cran-evaluate 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-jsonlite 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-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgkitten r-cran-pkgload r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppgsl r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr radiant raxml readline-common samtools sed sensible-utils seqtk sysvinit-utils tar tzdata ucf unzip util-linux x11-common zip zlib1g 343 upgraded, 90 newly installed, 27 to remove and 0 not upgraded. Need to get 369 MB of archives. After this operation, 654 MB 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 libc6 amd64 2.37-17 [2753 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-17 [603 kB] Get:4 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240330-1 [43.2 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240330-1 [71.9 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40-5 [163 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2+b2 [74.9 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40-5 [194 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40-5 [135 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40-5 [32.0 kB] Get:12 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-4 [616 kB] Get:13 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40-5 [1205 kB] Get:14 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.6.1+really5.4.5-1 [240 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:16 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:17 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.6 [1510 kB] Get:18 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-7 [32.2 kB] Get:19 http://deb.debian.org/debian sid/main amd64 lsb-base all 11.6 [4584 B] Get:20 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23 [252 kB] Get:21 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.17 [89.0 kB] Get:22 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:26 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-2 [61.4 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.4-1+b1 [364 kB] Get:28 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40-5 [100 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libcbor0.10 amd64 0.10.2-1.2 [28.2 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.4-1+b1 [126 kB] Get:32 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3.1 [87.6 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libfido2-1 amd64 1.14.0-1+b2 [77.7 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:35 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b3 [90.3 kB] Get:37 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-4 [973 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2.1 [11.4 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-2 [16.9 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2.1 [48.5 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [38.0 kB] Get:42 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3.2 [2899 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [697 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.23-5.1+b1 [73.0 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.23-5.1+b1 [48.8 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libperl5.38t64 amd64 5.38.2-3.2+b2 [4279 kB] Get:47 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3.2+b2 [236 kB] Get:48 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3.2+b2 [1644 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.3-7 [67.7 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.3-7 [54.4 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.3-7 [265 kB] Get:53 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.86 [119 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:55 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.4+20240113-1 [104 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:61 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libedit2 amd64 3.1-20230828-1 [93.1 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2.4 [20.2 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:69 http://deb.debian.org/debian sid/main amd64 openssh-client amd64 1:9.7p1-4 [965 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.2.1-3 [2244 kB] Get:71 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3.1 [2950 kB] Get:72 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:73 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:74 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:75 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:76 http://deb.debian.org/debian sid/main amd64 gzip amd64 1.12-1.1 [133 kB] Get:77 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:78 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271+b3 [10.2 kB] Get:80 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240330-1 [713 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.16+dfsg-2 [185 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.61.0-1 [75.3 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.2-1 [425 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.7.1-2 [440 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.7.1-2 [432 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:91 http://deb.debian.org/debian sid/main amd64 bcftools amd64 1.19-1+b1 [738 kB] Get:92 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libnettle8t64 amd64 3.9.1-2.2 [296 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libhogweed6t64 amd64 3.9.1-2.2 [328 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.5-2 [1437 kB] Get:99 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.0 [986 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:106 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-3 [649 kB] Get:107 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:109 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.0 [1379 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:111 http://deb.debian.org/debian sid/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:112 http://deb.debian.org/debian sid/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:113 http://deb.debian.org/debian sid/main amd64 usrmerge all 39 [13.1 kB] Get:114 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:115 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libasound2-data all 1.2.11-1 [20.9 kB] Get:117 http://deb.debian.org/debian sid/main amd64 openjdk-11-jre amd64 11.0.23~7ea-1 [194 kB] Get:118 http://deb.debian.org/debian sid/main amd64 openjdk-11-jre-headless amd64 11.0.23~7ea-1 [38.3 MB] Get:119 http://deb.debian.org/debian sid/main amd64 libasound2t64 amd64 1.2.11-1+b1 [369 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libgl1-mesa-dri amd64 24.0.5-1 [8278 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get:129 http://deb.debian.org/debian sid/main amd64 ibverbs-providers amd64 50.0-2+b1 [342 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libibverbs1 amd64 50.0-2+b1 [61.7 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get:134 http://deb.debian.org/debian sid/main amd64 libllvm17t64 amd64 1:17.0.6-9+b2 [23.7 MB] Get:135 http://deb.debian.org/debian sid/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get:136 http://deb.debian.org/debian sid/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get:137 http://deb.debian.org/debian sid/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get:143 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14-20240330-1 [9216 B] Get:144 http://deb.debian.org/debian sid/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get:147 http://deb.debian.org/debian sid/main amd64 librdmacm1t64 amd64 50.0-2+b1 [70.2 kB] Get:148 http://deb.debian.org/debian sid/main amd64 libucx0 amd64 1.16.0+ds-5 [1109 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libopenmpi3t64 amd64 4.1.6-9 [2429 kB] Get:150 http://deb.debian.org/debian sid/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [132 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [54.1 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libpciaccess0 amd64 0.17-3 [51.6 kB] Get:153 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:154 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:155 http://deb.debian.org/debian sid/main amd64 libx11-xcb1 amd64 2:1.8.7-1 [232 kB] Get:156 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:157 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:158 http://deb.debian.org/debian sid/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get:159 http://deb.debian.org/debian sid/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB] Get:162 http://deb.debian.org/debian sid/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libpmix2t64 amd64 5.0.2-3 [652 kB] Get:164 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2.4 [20.1 kB] Get:165 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.0-2.4 [206 kB] Get:166 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2.4 [571 kB] Get:167 http://deb.debian.org/debian sid/main amd64 libgsl-dev amd64 2.7.1+dfsg-6+b1 [1146 kB] Get:168 http://deb.debian.org/debian sid/main amd64 r-cran-rcppgsl amd64 0.3.13-1 [203 kB] Get:169 http://deb.debian.org/debian sid/main amd64 libgslcblas0 amd64 2.7.1+dfsg-6+b1 [107 kB] Get:170 http://deb.debian.org/debian sid/main amd64 libgsl27 amd64 2.7.1+dfsg-6+b1 [934 kB] Get:171 http://deb.debian.org/debian sid/main amd64 r-cran-ps amd64 1.7.6-1 [310 kB] Get:172 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.3-1 [1669 kB] Get:173 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.2-1 [1325 kB] Get:174 http://deb.debian.org/debian sid/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:175 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:176 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:177 http://deb.debian.org/debian sid/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:178 http://deb.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:179 http://deb.debian.org/debian sid/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:180 http://deb.debian.org/debian sid/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:181 http://deb.debian.org/debian sid/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:182 http://deb.debian.org/debian sid/main amd64 zip amd64 3.0-13 [230 kB] Get:183 http://deb.debian.org/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:184 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:185 http://deb.debian.org/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:186 http://deb.debian.org/debian sid/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:188 http://deb.debian.org/debian sid/main amd64 libopenblas-pthread-dev amd64 0.3.27+ds-1 [4779 kB] Get:189 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get:190 http://deb.debian.org/debian sid/main amd64 libopenblas0-pthread amd64 0.3.27+ds-1 [6815 kB] Get:191 http://deb.debian.org/debian sid/main amd64 libopenblas0 amd64 0.3.27+ds-1 [39.0 kB] Get:192 http://deb.debian.org/debian sid/main amd64 libopenblas-dev amd64 0.3.27+ds-1 [52.3 kB] Get:193 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:194 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:195 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:196 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:197 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:198 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get:199 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:200 http://deb.debian.org/debian sid/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:201 http://deb.debian.org/debian sid/main amd64 java-common all 0.75 [6640 B] Get:202 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:203 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:204 http://deb.debian.org/debian sid/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get:205 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.2-1 [895 kB] Get:206 http://deb.debian.org/debian sid/main amd64 libnss3 amd64 2:3.99-1 [1408 kB] Get:207 http://deb.debian.org/debian sid/main amd64 libpcsclite1 amd64 2.0.3-1 [51.0 kB] Get:208 http://deb.debian.org/debian sid/main amd64 libvulkan1 amd64 1.3.275.0-1 [124 kB] Get:209 http://deb.debian.org/debian sid/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get:210 http://deb.debian.org/debian sid/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get:211 http://deb.debian.org/debian sid/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get:212 http://deb.debian.org/debian sid/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get:213 http://deb.debian.org/debian sid/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get:214 http://deb.debian.org/debian sid/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get:215 http://deb.debian.org/debian sid/main amd64 libglx-mesa0 amd64 24.0.5-1 [151 kB] Get:216 http://deb.debian.org/debian sid/main amd64 libglapi-mesa amd64 24.0.5-1 [36.3 kB] Get:217 http://deb.debian.org/debian sid/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get:218 http://deb.debian.org/debian sid/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get:219 http://deb.debian.org/debian sid/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get:220 http://deb.debian.org/debian sid/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get:221 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:222 http://deb.debian.org/debian sid/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get:223 http://deb.debian.org/debian sid/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get:224 http://deb.debian.org/debian sid/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get:225 http://deb.debian.org/debian sid/main amd64 libgl1 amd64 1.7.0-1 [89.7 kB] Get:226 http://deb.debian.org/debian sid/main amd64 libglx0 amd64 1.7.0-1 [34.7 kB] Get:227 http://deb.debian.org/debian sid/main amd64 libglvnd0 amd64 1.7.0-1 [51.3 kB] Get:228 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.78.4-6 [275 kB] Get:229 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.78.4-6 [1222 kB] Get:230 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:231 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get:232 http://deb.debian.org/debian sid/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB] Get:233 http://deb.debian.org/debian sid/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get:234 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:235 http://deb.debian.org/debian sid/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get:236 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get:237 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b3 [439 kB] Get:238 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:239 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:240 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:241 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-3 [530 kB] Get:242 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240330-1 [136 kB] Get:243 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:244 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.52.1+ds-1 [35.1 kB] Get:245 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.52.1+ds-1 [216 kB] Get:246 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.52.1+ds-1 [48.3 kB] Get:247 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get:248 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:249 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:250 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:251 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:252 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get:253 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-4 [69.3 kB] Get:254 http://deb.debian.org/debian sid/main amd64 tzdata all 2024a-2 [255 kB] Get:255 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:256 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:257 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:258 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get:259 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get:260 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:261 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:262 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.2 [10.9 kB] Get:263 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.2 [82.6 kB] Get:264 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:265 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:266 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:267 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.3.3-3+b1 [26.8 MB] Get:268 http://deb.debian.org/debian sid/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get:269 http://deb.debian.org/debian sid/main amd64 littler all 0.3.20-1 [16.0 kB] Get:270 http://deb.debian.org/debian sid/main amd64 r-cran-pkgkitten all 0.2.3-1 [26.7 kB] Get:271 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.12-1 [2071 kB] Get:272 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40-5 [147 kB] Get:273 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get:274 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get:275 http://deb.debian.org/debian sid/main amd64 python3-setproctitle amd64 1.3.3-1+b1 [19.5 kB] Get:276 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml.clib amd64 0.2.8-1 [186 kB] Get:277 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.22.0+ds-1+b2 [4646 kB] Get:278 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get:279 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get:280 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:281 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:282 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get:283 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get:284 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get:285 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.3-7 [140 kB] Get:286 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:287 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:288 http://deb.debian.org/debian sid/main amd64 libpcre3 amd64 2:8.39-15+b1 [342 kB] Get:289 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:290 http://deb.debian.org/debian sid/main amd64 adapterremoval amd64 2.3.3-2 [191 kB] Get:291 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get:292 http://deb.debian.org/debian sid/main amd64 shared-mime-info amd64 2.4-4 [759 kB] Get:293 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-3+b2 [138 kB] Get:294 http://deb.debian.org/debian sid/main amd64 gtk-update-icon-cache amd64 3.24.41-4 [46.6 kB] Get:295 http://deb.debian.org/debian sid/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get:296 http://deb.debian.org/debian sid/main amd64 adwaita-icon-theme all 46.0-1 [614 kB] Get:297 http://deb.debian.org/debian sid/main amd64 ant-optional all 1.10.14-1 [455 kB] Get:298 http://deb.debian.org/debian sid/main amd64 openjdk-17-jre-headless amd64 17.0.11~7ea-1+b1 [43.8 MB] Get:299 http://deb.debian.org/debian sid/main amd64 libgtk2.0-common all 2.24.33-4 [2661 kB] Get:300 http://deb.debian.org/debian sid/main amd64 at-spi2-common all 2.52.0-1 [166 kB] Get:301 http://deb.debian.org/debian sid/main amd64 libatk1.0-0t64 amd64 2.52.0-1 [50.8 kB] Get:302 http://deb.debian.org/debian sid/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get:303 http://deb.debian.org/debian sid/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get:304 http://deb.debian.org/debian sid/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get:305 http://deb.debian.org/debian sid/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get:306 http://deb.debian.org/debian sid/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB] Get:307 http://deb.debian.org/debian sid/main amd64 libgtk2.0-0t64 amd64 2.24.33-4 [1816 kB] Get:308 http://deb.debian.org/debian sid/main amd64 openjdk-17-jre amd64 17.0.11~7ea-1+b1 [185 kB] Get:309 http://deb.debian.org/debian sid/main amd64 default-jre amd64 2:1.17-75 [1056 B] Get:310 http://deb.debian.org/debian sid/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get:311 http://deb.debian.org/debian sid/main amd64 ant all 1.10.14-1 [2162 kB] Get:312 http://deb.debian.org/debian sid/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get:313 http://deb.debian.org/debian sid/main amd64 bowtie2 amd64 2.5.2-1 [1438 kB] Get:314 http://deb.debian.org/debian sid/main amd64 bwa amd64 0.7.17-7+b3 [212 kB] Get:315 http://deb.debian.org/debian sid/main amd64 openmpi-common all 4.1.6-9 [169 kB] Get:316 http://deb.debian.org/debian sid/main amd64 openmpi-bin amd64 4.1.6-9 [226 kB] Get:317 http://deb.debian.org/debian sid/main amd64 examl amd64 3.0.22-5 [954 kB] Get:318 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240330-1 [147 kB] Get:319 http://deb.debian.org/debian sid/main amd64 gcc-10-base amd64 10.5.0-4 [36.7 kB] Get:320 http://deb.debian.org/debian sid/main amd64 gcc-9-base amd64 9.5.0-6 [29.0 kB] Get:321 http://deb.debian.org/debian sid/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get:322 http://deb.debian.org/debian sid/main amd64 libapache-pom-java all 29-2 [5276 B] Get:323 http://deb.debian.org/debian sid/main amd64 libargs4j-java all 2.33-2 [138 kB] Get:324 http://deb.debian.org/debian sid/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:325 http://deb.debian.org/debian sid/main amd64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get:326 http://deb.debian.org/debian sid/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get:327 http://deb.debian.org/debian sid/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get:328 http://deb.debian.org/debian sid/main amd64 libcommons-codec-java all 1.16.0-1 [297 kB] Get:329 http://deb.debian.org/debian sid/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get:330 http://deb.debian.org/debian sid/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get:331 http://deb.debian.org/debian sid/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get:332 http://deb.debian.org/debian sid/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get:333 http://deb.debian.org/debian sid/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get:334 http://deb.debian.org/debian sid/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get:335 http://deb.debian.org/debian sid/main amd64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] Get:336 http://deb.debian.org/debian sid/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB] Get:337 http://deb.debian.org/debian sid/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get:338 http://deb.debian.org/debian sid/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB] Get:339 http://deb.debian.org/debian sid/main amd64 libcommons-io-java all 2.16.0-1 [484 kB] Get:340 http://deb.debian.org/debian sid/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get:341 http://deb.debian.org/debian sid/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get:342 http://deb.debian.org/debian sid/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get:343 http://deb.debian.org/debian sid/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get:344 http://deb.debian.org/debian sid/main amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B] Get:345 http://deb.debian.org/debian sid/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get:346 http://deb.debian.org/debian sid/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get:347 http://deb.debian.org/debian sid/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get:348 http://deb.debian.org/debian sid/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get:349 http://deb.debian.org/debian sid/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get:350 http://deb.debian.org/debian sid/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2+b1 [1049 kB] Get:351 http://deb.debian.org/debian sid/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-6+b1 [155 kB] Get:352 http://deb.debian.org/debian sid/main amd64 libngs-jni amd64 3.0.3+dfsg-6+b1 [23.7 kB] Get:353 http://deb.debian.org/debian sid/main amd64 libngs-java amd64 3.0.3+dfsg-6+b1 [111 kB] Get:354 http://deb.debian.org/debian sid/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get:355 http://deb.debian.org/debian sid/main amd64 libsnappy1v5 amd64 1.1.10-1+b1 [27.6 kB] Get:356 http://deb.debian.org/debian sid/main amd64 libsnappy-jni amd64 1.1.10.5-2 [6396 B] Get:357 http://deb.debian.org/debian sid/main amd64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get:358 http://deb.debian.org/debian sid/main amd64 libhtsjdk-java all 4.1.0+dfsg-1 [1833 kB] Get:359 http://deb.debian.org/debian sid/main amd64 libgkl-java all 0.8.11+dfsg-2 [24.7 kB] Get:360 http://deb.debian.org/debian sid/main amd64 librngom-java all 2.3.0.1-10.1 [290 kB] Get:361 http://deb.debian.org/debian sid/main amd64 libxsom-java all 2.3.0.1-10.1 [400 kB] Get:362 http://deb.debian.org/debian sid/main amd64 libtxw2-java all 2.3.0.1-10.1 [134 kB] Get:363 http://deb.debian.org/debian sid/main amd64 libjaxb-java all 2.3.0.1-10.1 [1973 kB] Get:364 http://deb.debian.org/debian sid/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get:365 http://deb.debian.org/debian sid/main amd64 libmaven-parent-java all 35-1 [6140 B] Get:366 http://deb.debian.org/debian sid/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get:367 http://deb.debian.org/debian sid/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get:368 http://deb.debian.org/debian sid/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get:369 http://deb.debian.org/debian sid/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get:370 http://deb.debian.org/debian sid/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get:371 http://deb.debian.org/debian sid/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get:372 http://deb.debian.org/debian sid/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get:373 http://deb.debian.org/debian sid/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get:374 http://deb.debian.org/debian sid/main amd64 libmaven3-core-java all 3.8.7-2 [1573 kB] Get:375 http://deb.debian.org/debian sid/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get:376 http://deb.debian.org/debian sid/main amd64 libpicard-java all 3.1.1+dfsg-1 [1743 kB] Get:377 http://deb.debian.org/debian sid/main amd64 picard-tools all 3.1.1+dfsg-1 [311 kB] Get:378 http://deb.debian.org/debian sid/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get:379 http://deb.debian.org/debian sid/main amd64 libxz-java all 1.9-1 [143 kB] Get:380 http://deb.debian.org/debian sid/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get:381 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.0-2.4 [25.0 kB] Get:382 http://deb.debian.org/debian sid/main amd64 libuv1t64 amd64 1.48.0-1.1 [147 kB] Get:383 http://deb.debian.org/debian sid/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get:384 http://deb.debian.org/debian sid/main amd64 mafft amd64 7.505-1 [1078 kB] Get:385 http://deb.debian.org/debian sid/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:386 http://deb.debian.org/debian sid/main amd64 r-cran-iterators all 1.0.14-1 [337 kB] Get:387 http://deb.debian.org/debian sid/main amd64 r-cran-foreach all 1.5.2-1 [122 kB] Get:388 http://deb.debian.org/debian sid/main amd64 r-cran-gam amd64 1.22-3-1 [390 kB] Get:389 http://deb.debian.org/debian sid/main amd64 r-cran-gtable all 0.3.4+dfsg-1 [221 kB] Get:390 http://deb.debian.org/debian sid/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:391 http://deb.debian.org/debian sid/main amd64 r-cran-mass amd64 7.3-60.0.1-1 [1118 kB] Get:392 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:393 http://deb.debian.org/debian sid/main amd64 r-cran-nlme amd64 3.1.164-1 [2280 kB] Get:394 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.6-5-1 [3789 kB] Get:395 http://deb.debian.org/debian sid/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get:396 http://deb.debian.org/debian sid/main amd64 r-cran-farver amd64 2.1.1-2 [1405 kB] Get:397 http://deb.debian.org/debian sid/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:398 http://deb.debian.org/debian sid/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:399 http://deb.debian.org/debian sid/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:400 http://deb.debian.org/debian sid/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:401 http://deb.debian.org/debian sid/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:402 http://deb.debian.org/debian sid/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get:403 http://deb.debian.org/debian sid/main amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3405 kB] Get:404 http://deb.debian.org/debian sid/main amd64 r-cran-inline all 0.3.19-2 [129 kB] Get:405 http://deb.debian.org/debian sid/main amd64 seqtk amd64 1.4-2 [34.6 kB] Get:406 http://deb.debian.org/debian sid/main amd64 mapdamage all 2.2.1+dfsg-3 [41.9 kB] Get:407 http://deb.debian.org/debian sid/main amd64 python3-humanfriendly all 10.0-5 [85.4 kB] Get:408 http://deb.debian.org/debian sid/main amd64 python3-coloredlogs all 15.0.1-1 [47.4 kB] Get:409 http://deb.debian.org/debian sid/main amd64 python3-configargparse all 1.7-1 [31.3 kB] Get:410 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml all 0.17.21-1 [103 kB] Get:411 http://deb.debian.org/debian sid/main amd64 phylip amd64 1:3.697+dfsg-4 [957 kB] Get:412 http://deb.debian.org/debian sid/main amd64 radiant all 2.8.1+dfsg-2 [181 kB] Get:413 http://deb.debian.org/debian sid/main amd64 raxml amd64 8.2.13+dfsg-1 [1480 kB] Get:414 http://deb.debian.org/debian sid/main amd64 paleomix amd64 1.3.8-1 [984 kB] Get:415 http://deb.debian.org/debian sid/main amd64 r-cran-brio amd64 1.1.4-1 [37.4 kB] Get:416 http://deb.debian.org/debian sid/main amd64 r-cran-processx amd64 3.8.3-1 [345 kB] Get:417 http://deb.debian.org/debian sid/main amd64 r-cran-callr all 3.7.5-1 [430 kB] Get:418 http://deb.debian.org/debian sid/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB] Get:419 http://deb.debian.org/debian sid/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:420 http://deb.debian.org/debian sid/main amd64 r-cran-desc all 1.4.3-1 [351 kB] Get:421 http://deb.debian.org/debian sid/main amd64 r-cran-diffobj amd64 0.3.5-1+b1 [1122 kB] Get:422 http://deb.debian.org/debian sid/main amd64 r-cran-digest amd64 0.6.35-1 [203 kB] Get:423 http://deb.debian.org/debian sid/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get:424 http://deb.debian.org/debian sid/main amd64 r-cran-evaluate all 0.23-1 [90.6 kB] Get:425 http://deb.debian.org/debian sid/main amd64 r-cran-fs amd64 1.6.3+dfsg-1+b1 [228 kB] Get:426 http://deb.debian.org/debian sid/main amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [443 kB] Get:427 http://deb.debian.org/debian sid/main amd64 r-cran-pkgbuild all 1.4.3-1 [210 kB] Get:428 http://deb.debian.org/debian sid/main amd64 r-cran-rprojroot all 2.0.4-1 [124 kB] Get:429 http://deb.debian.org/debian sid/main amd64 r-cran-pkgload all 1.3.4-1 [208 kB] Get:430 http://deb.debian.org/debian sid/main amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] Get:431 http://deb.debian.org/debian sid/main amd64 r-cran-rstudioapi all 0.16.0-1 [292 kB] Get:432 http://deb.debian.org/debian sid/main amd64 r-cran-waldo all 0.5.2-1 [120 kB] Get:433 http://deb.debian.org/debian sid/main amd64 r-cran-testthat amd64 3.2.1-1 [1644 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 369 MB in 5s (78.5 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23209 files and directories currently installed.) Preparing to unpack .../login_1%3a4.13+dfsg1-4_amd64.deb ... Unpacking login (1:4.13+dfsg1-4) over (1:4.8.1-1) ... Setting up login (1:4.13+dfsg1-4) ... Installing new version of config file /etc/login.defs ... Installing new version of config file /etc/pam.d/login ... (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 ... 23222 files and directories currently installed.) Preparing to unpack .../util-linux_2.40-5_amd64.deb ... Unpacking util-linux (2.40-5) over (2.36.1-8+deb11u1) ... dpkg: warning: unable to delete old directory '/usr/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/usr/lib/udev': Directory not empty Setting up util-linux (2.40-5) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23191 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.22.6_amd64.deb ... Unpacking dpkg (1.22.6) over (1.20.13) ... Setting up dpkg (1.22.6) ... Installing new version of config file /etc/cron.daily/dpkg ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23180 files and directories currently installed.) Preparing to unpack .../x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) over (1:7.7+22) ... Preparing to unpack .../debianutils_5.17_amd64.deb ... Unpacking debianutils (5.17) over (4.11.2) ... Setting up debianutils (5.17) ... update-alternatives: using /usr/bin/which.debianutils to provide /usr/bin/which (which) in auto mode (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23182 files and directories currently installed.) Preparing to unpack .../bash_5.2.21-2_amd64.deb ... Unpacking bash (5.2.21-2) over (5.1-2+deb11u1) ... Setting up bash (5.2.21-2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode Selecting previously unselected package libcap2: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 ... 23183 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.66-5_amd64.deb ... Unpacking libcap2:amd64 (1:2.66-5) ... Setting up libcap2:amd64 (1:2.66-5) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23195 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40-5_amd64.deb ... Unpacking bsdutils (1:2.40-5) over (1:2.36.1-8+deb11u1) ... Setting up bsdutils (1:2.40-5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23195 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.3.0+dfsg-2+b1_amd64.deb ... Unpacking libgmp10:amd64 (2:6.3.0+dfsg-2+b1) over (2:6.2.1+dfsg-1+deb11u1) ... Setting up libgmp10:amd64 (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package libcbor0.10: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 ... 23196 files and directories currently installed.) Preparing to unpack .../libcbor0.10_0.10.2-1.2_amd64.deb ... Unpacking libcbor0.10:amd64 (0.10.2-1.2) ... Preparing to unpack .../libudev1_255.4-1+b1_amd64.deb ... Unpacking libudev1:amd64 (255.4-1+b1) over (247.3-7+deb11u4) ... Setting up libudev1:amd64 (255.4-1+b1) ... (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 ... 23205 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.3.dfsg-3.1) over (1:1.2.11.dfsg-2+deb11u2) ... Setting up zlib1g:amd64 (1:1.3.dfsg-3.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23205 files and directories currently installed.) Preparing to unpack .../libfido2-1_1.14.0-1+b2_amd64.deb ... Unpacking libfido2-1:amd64 (1.14.0-1+b2) over (1.6.0-2) ... Preparing to unpack .../libsemanage-common_3.5-1_all.deb ... Unpacking libsemanage-common (3.5-1) over (3.1-1) ... Setting up libsemanage-common (3.5-1) ... Installing new version of config file /etc/selinux/semanage.conf ... Selecting previously unselected package libsepol2: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 ... 23206 files and directories currently installed.) Preparing to unpack .../libsepol2_3.5-2_amd64.deb ... Unpacking libsepol2:amd64 (3.5-2) ... Setting up libsepol2:amd64 (3.5-2) ... Selecting previously unselected package libsemanage2: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 ... 23210 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.5-1+b3_amd64.deb ... Unpacking libsemanage2:amd64 (3.5-1+b3) ... Setting up libsemanage2:amd64 (3.5-1+b3) ... (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 ... 23215 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.13+dfsg1-4_amd64.deb ... Unpacking passwd (1:4.13+dfsg1-4) over (1:4.8.1-1) ... Setting up passwd (1:4.13+dfsg1-4) ... Installing new version of config file /etc/default/useradd ... (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 ... 23249 files and directories currently installed.) Removing libsemanage1:amd64 (3.1-1+b2) ... (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 ... 23244 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.2-2.1_all.deb ... Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.0-2) ... Setting up libaudit-common (1:3.1.2-2.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23244 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.4-2_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.4-2) over (0.7.9-2.2+b1) ... Setting up libcap-ng0:amd64 (0.8.4-2) ... (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 ... 23245 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.1.2-2.1) over (1:3.0-2) ... Setting up libaudit1:amd64 (1:3.1.2-2.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23245 files and directories currently installed.) Preparing to unpack .../libbz2-1.0_1.0.8-5.1_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.8-5.1) over (1.0.8-4) ... Setting up libbz2-1.0:amd64 (1.0.8-5.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23245 files and directories currently installed.) Preparing to unpack .../perl_5.38.2-3.2+b2_amd64.deb ... Unpacking perl (5.38.2-3.2+b2) over (5.32.1-4+deb11u3) ... Selecting previously unselected package perl-modules-5.38. Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... Unpacking perl-modules-5.38 (5.38.2-3.2) ... dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libsasl2-modules-db:amd64 depends on libdb5.3. libpython3.9-stdlib:amd64 depends on libdb5.3. libperl5.32:amd64 depends on libdb5.3. libpam-modules:amd64 depends on libdb5.3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 24659 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg1-0.8) ... Selecting previously unselected package libdb5.3t64: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 ... 24653 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... dpkg: libgdbm6:amd64: dependency problems, but removing anyway as you requested: libperl5.32:amd64 depends on libgdbm6 (>= 1.18-3). libgdbm-compat4:amd64 depends on libgdbm6 (>= 1.16). (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 ... 24659 files and directories currently installed.) Removing libgdbm6:amd64 (1.19-2) ... Selecting previously unselected package libgdbm6t64: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 ... 24653 files and directories currently installed.) Preparing to unpack .../libgdbm6t64_1.23-5.1+b1_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.23-5.1+b1) ... dpkg: libgdbm-compat4:amd64: dependency problems, but removing anyway as you requested: libperl5.32:amd64 depends on libgdbm-compat4 (>= 1.18-3). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 24661 files and directories currently installed.) Removing libgdbm-compat4:amd64 (1.19-2) ... Selecting previously unselected package libgdbm-compat4t64: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 ... 24655 files and directories currently installed.) Preparing to unpack .../libgdbm-compat4t64_1.23-5.1+b1_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.23-5.1+b1) ... Selecting previously unselected package libperl5.38t64:amd64. Preparing to unpack .../libperl5.38t64_5.38.2-3.2+b2_amd64.deb ... Unpacking libperl5.38t64:amd64 (5.38.2-3.2+b2) ... Preparing to unpack .../perl-base_5.38.2-3.2+b2_amd64.deb ... Unpacking perl-base (5.38.2-3.2+b2) over (5.32.1-4+deb11u3) ... Setting up perl-base (5.38.2-3.2+b2) ... (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 ... 25191 files and directories currently installed.) Preparing to unpack .../libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) over (2.1.27+dfsg-2.1+deb11u1) ... Preparing to unpack .../libpam0g_1.5.3-7_amd64.deb ... Unpacking libpam0g:amd64 (1.5.3-7) over (1.4.0-9+deb11u1) ... Setting up libpam0g:amd64 (1.5.3-7) ... (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 ... 25188 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-7_amd64.deb ... Unpacking libpam-modules-bin (1.5.3-7) over (1.4.0-9+deb11u1) ... Replacing files in old package libpam-modules:amd64 (1.4.0-9+deb11u1) ... Setting up libpam-modules-bin (1.5.3-7) ... (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 ... 25192 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-7_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.3-7) over (1.4.0-9+deb11u1) ... dpkg: warning: unable to delete old directory '/lib/x86_64-linux-gnu/security': Directory not empty Setting up libpam-modules:amd64 (1.5.3-7) ... Installing new version of config file /etc/security/limits.conf ... Installing new version of config file /etc/security/namespace.init ... Installing new version of config file /etc/security/sepermit.conf ... (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 ... 25193 files and directories currently installed.) Preparing to unpack .../debconf_1.5.86_all.deb ... Unpacking debconf (1.5.86) over (1.5.77) ... Setting up debconf (1.5.86) ... Installing new version of config file /etc/debconf.conf ... (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 ... 25191 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.36-4_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-4) over (1:4.4.18-4) ... Setting up libcrypt1:amd64 (1:4.4.36-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25191 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.137_all.deb ... moving unchanged adduser.conf to adduser.conf.update-old. New dpkg-conffile will come from the package. Unpacking adduser (3.137) over (3.118+deb11u1) ... Setting up adduser (3.137) ... Installing new version of config file /etc/deluser.conf ... (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 ... 25153 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-2_amd64.deb ... Unpacking libmd0:amd64 (1.1.0-2) over (1.0.3-3) ... Setting up libmd0:amd64 (1.1.0-2) ... (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 ... 25153 files and directories currently installed.) Preparing to unpack .../libbsd0_0.12.2-1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-1) over (0.11.3-1+deb11u1) ... Preparing to unpack .../libncurses6_6.4+20240113-1_amd64.deb ... Unpacking libncurses6:amd64 (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Preparing to unpack .../libncursesw6_6.4+20240113-1_amd64.deb ... Unpacking libncursesw6:amd64 (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Preparing to unpack .../libtinfo6_6.4+20240113-1_amd64.deb ... Unpacking libtinfo6:amd64 (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Setting up libtinfo6:amd64 (6.4+20240113-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25152 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4+20240113-1_amd64.deb ... Unpacking ncurses-bin (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-bin (6.4+20240113-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25152 files and directories currently installed.) Preparing to unpack .../0-libedit2_3.1-20230828-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20230828-1) over (3.1-20191231-2+b1) ... Preparing to unpack .../1-libgssapi-krb5-2_1.20.1-6+b1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-6+b1) over (1.18.3-6+deb11u4) ... Preparing to unpack .../2-libkrb5-3_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-6+b1) over (1.18.3-6+deb11u4) ... Preparing to unpack .../3-libk5crypto3_1.20.1-6+b1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-6+b1) over (1.18.3-6+deb11u4) ... Preparing to unpack .../4-libkrb5support0_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6+b1) over (1.18.3-6+deb11u4) ... Preparing to unpack .../5-libcom-err2_1.47.0-2.4_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.0-2.4) over (1.46.2-2) ... Preparing to unpack .../6-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) over (1.6.1-2) ... Preparing to unpack .../7-openssh-client_1%3a9.7p1-4_amd64.deb ... Unpacking openssh-client (1:9.7p1-4) over (1:8.4p1-5+deb11u3) ... Selecting previously unselected package libssl3t64:amd64. Preparing to unpack .../8-libssl3t64_3.2.1-3_amd64.deb ... Unpacking libssl3t64:amd64 (3.2.1-3) ... Setting up libssl3t64:amd64 (3.2.1-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25170 files and directories currently installed.) Preparing to unpack .../coreutils_9.4-3.1_amd64.deb ... Unpacking coreutils (9.4-3.1) over (8.32-4+b1) ... Setting up coreutils (9.4-3.1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25179 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.3_amd64.deb ... Unpacking base-passwd (3.6.3) over (3.5.51) ... Setting up base-passwd (3.6.3) ... (Reading database ... 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Unpacking libnghttp2-14:amd64 (1.61.0-1) over (1.43.0-1+deb11u1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../libunistring5_1.2-1_amd64.deb ... Unpacking libunistring5:amd64 (1.2-1) ... Setting up libunistring5:amd64 (1.2-1) ... dpkg: libssh2-1:amd64: dependency problems, but removing anyway as you requested: libcurl4:amd64 depends on libssh2-1 (>= 1.7.0). libcurl3-gnutls:amd64 depends on libssh2-1 (>= 1.7.0). (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25187 files and directories currently installed.) Preparing to unpack .../libcurl4t64_8.7.1-2_amd64.deb ... Unpacking libcurl4t64:amd64 (8.7.1-2) ... dpkg: libpsl5:amd64: dependency problems, but removing anyway as you requested: libcurl3-gnutls:amd64 depends on libpsl5 (>= 0.16.0). (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25195 files and directories currently installed.) Removing libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u11) ... Selecting previously unselected package libcurl3t64-gnutls: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 ... 25186 files and directories currently installed.) Preparing to unpack .../libcurl3t64-gnutls_8.7.1-2_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.7.1-2) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../libhtscodecs2_1.6.0-1+b1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.0-1+b1) ... Preparing to unpack .../bcftools_1.19-1+b1_amd64.deb ... Unpacking bcftools (1.19-1+b1) over (1.11-1) ... 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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 ... 25197 files and directories currently installed.) Preparing to unpack .../libhts3t64_1.19+ds-1.1+b1_amd64.deb ... Unpacking libhts3t64:amd64 (1.19+ds-1.1+b1) ... dpkg: libhogweed6:amd64: dependency problems, but removing anyway as you requested: librtmp1:amd64 depends on libhogweed6. libgnutls30:amd64 depends on libhogweed6 (>= 3.6). (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 ... 25214 files and directories currently installed.) Removing libhogweed6:amd64 (3.7.3-1) ... dpkg: libnettle8:amd64: dependency problems, but removing anyway as you requested: librtmp1:amd64 depends on libnettle8. libgnutls30:amd64 depends on libnettle8 (>= 3.7~). Removing libnettle8:amd64 (3.7.3-1) ... dpkg: libgnutls30:amd64: dependency problems, but removing anyway as you requested: librtmp1:amd64 depends on libgnutls30 (>= 3.6.14). libldap-2.4-2:amd64 depends on libgnutls30 (>= 3.7.0). libcups2:amd64 depends on libgnutls30 (>= 3.7.0). apt depends on libgnutls30 (>= 3.7.0). Removing libgnutls30:amd64 (3.7.1-5+deb11u4) ... Selecting previously unselected package libnettle8t64: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 ... 25173 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.9.1-2.2_amd64.deb ... Unpacking libnettle8t64:amd64 (3.9.1-2.2) ... Setting up libnettle8t64:amd64 (3.9.1-2.2) ... Selecting previously unselected package libhogweed6t64: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 ... 25182 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.9.1-2.2_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.9.1-2.2) ... Setting up libhogweed6t64:amd64 (3.9.1-2.2) ... Selecting previously unselected package libffi8: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 ... 25189 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.6-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.6-1) ... Setting up libffi8:amd64 (3.4.6-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25194 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.3-4_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.3-4) over (0.23.22-1) ... Setting up libp11-kit0:amd64 (0.25.3-4) ... Selecting previously unselected package libgnutls30t64: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 ... 25194 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.5-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.5-2) ... Setting up libgnutls30t64:amd64 (3.8.5-2) ... (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 ... 25223 files and directories currently installed.) Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) over (2.4+20151223.gitfa8646d.1-2+b2) ... Preparing to unpack .../libidn2-0_2.3.7-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.7-2) over (2.3.0-5) ... Setting up libidn2-0:amd64 (2.3.7-2) ... (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 ... 25225 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.19.0-3+b2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.19.0-3+b2) over (4.16.0-2+deb11u1) ... Setting up libtasn1-6:amd64 (4.19.0-3+b2) ... (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 ... 25226 files and directories currently installed.) Preparing to unpack .../libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) over (1.0.9-2+b2) ... Preparing to unpack .../libdeflate0_1.20-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.20-1) over (1.7-1) ... dpkg: libapt-pkg6.0:amd64: dependency problems, but removing anyway as you requested: apt depends on libapt-pkg6.0 (>= 2.2.4). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25227 files and directories currently installed.) Removing libapt-pkg6.0:amd64 (2.2.4) ... Selecting previously unselected package libapt-pkg6.0t64:amd64. (Reading database ... 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Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-automatic.gpg ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25229 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.0_amd64.deb ... Unpacking apt (2.9.0) over (2.2.4) ... Setting up apt (2.9.0) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt-compat ... Removing obsolete conffile /etc/kernel/postinst.d/apt-auto-removal ... Selecting previously unselected package libnumber-compare-perl. (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 ... 25222 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-3_all.deb ... Unpacking libnumber-compare-perl (0.03-3) ... Setting up libnumber-compare-perl (0.03-3) ... Selecting previously unselected package libtext-glob-perl. (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25236 files and directories currently installed.) Preparing to unpack .../libfile-find-rule-perl_0.34-3_all.deb ... Unpacking libfile-find-rule-perl (0.34-3) ... Setting up perl-modules-5.38 (5.38.2-3.2) ... Setting up libgdbm6t64:amd64 (1.23-5.1+b1) ... Setting up libgdbm-compat4t64:amd64 (1.23-5.1+b1) ... Setting up libperl5.38t64:amd64 (5.38.2-3.2+b2) ... Setting up perl (5.38.2-3.2+b2) ... Setting up libfile-find-rule-perl (0.34-3) ... Selecting previously unselected package usrmerge. (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 ... 25251 files and directories currently installed.) Preparing to unpack .../archives/usrmerge_39_all.deb ... Unpacking usrmerge (39) ... Setting up usrmerge (39) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25258 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4+20240113-1_all.deb ... Unpacking ncurses-base (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-base (6.4+20240113-1) ... (Reading database ... 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Unpacking openjdk-11-jre-headless:amd64 (11.0.23~7ea-1) over (11.0.22+7-1~deb11u1) ... (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 ... 25260 files and directories currently installed.) Removing libasound2:amd64 (1.2.4-1.1) ... Selecting previously unselected package libasound2t64: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 ... 25252 files and directories currently installed.) Preparing to unpack .../libasound2t64_1.2.11-1+b1_amd64.deb ... Unpacking libasound2t64:amd64 (1.2.11-1+b1) ... Preparing to unpack .../libavahi-client3_0.8-13+b2_amd64.deb ... Unpacking libavahi-client3:amd64 (0.8-13+b2) over (0.8-5+deb11u2) ... Preparing to unpack .../libavahi-common3_0.8-13+b2_amd64.deb ... Unpacking libavahi-common3:amd64 (0.8-13+b2) over (0.8-5+deb11u2) ... Preparing to unpack .../libavahi-common-data_0.8-13+b2_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.8-13+b2) over (0.8-5+deb11u2) ... Preparing to unpack .../libdbus-1-3_1.14.10-4+b1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.14.10-4+b1) over (1.12.28-0+deb11u1) ... (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 ... 25263 files and directories currently installed.) Removing libcups2:amd64 (2.3.3op2-3+deb11u6) ... Selecting previously unselected package libcups2t64: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 ... 25255 files and directories currently installed.) Preparing to unpack .../libcups2t64_2.4.7-1.2+b1_amd64.deb ... Unpacking libcups2t64:amd64 (2.4.7-1.2+b1) ... Preparing to unpack .../libgl1-mesa-dri_24.0.5-1_amd64.deb ... Unpacking libgl1-mesa-dri:amd64 (24.0.5-1) over (20.3.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25264 files and directories currently installed.) Removing libelf1:amd64 (0.183-1) ... Selecting previously unselected package libelf1t64: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 ... 25251 files and directories currently installed.) Preparing to unpack .../00-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Preparing to unpack .../01-libnl-route-3-200_3.7.0-0.3_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.7.0-0.3) over (3.4.0-1+b1) ... Preparing to unpack .../02-libnl-3-200_3.7.0-0.3_amd64.deb ... Unpacking libnl-3-200:amd64 (3.7.0-0.3) over (3.4.0-1+b1) ... Preparing to unpack .../03-ibverbs-providers_50.0-2+b1_amd64.deb ... Unpacking ibverbs-providers:amd64 (50.0-2+b1) over (33.2-1) ... Preparing to unpack .../04-libibverbs1_50.0-2+b1_amd64.deb ... Unpacking libibverbs1:amd64 (50.0-2+b1) over (33.2-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../05-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Preparing to unpack .../06-libxml2_2.9.14+dfsg-1.3+b2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b2) over (2.9.10+dfsg-6.7+deb11u4) ... Preparing to unpack .../07-libz3-4_4.8.12-3.1+b2_amd64.deb ... Unpacking libz3-4:amd64 (4.8.12-3.1+b2) over (4.8.10-1) ... Selecting previously unselected package libllvm17t64:amd64. Preparing to unpack .../08-libllvm17t64_1%3a17.0.6-9+b2_amd64.deb ... Unpacking libllvm17t64:amd64 (1:17.0.6-9+b2) ... Selecting previously unselected package libamd-comgr2:amd64. Preparing to unpack .../09-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b1_amd64.deb ... Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Preparing to unpack .../10-libdrm-common_2.4.120-2_all.deb ... Unpacking libdrm-common (2.4.120-2) over (2.4.104-1) ... Preparing to unpack .../11-libdrm2_2.4.120-2_amd64.deb ... Unpacking libdrm2:amd64 (2.4.120-2) over (2.4.104-1) ... Preparing to unpack .../12-libdrm-amdgpu1_2.4.120-2_amd64.deb ... Unpacking libdrm-amdgpu1:amd64 (2.4.120-2) over (2.4.104-1) ... Preparing to unpack .../13-libnuma1_2.0.18-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.18-1) over (2.0.12-1+b1) ... Selecting previously unselected package libhsakmt1:amd64. Preparing to unpack .../14-libhsakmt1_5.7.0-1_amd64.deb ... Unpacking libhsakmt1:amd64 (5.7.0-1) ... Selecting previously unselected package libhsa-runtime64-1. Preparing to unpack .../15-libhsa-runtime64-1_5.7.1-2_amd64.deb ... Unpacking libhsa-runtime64-1 (5.7.1-2) ... Selecting previously unselected package libamdhip64-5. Preparing to unpack .../16-libamdhip64-5_5.7.1-3_amd64.deb ... Unpacking libamdhip64-5 (5.7.1-3) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../17-libatomic1_14-20240330-1_amd64.deb ... Unpacking libatomic1:amd64 (14-20240330-1) ... Preparing to unpack .../18-libpsm-infinipath1_3.3+20.604758e7-6.3_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3) over (3.3+20.604758e7-6.1) ... Preparing to unpack .../19-libpsm2-2_11.2.185-2_amd64.deb ... Unpacking libpsm2-2 (11.2.185-2) over (11.2.185-1) ... Preparing to unpack .../20-libfabric1_1.17.0-3+b1_amd64.deb ... Unpacking libfabric1:amd64 (1.17.0-3+b1) over (1.11.0-2) ... dpkg: librdmacm1:amd64: dependency problems, but removing anyway as you requested: libucx0:amd64 depends on librdmacm1 (>= 23). (Reading database ... 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Unpacking libucx0:amd64 (1.16.0+ds-5) over (1.10.1~rc1+really.1.10.0-1) ... dpkg: libopenmpi3:amd64: dependency problems, but removing anyway as you requested: openmpi-bin depends on libopenmpi3 (>= 4.1.0). examl depends on libopenmpi3 (>= 4.1.0). (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 ... 25326 files and directories currently installed.) Removing libopenmpi3:amd64 (4.1.0-10) ... Selecting previously unselected package libopenmpi3t64: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 ... 25158 files and directories currently installed.) Preparing to unpack .../libopenmpi3t64_4.1.6-9_amd64.deb ... Unpacking libopenmpi3t64:amd64 (4.1.6-9) ... (Reading database ... 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(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 ... 25244 files and directories currently installed.) Preparing to unpack .../00-libevent-core-2.1-7t64_2.1.12-stable-8.1+b3_amd64.deb ... Unpacking libevent-core-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. Preparing to unpack .../01-libevent-pthreads-2.1-7t64_2.1.12-stable-8.1+b3_amd64.deb ... Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:amd64 (1.47.0-2.4) ... Setting up libcom-err2:amd64 (1.47.0-2.4) ... Setting up libext2fs2t64:amd64 (1.47.0-2.4) ... (Reading database ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Preparing to unpack .../01-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) over (8.1-1) ... Preparing to unpack .../02-tzdata_2024a-2_all.deb ... Unpacking tzdata (2024a-2) over (2024a-0+deb11u1) ... Preparing to unpack .../03-libtcl8.6_8.6.14+dfsg-1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1) over (8.6.11+dfsg-1) ... 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Setting up bwa (0.7.17-7+b3) ... Setting up libglvnd0:amd64 (1.7.0-1) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up radiant (2.8.1+dfsg-2) ... Setting up libtirpc-common (1.3.4+ds-1.2) ... Setting up libmjson-java (1.4.0-3) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up unzip (6.0-28) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libsqlite3-0:amd64 (3.45.2-1) ... Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Setting up libuv1t64:amd64 (1.48.0-1.1) ... Setting up phylip (1:3.697+dfsg-4) ... Setting up x11-common (1:7.7+23) ... Installing new version of config file /etc/X11/Xsession ... Installing new version of config file /etc/X11/Xsession.d/20x11-common_process-args ... Installing new version of config file /etc/X11/Xsession.d/90x11-common_ssh-agent ... Installing new version of config file /etc/init.d/x11-common ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libsensors-config (1:3.6.0-9) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up libgsl27:amd64 (2.7.1+dfsg-6+b1) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libgomp1:amd64 (14-20240330-1) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up libsnappy1v5:amd64 (1.1.10-1+b1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Apr 14 15:44:26 UTC 2024. Universal Time is now: Sun Apr 14 15:44:26 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.15-1) ... Setting up libasound2-data (1.2.11-1) ... Setting up gcc-10-base:amd64 (10.5.0-4) ... Setting up zip (3.0-13) ... Setting up librhino-java (1.7.14-2.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libglib2.0-0t64:amd64 (2.78.4-6) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... Setting up libasound2t64:amd64 (1.2.11-1+b1) ... Setting up libmunge2:amd64 (0.5.15-4) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:amd64 (0.8-13+b2) ... Setting up libncurses6:amd64 (6.4+20240113-1) ... Setting up libdbus-1-3:amd64 (1.14.10-4+b1) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libquadmath0:amd64 (14-20240330-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libhwloc15:amd64 (2.10.0-1+b1) ... Setting up libatomic1:amd64 (14-20240330-1) ... Setting up libxz-java (1.9-1) ... Setting up libss2:amd64 (1.47.0-2.4) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... Setting up fonts-dejavu-core (2.37-8) ... Removing obsolete conffile /etc/fonts/conf.avail/20-unhint-small-dejavu-lgc-sans-mono.conf ... Removing obsolete conffile /etc/fonts/conf.avail/20-unhint-small-dejavu-sans-mono.conf ... Removing obsolete conffile /etc/fonts/conf.avail/57-dejavu-sans-mono.conf ... Removing obsolete conffile /etc/fonts/conf.avail/58-dejavu-lgc-sans-mono.conf ... Setting up libpcsclite1:amd64 (2.0.3-1) ... Setting up libsensors5:amd64 (1:3.6.0-9) ... Setting up libncursesw6:amd64 (6.4+20240113-1) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libglapi-mesa:amd64 (24.0.5-1) ... Setting up logsave (1.47.0-2.4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14-20240330-1) ... Setting up libvulkan1:amd64 (1.3.275.0-1) ... Setting up libwebp7:amd64 (1.3.2-0.4+b1) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up libgif7:amd64 (5.2.2-1) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10.1) ... Setting up librngom-java (2.3.0.1-10.1) ... Setting up libnuma1:amd64 (2.0.18-1) ... Setting up mount (2.40-5) ... Setting up libfreemarker-java (2.3.32-2) ... Setting up sensible-utils (0.0.22) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.52.0-1) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libnl-3-200:amd64 (3.7.0-0.3) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up openmpi-common (4.1.6-9) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libgtk2.0-common (2.24.33-4) ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libxsom-java (2.3.0.1-10.1) ... Setting up libfido2-1:amd64 (1.14.0-1+b2) ... Setting up openssl (3.2.1-3) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libsnappy-jni (1.1.10.5-2) ... Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Setting up bedtools (2.31.1+dfsg-2) ... Setting up libargs4j-java (2.33-2) ... Setting up gcc-9-base:amd64 (9.5.0-6) ... Setting up raxml (8.2.13+dfsg-1) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libgsl-dev (2.7.1+dfsg-6+b1) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up libopenblas0-pthread:amd64 (0.3.27+ds-1) ... Setting up libatk1.0-0t64:amd64 (2.52.0-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Setting up libglib2.0-0:amd64 (2.78.4-6) ... Setting up fontconfig-config (2.15.0-1.1) ... Installing new version of config file /etc/fonts/conf.d/README ... Installing new version of config file /etc/fonts/fonts.conf ... Setting up libmaven-parent-java (35-1) ... Setting up libedit2:amd64 (3.1-20230828-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-13+b2) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up e2fsprogs (1.47.0-2.4) ... Installing new version of config file /etc/mke2fs.conf ... Setting up libnss3:amd64 (2:3.99-1) ... Setting up libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3) ... Setting up libxnvctrl0:amd64 (535.171.04-1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 37 added, 20 removed; done. Setting up libllvm17t64:amd64 (1:17.0.6-9+b2) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b3) ... Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up shared-mime-info (2.4-4) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libxrandr2:amd64 (2:1.5.4-1) ... Setting up ucf (3.0043+nmu1) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up libopenblas0:amd64 (0.3.27+ds-1) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b2) ... Setting up libsnappy-java (1.1.10.5-2) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up ca-certificates-java (20240118) ... Installing new version of config file /etc/ca-certificates/update.d/jks-keystore ... Removing debian:chambers_of_commerce_root_-_2008.pem Removing debian:cybertrust_global_root.pem Removing debian:dst_root_ca_x3.pem Removing debian:e-tugra_certification_authority.pem Removing debian:ec-acc.pem Removing debian:geotrust_primary_certification_authority_-_g2.pem Removing debian:global_chambersign_root_-_2008.pem Removing debian:globalsign_root_ca_-_r2.pem Removing debian:hellenic_academic_and_research_institutions_rootca_2011.pem Removing debian:hongkong_post_root_ca_1.pem Removing debian:network_solutions_certificate_authority.pem Removing debian:quovadis_root_ca.pem Removing debian:sonera_class_2_root_ca.pem Removing debian:staat_der_nederlanden_ev_root_ca.pem Removing debian:staat_der_nederlanden_root_ca_-_g3.pem Removing debian:trustcor_eca-1.pem Removing debian:trustcor_rootcert_ca-1.pem Removing debian:trustcor_rootcert_ca-2.pem Removing debian:trustis_fps_root_ca.pem Removing debian:verisign_universal_root_certification_authority.pem Replacing debian:ACCVRAIZ1.pem Replacing debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Replacing debian:Actalis_Authentication_Root_CA.pem Replacing debian:AffirmTrust_Commercial.pem Replacing debian:AffirmTrust_Networking.pem Replacing debian:AffirmTrust_Premium.pem Replacing debian:AffirmTrust_Premium_ECC.pem Replacing debian:Amazon_Root_CA_1.pem Replacing debian:Amazon_Root_CA_2.pem Replacing debian:Amazon_Root_CA_3.pem Replacing debian:Amazon_Root_CA_4.pem Replacing debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Replacing debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Replacing debian:Baltimore_CyberTrust_Root.pem Replacing debian:Buypass_Class_2_Root_CA.pem Replacing debian:Buypass_Class_3_Root_CA.pem Replacing debian:CA_Disig_Root_R2.pem Replacing debian:CFCA_EV_ROOT.pem Replacing debian:COMODO_Certification_Authority.pem Replacing debian:COMODO_ECC_Certification_Authority.pem Replacing debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Replacing debian:Certigna.pem Replacing debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Replacing debian:Certum_Trusted_Network_CA.pem Replacing debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Replacing 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 Replacing debian:D-TRUST_Root_Class_3_CA_2_2009.pem Replacing debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Replacing debian:DigiCert_Assured_ID_Root_CA.pem Replacing debian:DigiCert_Assured_ID_Root_G2.pem Replacing debian:DigiCert_Assured_ID_Root_G3.pem Replacing debian:DigiCert_Global_Root_CA.pem Replacing debian:DigiCert_Global_Root_G2.pem Replacing debian:DigiCert_Global_Root_G3.pem Replacing 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 Replacing debian:DigiCert_Trusted_Root_G4.pem Replacing debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Replacing debian:Entrust_Root_Certification_Authority.pem Replacing debian:Entrust_Root_Certification_Authority_-_EC1.pem Replacing debian:Entrust_Root_Certification_Authority_-_G2.pem Replacing debian:Entrust_Root_Certification_Authority_-_G4.pem Replacing debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Replacing debian:GTS_Root_R1.pem Replacing debian:GTS_Root_R2.pem Replacing debian:GTS_Root_R3.pem Replacing debian:GTS_Root_R4.pem Replacing debian:GlobalSign_ECC_Root_CA_-_R4.pem Replacing debian:GlobalSign_ECC_Root_CA_-_R5.pem Replacing debian:GlobalSign_Root_CA.pem Replacing debian:GlobalSign_Root_CA_-_R3.pem Replacing debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Replacing debian:Go_Daddy_Class_2_CA.pem Replacing 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 Replacing debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Replacing debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Replacing debian:Hongkong_Post_Root_CA_3.pem Replacing debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Replacing debian:IdenTrust_Commercial_Root_CA_1.pem Replacing debian:IdenTrust_Public_Sector_Root_CA_1.pem Replacing debian:Izenpe.com.pem Replacing debian:Microsec_e-Szigno_Root_CA_2009.pem Replacing debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Replacing debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Replacing debian:NAVER_Global_Root_Certification_Authority.pem Replacing debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Replacing debian:OISTE_WISeKey_Global_Root_GB_CA.pem Replacing debian:OISTE_WISeKey_Global_Root_GC_CA.pem Replacing debian:QuoVadis_Root_CA_1_G3.pem Replacing debian:QuoVadis_Root_CA_2.pem Replacing debian:QuoVadis_Root_CA_2_G3.pem Replacing debian:QuoVadis_Root_CA_3.pem Replacing debian:QuoVadis_Root_CA_3_G3.pem Replacing debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Replacing debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Replacing debian:SSL.com_Root_Certification_Authority_ECC.pem Replacing debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Replacing debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Replacing debian:SecureSign_RootCA11.pem Replacing debian:SecureTrust_CA.pem Replacing debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Replacing debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Replacing debian:Security_Communication_Root_CA.pem Replacing debian:Starfield_Class_2_CA.pem Replacing debian:Starfield_Root_Certificate_Authority_-_G2.pem Replacing debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Replacing debian:SwissSign_Gold_CA_-_G2.pem Replacing debian:SwissSign_Silver_CA_-_G2.pem Replacing debian:T-TeleSec_GlobalRoot_Class_2.pem Replacing debian:T-TeleSec_GlobalRoot_Class_3.pem Replacing debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Replacing debian:TWCA_Global_Root_CA.pem Replacing debian:TWCA_Root_Certification_Authority.pem Replacing debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Replacing debian:Trustwave_Global_Certification_Authority.pem Replacing debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Replacing debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Replacing debian:UCA_Extended_Validation_Root.pem Replacing debian:UCA_Global_G2_Root.pem Replacing debian:USERTrust_ECC_Certification_Authority.pem Replacing debian:USERTrust_RSA_Certification_Authority.pem Replacing debian:XRamp_Global_CA_Root.pem Replacing debian:certSIGN_ROOT_CA.pem Replacing debian:certSIGN_Root_CA_G2.pem Replacing debian:e-Szigno_Root_CA_2017.pem Replacing debian:ePKI_Root_Certification_Authority.pem Replacing debian:emSign_ECC_Root_CA_-_C3.pem Replacing debian:emSign_ECC_Root_CA_-_G3.pem Replacing debian:emSign_Root_CA_-_C1.pem Replacing debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up libcommons-codec-java (1.16.0-1) ... Setting up libtxw2-java (2.3.0.1-10.1) ... Setting up libavahi-client3:amd64 (0.8-13+b2) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libopenblas-pthread-dev:amd64 (0.3.27+ds-1) ... update-alternatives: updating alternative /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so because link group libopenblas.so-x86_64-linux-gnu has changed slave links Setting up libjaxb-java (2.3.0.1-10.1) ... Setting up libpaper1:amd64 (1.1.29) ... Setting up gtk-update-icon-cache (3.24.41-4) ... Setting up libibverbs1:amd64 (50.0-2+b1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up libcurl4t64:amd64 (8.7.1-2) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.2) ... Setting up ibverbs-providers:amd64 (50.0-2+b1) ... Removing obsolete conffile /etc/libibverbs.d/i40iw.driver ... Setting up libcommons-io-java (2.16.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up openssh-client (1:9.7p1-4) ... Installing new version of config file /etc/ssh/ssh_config ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up libpango-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up openjdk-11-jre-headless:amd64 (11.0.23~7ea-1) ... Installing new version of config file /etc/java-11-openjdk/security/default.policy ... Installing new version of config file /etc/java-11-openjdk/security/java.security ... Installing new version of config file /etc/java-11-openjdk/security/public_suffix_list.dat ... Setting up libgl1-mesa-dri:amd64 (24.0.5-1) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-2) ... Setting up libpaper-utils (1.1.29) ... Setting up libhwloc-plugins:amd64 (2.10.0-1+b1) ... Setting up libcairo2:amd64 (1.18.0-3) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up libopenblas-dev:amd64 (0.3.27+ds-1) ... Setting up adwaita-icon-theme (46.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libpmix2t64:amd64 (5.0.2-3) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11~7ea-1+b1) ... 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 libhttpclient-java (4.5.14-1) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up librdmacm1t64:amd64 (50.0-2+b1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libpangoft2-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ... Setting up libhsakmt1:amd64 (5.7.0-1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-6+b1) ... Setting up libfabric1:amd64 (1.17.0-3+b1) ... Setting up python3.11 (3.11.9-1) ... Setting up libngs-jni:amd64 (3.0.3+dfsg-6+b1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:amd64 (24.0.5-1) ... Setting up libglx0:amd64 (1.7.0-1) ... Setting up libmaven3-core-java (3.8.7-2) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up bcftools (1.19-1+b1) ... Setting up python3 (3.11.8-1) ... Setting up samtools (1.19.2-1+b1) ... Setting up bowtie2 (2.5.2-1) ... Setting up libgl1:amd64 (1.7.0-1) ... Setting up python3-humanfriendly (10.0-5) ... Setting up r-base-core (4.3.3-3+b1) ... Installing new version of config file /etc/R/Makeconf ... Installing new version of config file /etc/R/Renviron.site ... Installing new version of config file /etc/R/repositories ... Replacing config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.5.2-1) ... Setting up python3-setproctitle:amd64 (1.3.3-1+b1) ... Setting up r-cran-labeling (0.4.3-1) ... Setting up libgtk2.0-0t64:amd64 (2.24.33-4) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-ps (1.7.6-1) ... Setting up r-cran-nlme (3.1.164-1) ... Setting up r-cran-farver (2.1.1-2) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libhsa-runtime64-1 (5.7.1-2) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:amd64 (3.0.3+dfsg-6+b1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.3-1) ... Setting up python3-coloredlogs (15.0.1-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up libhtsjdk-java (4.1.0+dfsg-1) ... Setting up libbarclay-java (5.0.0+dfsg-1) ... Setting up r-cran-littler (0.3.20-1) ... Setting up python3-configargparse (1.7-1) ... Setting up r-cran-fs (1.6.3+dfsg-1+b1) ... Setting up r-cran-rcpp (1.0.12-1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-cran-brio (1.1.4-1) ... Setting up r-cran-inline (0.3.19-2) ... Setting up r-cran-diffobj (0.3.5-1+b1) ... Setting up r-cran-rlang (1.1.3-1) ... Setting up python3-pysam (0.22.0+ds-1+b2) ... Setting up littler (0.3.20-1) ... Setting up r-cran-withr (3.0.0+dfsg-1) ... Setting up libgkl-java (0.8.11+dfsg-2) ... Setting up r-cran-processx (3.8.3-1) ... Setting up r-cran-iterators (1.0.14-1) ... Setting up r-cran-digest (0.6.35-1) ... Setting up r-cran-evaluate (0.23-1) ... Setting up python3-ruamel.yaml.clib:amd64 (0.2.8-1) ... Setting up r-cran-foreach (1.5.2-1) ... Setting up r-cran-prettyunits (1.2.0-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-mass (7.3-60.0.1-1) ... Setting up r-cran-glue (1.7.0-1) ... Setting up r-cran-gam (1.22-3-1) ... Setting up r-cran-cli (3.6.2-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-cran-rprojroot (2.0.4-1) ... Setting up r-cran-jsonlite (1.8.8+dfsg-1) ... Setting up r-cran-rstudioapi (0.16.0-1) ... Setting up libpicard-java (3.1.1+dfsg-1) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-colorspace (2.1-0+dfsg-1) ... Setting up libamdhip64-5 (5.7.1-3) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-scales (1.3.0-1) ... Setting up r-cran-gtable (0.3.4+dfsg-1) ... Setting up r-cran-matrix (1.6-5-1) ... Setting up python3-ruamel.yaml (0.17.21-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up r-cran-rcppgsl (0.3.13-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up r-cran-ellipsis (0.3.2-2) ... Setting up libucx0:amd64 (1.16.0+ds-5) ... Setting up r-cran-callr (3.7.5-1) ... Setting up r-cran-desc (1.4.3-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-cran-waldo (0.5.2-1) ... Setting up libopenmpi3t64:amd64 (4.1.6-9) ... Setting up r-cran-pkgbuild (1.4.3-1) ... Setting up openmpi-bin (4.1.6-9) ... Installing new version of config file /etc/openmpi/openmpi-mca-params.conf ... Setting up r-cran-pkgload (1.3.4-1) ... Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... Setting up mapdamage (2.2.1+dfsg-3) ... Setting up r-cran-testthat (3.2.1-1) ... Setting up examl (3.0.22-5) ... Setting up libguava-java (32.0.1-1) ... Setting up liberror-prone-java (2.18.0-1) ... Processing triggers for libc-bin (2.37-17) ... Processing triggers for debianutils (5.17) ... Processing triggers for ca-certificates-java (20240118) ... done. Setting up default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:amd64 (17.0.11~7ea-1+b1) ... Setting up openjdk-11-jre:amd64 (11.0.23~7ea-1) ... Setting up default-jre (2:1.17-75) ... Setting up picard-tools (3.1.1+dfsg-1) ... Setting up ant (1.10.14-1) ... Setting up paleomix (1.3.8-1) ... Setting up ant-optional (1.10.14-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. 2m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', '-yf', 'dist-upgrade'] 2m29.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m30.2s DUMP: 1512f65556dc874d2a448b4a657aacc7 - 2m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'show', '--no-all-versions', 'paleomix'] 2m30.5s 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 2m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'show', '--no-all-versions', 'paleomix'] 2m30.5s INFO: apt-cache knows about the following packages: paleomix 2m30.5s INFO: Running scripts pre_install 2m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_database-server'] 2m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_database-server'] 2m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_exceptions'] 2m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_exceptions'] 2m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_extras'] 2m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_extras'] 2m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_foreign_architecture'] 2m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_foreign_architecture'] 2m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'policy'] 2m30.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 2m30.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'policy'] 2m30.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'policy', 'paleomix'] 2m30.6s 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 2m30.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'policy', 'paleomix'] 2m30.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', '-y', 'install', 'paleomix'] 2m31.4s DUMP: Reading package lists... Building dependency tree... Reading state information... paleomix is already the newest version (1.3.8-1). The following packages were automatically installed and are no longer required: ant ant-optional libaopalliance-java libargs4j-java libatinject-jsr330-api-java libcbor0 libcdi-api-java libcodemodel-java libcommons-cli-java libdtd-parser-java liberror-prone-java libfastinfoset-java libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libglib2.0-0 libguava-java libguice-java libicu67 libistack-commons-java libjaxb-api-java libjaxb-java libjsoup-java libjsr305-java libldap-2.4-2 libllvm11 libmaven-file-management-java libmaven-parent-java libmaven-resolver-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libmpdec3 libngs-sdk-dev libngs-sdk2 libperl5.32 libplexus-archiver-java libplexus-cipher-java libplexus-classworlds-java libplexus-component-annotations-java libplexus-interpolation-java libplexus-io-java libplexus-sec-dispatcher-java libplexus-utils2-java libpython3.9-minimal libpython3.9-stdlib libquadmath0 librelaxng-datatype-java librngom-java libsisu-inject-java libsisu-plexus-java libstax-ex-java libstreambuffer-java libtbb2 libtiff5 libtxw2-java libwagon-http-java libwagon-provider-api-java libwebp6 libxml-commons-resolver1.1-java libxsom-java perl-modules-5.32 python3.9 python3.9-minimal r-cran-assertthat r-cran-ellipsis r-cran-prettyunits Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', '-y', 'install', 'paleomix'] 2m31.4s INFO: Running scripts post_install 2m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_install_exceptions'] 2m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_install_exceptions'] 2m31.4s INFO: Running scripts post_distupgrade 2m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_distupgrade_exceptions'] 2m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_distupgrade_exceptions'] 2m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_distupgrade_zz_backports'] 2m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_distupgrade_zz_backports'] 2m31.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 2m33.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 2m33.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 2m34.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 2m34.3s INFO: Running scripts pre_install 2m34.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_database-server'] 2m34.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_database-server'] 2m34.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_exceptions'] 2m34.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_exceptions'] 2m34.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_extras'] 2m34.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_extras'] 2m34.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_foreign_architecture'] 2m34.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_foreign_architecture'] 2m34.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m34.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m34.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'policy'] 2m34.4s 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: 2m34.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'policy'] 2m34.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'policy', 'paleomix'] 2m34.4s 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 2m34.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-cache', 'policy', 'paleomix'] 2m34.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', '-y', 'install', 'paleomix=1.3.8-1'] 2m34.9s DUMP: Reading package lists... Building dependency tree... Reading state information... paleomix is already the newest version (1.3.8-1). The following packages were automatically installed and are no longer required: ant ant-optional libaopalliance-java libargs4j-java libatinject-jsr330-api-java libcbor0 libcdi-api-java libcodemodel-java libcommons-cli-java libdtd-parser-java liberror-prone-java libfastinfoset-java libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libglib2.0-0 libguava-java libguice-java libicu67 libistack-commons-java libjaxb-api-java libjaxb-java libjsoup-java libjsr305-java libldap-2.4-2 libllvm11 libmaven-file-management-java libmaven-parent-java libmaven-resolver-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libmpdec3 libngs-sdk-dev libngs-sdk2 libperl5.32 libplexus-archiver-java libplexus-cipher-java libplexus-classworlds-java libplexus-component-annotations-java libplexus-interpolation-java libplexus-io-java libplexus-sec-dispatcher-java libplexus-utils2-java libpython3.9-minimal libpython3.9-stdlib libquadmath0 librelaxng-datatype-java librngom-java libsisu-inject-java libsisu-plexus-java libstax-ex-java libstreambuffer-java libtbb2 libtiff5 libtxw2-java libwagon-http-java libwagon-provider-api-java libwebp6 libxml-commons-resolver1.1-java libxsom-java perl-modules-5.32 python3.9 python3.9-minimal r-cran-assertthat r-cran-ellipsis r-cran-prettyunits Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m34.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', '-y', 'install', 'paleomix=1.3.8-1'] 2m34.9s INFO: Running scripts post_install 2m34.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_install_exceptions'] 2m34.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_install_exceptions'] 2m35.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 2m36.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 2m36.4s INFO: /bin converted to /usr/bin by /usr merge 2m36.4s INFO: /lib converted to /usr/lib by /usr merge 2m36.4s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 2m36.4s INFO: /lib64 converted to /usr/lib64 by /usr merge 2m36.4s INFO: /sbin converted to /usr/sbin by /usr merge 2m38.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpuarkol71', '-ac', '--ignore-obsolete'] 2m45.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpuarkol71', '-ac', '--ignore-obsolete'] 2m45.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m45.7s DUMP: 0.15.6 2m45.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m45.7s INFO: Running adequate version 0.15.6 now. 2m45.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'paleomix'] 2m45.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'paleomix'] 2m45.8s INFO: Running scripts pre_remove 2m45.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m45.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m45.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m46.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m46.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m56.3s DUMP: UNOWNED SYMLINK /usr/lib/x86_64-linux-gnu/libmpi_usempi_ignore_tkr-gfortranso.40 -> libmpi_usempi_ignore_tkr-gfortran.so.40.30.0 2m56.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m56.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m56.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m56.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m56.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m56.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_remove_exceptions'] 2m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/pre_remove_exceptions'] 2m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m56.7s DUMP: install ok installed adapterremoval adapterremoval 2.3.3-2 install ok installed adduser adduser 3.137 install ok installed adwaita-icon-theme adwaita-icon-theme 46.0-1 install ok installed ant ant 1.10.14-1 install ok installed ant-optional ant-optional 1.10.14-1 install ok installed apt apt 2.9.0 install ok installed at-spi2-common at-spi2-common 2.52.0-1 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bcftools bcftools 1.19-1+b1 install ok installed bedtools bedtools 2.31.1+dfsg-2 install ok installed bowtie2 bowtie2 2.5.2-1 install ok installed bsdutils bsdutils 1:2.40-5 install ok installed bwa bwa 0.7.17-7+b3 install ok installed ca-certificates ca-certificates 20240203 install ok installed ca-certificates-java ca-certificates-java 20240118 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed default-jre default-jre 2:1.17-75 install ok installed default-jre-headless default-jre-headless 2:1.17-75 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed examl examl 3.0.22-5 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig fontconfig 2.15.0-1.1 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed gcc-10-base:amd64 gcc-10-base 10.5.0-4 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240330-1 install ok installed gcc-9-base:amd64 gcc-9-base 9.5.0-6 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gtk-update-icon-cache gtk-update-icon-cache 3.24.41-4 install ok installed gzip gzip 1.12-1.1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.17-2 install ok installed hostname hostname 3.23+nmu2 install ok installed ibverbs-providers:amd64 ibverbs-providers 50.0-2+b1 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed java-common java-common 0.75 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libactivation-java libactivation-java 1.2.0-2 install ok installed libamd-comgr2:amd64 libamd-comgr2 6.0+git20231212.4510c28+dfsg-3+b1 install ok installed libamdhip64-5 libamdhip64-5 5.7.1-3 install ok installed libaopalliance-java libaopalliance-java 20070526-7 install ok installed libapache-pom-java libapache-pom-java 29-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.0 install ok installed libargs4j-java libargs4j-java 2.33-2 install ok installed libasound2-data libasound2-data 1.2.11-1 install ok installed libasound2t64:amd64 libasound2t64 1.2.11-1+b1 install ok installed libatinject-jsr330-api-java libatinject-jsr330-api-java 1.0+ds1-5 install ok installed libatk1.0-0t64:amd64 libatk1.0-0t64 2.52.0-1 install ok installed libatomic1:amd64 libatomic1 14-20240330-1 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-13+b2 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-13+b2 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-13+b2 install ok installed libbarclay-java libbarclay-java 5.0.0+dfsg-1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.40-5 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-17 install ok installed libc6:amd64 libc6 2.37-17 install ok installed libcairo2:amd64 libcairo2 1.18.0-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcbor0:amd64 libcbor0 0.5.0+dfsg-2 install ok installed libcbor0.10:amd64 libcbor0.10 0.10.2-1.2 install ok installed libcdi-api-java libcdi-api-java 1.2-3 install ok installed libcodemodel-java libcodemodel-java 2.6+jaxb2.3.0.1-10.1 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcommons-cli-java libcommons-cli-java 1.6.0-1 install ok installed libcommons-codec-java libcommons-codec-java 1.16.0-1 install ok installed libcommons-compress-java libcommons-compress-java 1.25.0-1 install ok installed libcommons-io-java libcommons-io-java 2.16.0-1 install ok installed libcommons-jexl2-java libcommons-jexl2-java 2.1.1-6 install ok installed libcommons-lang3-java libcommons-lang3-java 3.14.0-1 install ok installed libcommons-logging-java libcommons-logging-java 1.3.0-1 install ok installed libcommons-math3-java libcommons-math3-java 3.6.1-3 install ok installed libcommons-parent-java libcommons-parent-java 56-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcups2t64:amd64 libcups2t64 2.4.7-1.2+b1 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.7.1-2 install ok installed libcurl4t64:amd64 libcurl4t64 8.7.1-2 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.14.10-4+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libdeflate0:amd64 libdeflate0 1.20-1 install ok installed libdom4j-java libdom4j-java 2.1.4-1 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.120-2 install ok installed libdrm-common libdrm-common 2.4.120-2 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.120-2 install ok installed libdrm-nouveau2:amd64 libdrm-nouveau2 2.4.120-2 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.120-2 install ok installed libdrm2:amd64 libdrm2 2.4.120-2 install ok installed libdtd-parser-java libdtd-parser-java 1.2-1 install ok installed libedit2:amd64 libedit2 3.1-20230828-1 install ok installed libelf1t64:amd64 libelf1t64 0.191-1+b1 install ok installed liberror-prone-java liberror-prone-java 2.18.0-1 install ok installed libevent-core-2.1-7t64:amd64 libevent-core-2.1-7t64 2.1.12-stable-8.1+b3 install ok installed libevent-pthreads-2.1-7t64:amd64 libevent-pthreads-2.1-7t64 2.1.12-stable-8.1+b3 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libfabric1:amd64 libfabric1 1.17.0-3+b1 install ok installed libfastinfoset-java libfastinfoset-java 1.2.12-3 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfido2-1:amd64 libfido2-1 1.14.0-1+b2 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1 install ok installed libfreemarker-java libfreemarker-java 2.3.32-2 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b3 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libgatk-native-bindings-java libgatk-native-bindings-java 1.0.0+dfsg-2 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240330-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.23-5.1+b1 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.23-5.1+b1 install ok installed libgdk-pixbuf-2.0-0:amd64 libgdk-pixbuf-2.0-0 2.42.10+dfsg-3+b2 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.42.10+dfsg-3 install ok installed libgeronimo-annotation-1.3-spec-java libgeronimo-annotation-1.3-spec-java 1.3-1 install ok installed libgeronimo-interceptor-3.0-spec-java libgeronimo-interceptor-3.0-spec-java 1.0.1-4 install ok installed libgfortran5:amd64 libgfortran5 14-20240330-1 install ok installed libgif7:amd64 libgif7 5.2.2-1 install ok installed libgkl-java libgkl-java 0.8.11+dfsg-2 install ok installed libgl1:amd64 libgl1 1.7.0-1 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 24.0.5-1 install ok installed libglapi-mesa:amd64 libglapi-mesa 24.0.5-1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.78.4-6 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.78.4-6 install ok installed libglvnd0:amd64 libglvnd0 1.7.0-1 install ok installed libglx-mesa0:amd64 libglx-mesa0 24.0.5-1 install ok installed libglx0:amd64 libglx0 1.7.0-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.5-2 install ok installed libgomp1:amd64 libgomp1 14-20240330-1 install ok installed libgoogle-gson-java libgoogle-gson-java 2.10.1-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgsl-dev libgsl-dev 2.7.1+dfsg-6+b1 install ok installed libgsl27:amd64 libgsl27 2.7.1+dfsg-6+b1 install ok installed libgslcblas0:amd64 libgslcblas0 2.7.1+dfsg-6+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-6+b1 install ok installed libgtk2.0-0t64:amd64 libgtk2.0-0t64 2.24.33-4 install ok installed libgtk2.0-common libgtk2.0-common 2.24.33-4 install ok installed libguava-java libguava-java 32.0.1-1 install ok installed libguice-java libguice-java 4.2.3-2 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2+b1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libhsa-runtime64-1 libhsa-runtime64-1 5.7.1-2 install ok installed libhsakmt1:amd64 libhsakmt1 5.7.0-1 install ok installed libhts3t64:amd64 libhts3t64 1.19+ds-1.1+b1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.0-1+b1 install ok installed libhtsjdk-java libhtsjdk-java 4.1.0+dfsg-1 install ok installed libhttpclient-java libhttpclient-java 4.5.14-1 install ok installed libhttpcore-java libhttpcore-java 4.4.16-1 install ok installed libhwloc-plugins:amd64 libhwloc-plugins 2.10.0-1+b1 install ok installed libhwloc15:amd64 libhwloc15 2.10.0-1+b1 install ok installed libibverbs1:amd64 libibverbs1 50.0-2+b1 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libicu72:amd64 libicu72 72.1-4+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libistack-commons-java libistack-commons-java 3.0.6-5 install ok installed libjaxb-api-java libjaxb-api-java 2.3.1-1 install ok installed libjaxb-java libjaxb-java 2.3.0.1-10.1 install ok installed libjaxen-java libjaxen-java 1.1.6-4 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjoptsimple-java libjoptsimple-java 5.0.4-4 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libjsoup-java libjsoup-java 1.15.3-1 install ok installed libjsr305-java libjsr305-java 0.1~+svn49-11 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-6+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-6+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-6+b1 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2+b1 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.16+dfsg-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed liblightcouch-java liblightcouch-java 0.2.0-1 install ok installed libllvm11:amd64 libllvm11 1:11.0.1-2 install ok installed libllvm17t64:amd64 libllvm17t64 1:17.0.6-9+b2 install ok installed liblog4j2-java liblog4j2-java 2.19.0-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmaven-file-management-java libmaven-file-management-java 3.0.0-1 install ok installed libmaven-parent-java libmaven-parent-java 35-1 install ok installed libmaven-resolver-java libmaven-resolver-java 1.6.3-1 install ok installed libmaven-shared-io-java libmaven-shared-io-java 3.0.0-4 install ok installed libmaven-shared-utils-java libmaven-shared-utils-java 3.3.4-1 install ok installed libmaven3-core-java libmaven3-core-java 3.8.7-2 install ok installed libmbedcrypto7t64:amd64 libmbedcrypto7t64 2.28.8-1 install ok installed libmbedtls14t64:amd64 libmbedtls14t64 2.28.8-1 install ok installed libmbedx509-1t64:amd64 libmbedx509-1t64 2.28.8-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmjson-java libmjson-java 1.4.0-3 install ok installed libmongodb-java libmongodb-java 3.6.3-2 install ok installed libmount1:amd64 libmount1 2.40-5 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-1 install ok installed libmunge2:amd64 libmunge2 0.5.15-4 install ok installed libncbi-ngs3:amd64 libncbi-ngs3 3.0.3+dfsg-6+b1 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.0.2+dfsg-2+b1 install ok installed libncurses6:amd64 libncurses6 6.4+20240113-1 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.61.0-1 install ok installed libngs-java:amd64 libngs-java 3.0.3+dfsg-6+b1 install ok installed libngs-jni:amd64 libngs-jni 3.0.3+dfsg-6+b1 install ok installed libngs-sdk-dev:amd64 libngs-sdk-dev 2.10.9-1 install ok installed libngs-sdk2:amd64 libngs-sdk2 2.10.9-1 install ok installed libnl-3-200:amd64 libnl-3-200 3.7.0-0.3 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.7.0-0.3 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b2 install ok installed libnspr4:amd64 libnspr4 2:4.35-1.1+b1 install ok installed libnss3:amd64 libnss3 2:3.99-1 install ok installed libnuma1:amd64 libnuma1 2.0.18-1 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libopenblas-dev:amd64 libopenblas-dev 0.3.27+ds-1 install ok installed libopenblas-pthread-dev:amd64 libopenblas-pthread-dev 0.3.27+ds-1 install ok installed libopenblas0:amd64 libopenblas0 0.3.27+ds-1 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.27+ds-1 install ok installed libopenmpi3t64:amd64 libopenmpi3t64 4.1.6-9 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.52.1+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.52.1+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.52.1+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 0.17-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpcre3:amd64 libpcre3 2:8.39-15+b1 install ok installed libpcsclite1:amd64 libpcsclite1 2.0.3-1 install ok installed libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u3 install ok installed libperl5.38t64:amd64 libperl5.38t64 5.38.2-3.2+b2 install ok installed libpicard-java libpicard-java 3.1.1+dfsg-1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libplexus-archiver-java libplexus-archiver-java 4.6.1-1 install ok installed libplexus-cipher-java libplexus-cipher-java 2.0-1 install ok installed libplexus-classworlds-java libplexus-classworlds-java 2.7.0-1 install ok installed libplexus-component-annotations-java libplexus-component-annotations-java 2.1.1-1 install ok installed libplexus-interpolation-java libplexus-interpolation-java 1.26-1 install ok installed libplexus-io-java libplexus-io-java 3.3.1-2 install ok installed libplexus-sec-dispatcher-java libplexus-sec-dispatcher-java 2.0-3 install ok installed libplexus-utils2-java libplexus-utils2-java 3.4.2-1 install ok installed libpmix2t64:amd64 libpmix2t64 5.0.2-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.43-5 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libpsm-infinipath1 libpsm-infinipath1 3.3+20.604758e7-6.3 install ok installed libpsm2-2 libpsm2-2 11.2.185-2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.8-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.9-1 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.9-1 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed libquadmath0:amd64 libquadmath0 14-20240330-1 install ok installed librdmacm1t64:amd64 librdmacm1t64 50.0-2+b1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-4 install ok installed librelaxng-datatype-java librelaxng-datatype-java 1.0+ds1-3.1 install ok installed librhino-java librhino-java 1.7.14-2.1 install ok installed librngom-java librngom-java 2.3.0.1-10.1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b4 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-6 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-6 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsensors-config libsensors-config 1:3.6.0-9 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-9 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.4+b1 install ok installed libsisu-inject-java libsisu-inject-java 0.3.4-2 install ok installed libsisu-plexus-java libsisu-plexus-java 0.3.4-3 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 2.40-5 install ok installed libsnappy-java libsnappy-java 1.1.10.5-2 install ok installed libsnappy-jni libsnappy-jni 1.1.10.5-2 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.1.10-1+b1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.2-1 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-4.1+b2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libssl3t64:amd64 libssl3t64 3.2.1-3 install ok installed libstax-ex-java libstax-ex-java 1.7.8-3 install ok installed libstdc++6:amd64 libstdc++6 14-20240330-1 install ok installed libstreambuffer-java libstreambuffer-java 1.5.4-1.1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtbb2:amd64 libtbb2 2020.3-1 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.14+dfsg-1 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff5:amd64 libtiff5 4.2.0-1+deb11u5 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.2 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.2 install ok installed libtk8.6:amd64 libtk8.6 8.6.14-1 install ok installed libtxw2-java libtxw2-java 2.3.0.1-10.1 install ok installed libucx0:amd64 libucx0 1.16.0+ds-5 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40-5 install ok installed libuv1t64:amd64 libuv1t64 1.48.0-1.1 install ok installed libvulkan1:amd64 libvulkan1 1.3.275.0-1 install ok installed libwagon-http-java libwagon-http-java 3.5.3-1 install ok installed libwagon-provider-api-java libwagon-provider-api-java 3.5.3-1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2.1+deb11u2 install ok installed libwebp7:amd64 libwebp7 1.3.2-0.4+b1 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-dri2-0:amd64 libxcb-dri2-0 1.15-1 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.15-1 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.15-1 install ok installed libxcb-present0:amd64 libxcb-present0 1.15-1 install ok installed libxcb-randr0:amd64 libxcb-randr0 1.15-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb-sync1:amd64 libxcb-sync1 1.15-1 install ok installed libxcb-xfixes0:amd64 libxcb-xfixes0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxcomposite1:amd64 libxcomposite1 1:0.4.5-1 install ok installed libxcursor1:amd64 libxcursor1 1:1.2.1-1 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.6-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxfixes3:amd64 libxfixes3 1:6.0.0-2 install ok installed libxft2:amd64 libxft2 2.3.6-1+b1 install ok installed libxi6:amd64 libxi6 2:1.8.1-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3 install ok installed libxml-commons-resolver1.1-java libxml-commons-resolver1.1-java 1.2-11 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3+b2 install ok installed libxnvctrl0:amd64 libxnvctrl0 535.171.04-1 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.4-1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxshmfence1:amd64 libxshmfence1 1.3-1 install ok installed libxsom-java libxsom-java 2.3.0.1-10.1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2 install ok installed libxtst6:amd64 libxtst6 2:1.2.3-1.1 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libxz-java libxz-java 1.9-1 install ok installed libz3-4:amd64 libz3-4 4.8.12-3.1+b2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed littler littler 0.3.20-1 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed lsb-base lsb-base 11.6 install ok installed mafft mafft 7.505-1 install ok installed mapdamage mapdamage 2.2.1+dfsg-3 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40-5 install ok installed ncbi-vdb-data ncbi-vdb-data 3.0.2+dfsg-2 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.3.2-1+b1 install ok installed openjdk-11-jre:amd64 openjdk-11-jre 11.0.23~7ea-1 install ok installed openjdk-11-jre-headless:amd64 openjdk-11-jre-headless 11.0.23~7ea-1 install ok installed openjdk-17-jre:amd64 openjdk-17-jre 17.0.11~7ea-1+b1 install ok installed openjdk-17-jre-headless:amd64 openjdk-17-jre-headless 17.0.11~7ea-1+b1 install ok installed openmpi-bin openmpi-bin 4.1.6-9 install ok installed openmpi-common openmpi-common 4.1.6-9 install ok installed openssh-client openssh-client 1:9.7p1-4 install ok installed openssl openssl 3.2.1-3 install ok installed paleomix paleomix 1.3.8-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl perl 5.38.2-3.2+b2 install ok installed perl-base perl-base 5.38.2-3.2+b2 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.1-4+deb11u3 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3.2 install ok installed phylip phylip 1:3.697+dfsg-4 install ok installed picard-tools picard-tools 3.1.1+dfsg-1 install ok installed python3 python3 3.11.8-1 install ok installed python3-coloredlogs python3-coloredlogs 15.0.1-1 install ok installed python3-configargparse python3-configargparse 1.7-1 install ok installed python3-humanfriendly python3-humanfriendly 10.0-5 install ok installed python3-minimal python3-minimal 3.11.8-1 install ok installed python3-pysam python3-pysam 0.22.0+ds-1+b2 install ok installed python3-ruamel.yaml python3-ruamel.yaml 0.17.21-1 install ok installed python3-ruamel.yaml.clib:amd64 python3-ruamel.yaml.clib 0.2.8-1 install ok installed python3-setproctitle:amd64 python3-setproctitle 1.3.3-1+b1 install ok installed python3.11 python3.11 3.11.9-1 install ok installed python3.11-minimal python3.11-minimal 3.11.9-1 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed r-base-core r-base-core 4.3.3-3+b1 install ok installed r-cran-assertthat r-cran-assertthat 0.2.1-2 install ok installed r-cran-brio r-cran-brio 1.1.4-1 install ok installed r-cran-callr r-cran-callr 3.7.5-1 install ok installed r-cran-cli r-cran-cli 3.6.2-1 install ok installed r-cran-codetools r-cran-codetools 0.2-20-1 install ok installed r-cran-colorspace r-cran-colorspace 2.1-0+dfsg-1 install ok installed r-cran-crayon r-cran-crayon 1.5.2-1 install ok installed r-cran-desc r-cran-desc 1.4.3-1 install ok installed r-cran-diffobj r-cran-diffobj 0.3.5-1+b1 install ok installed r-cran-digest r-cran-digest 0.6.35-1 install ok installed r-cran-ellipsis r-cran-ellipsis 0.3.2-2 install ok installed r-cran-evaluate r-cran-evaluate 0.23-1 install ok installed r-cran-fansi r-cran-fansi 1.0.5-1 install ok installed r-cran-farver r-cran-farver 2.1.1-2 install ok installed r-cran-foreach r-cran-foreach 1.5.2-1 install ok installed r-cran-fs r-cran-fs 1.6.3+dfsg-1+b1 install ok installed r-cran-gam r-cran-gam 1.22-3-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.4.4+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.7.0-1 install ok installed r-cran-gtable r-cran-gtable 0.3.4+dfsg-1 install ok installed r-cran-inline r-cran-inline 0.3.19-2 install ok installed r-cran-isoband r-cran-isoband 0.2.7-1 install ok installed r-cran-iterators r-cran-iterators 1.0.14-1 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.8+dfsg-1 install ok installed r-cran-labeling r-cran-labeling 0.4.3-1 install ok installed r-cran-lattice r-cran-lattice 0.22-6-1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.20-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-mass r-cran-mass 7.3-60.0.1-1 install ok installed r-cran-matrix r-cran-matrix 1.6-5-1 install ok installed r-cran-mgcv r-cran-mgcv 1.9-1-1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-2 install ok installed r-cran-nlme r-cran-nlme 3.1.164-1 install ok installed r-cran-pillar r-cran-pillar 1.9.0+dfsg-1 install ok installed r-cran-pkgbuild r-cran-pkgbuild 1.4.3-1 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-pkgload r-cran-pkgload 1.3.4-1 install ok installed r-cran-praise r-cran-praise 1.0.0-4 install ok installed r-cran-prettyunits r-cran-prettyunits 1.2.0-1 install ok installed r-cran-processx r-cran-processx 3.8.3-1 install ok installed r-cran-ps r-cran-ps 1.7.6-1 install ok installed r-cran-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-3-1 install ok installed r-cran-rcpp r-cran-rcpp 1.0.12-1 install ok installed r-cran-rcppgsl r-cran-rcppgsl 0.3.13-1 install ok installed r-cran-rematch2 r-cran-rematch2 2.1.2-2 install ok installed r-cran-rlang r-cran-rlang 1.1.3-1 install ok installed r-cran-rprojroot r-cran-rprojroot 2.0.4-1 install ok installed r-cran-rstudioapi r-cran-rstudioapi 0.16.0-1 install ok installed r-cran-scales r-cran-scales 1.3.0-1 install ok installed r-cran-testthat r-cran-testthat 3.2.1-1 install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-2 install ok installed r-cran-utf8 r-cran-utf8 1.2.4-1 install ok installed r-cran-vctrs r-cran-vctrs 0.6.5-1 install ok installed r-cran-viridislite r-cran-viridislite 0.4.2-2 install ok installed r-cran-waldo r-cran-waldo 0.5.2-1 install ok installed r-cran-withr r-cran-withr 3.0.0+dfsg-1 install ok installed radiant radiant 2.8.1+dfsg-2 install ok installed raxml raxml 8.2.13+dfsg-1 install ok installed readline-common readline-common 8.2-4 install ok installed samtools samtools 1.19.2-1+b1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.22 install ok installed seqtk seqtk 1.4-2 install ok installed shared-mime-info shared-mime-info 2.4-4 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-2 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usrmerge usrmerge 39 install ok installed util-linux util-linux 2.40-5 install ok installed x11-common x11-common 1:7.7+23 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 2m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', 'remove', 'adapterremoval', 'adwaita-icon-theme', 'ant', 'ant-optional', 'at-spi2-common', 'bcftools', 'bedtools', 'bowtie2', 'bwa', 'ca-certificates', 'ca-certificates-java', 'default-jre', 'default-jre-headless', 'examl', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'ibverbs-providers:amd64', 'java-common', 'libactivation-java', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libaopalliance-java', 'libapache-pom-java', 'libargs4j-java', 'libasound2-data', 'libasound2t64:amd64', 'libatinject-jsr330-api-java', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcbor0:amd64', 'libcbor0.10:amd64', 'libcdi-api-java', 'libcodemodel-java', 'libcommons-cli-java', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdom4j-java', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libdtd-parser-java', 'libedit2:amd64', 'libelf1t64:amd64', 'liberror-prone-java', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfastinfoset-java', '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', 'libgeronimo-annotation-1.3-spec-java', 'libgeronimo-interceptor-3.0-spec-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgkl-java', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgtk2.0-0t64:amd64', 'libgtk2.0-common', 'libguava-java', 'libguice-java', 'libharfbuzz0b:amd64', 'libhsa-runtime64-1', 'libhsakmt1:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libistack-commons-java', 'libjaxb-api-java', 'libjaxb-java', 'libjaxen-java', 'libjbig0:amd64', 'libjoptsimple-java', 'libjpeg62-turbo:amd64', 'libjsoup-java', 'libjsr305-java', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblightcouch-java', 'libllvm11:amd64', 'libllvm17t64:amd64', 'liblog4j2-java', 'libmaven-file-management-java', 'libmaven-parent-java', 'libmaven-resolver-java', 'libmaven-shared-io-java', 'libmaven-shared-utils-java', 'libmaven3-core-java', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedx509-1t64:amd64', 'libmjson-java', 'libmongodb-java', 'libmpdec3:amd64', 'libmunge2:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngs-sdk-dev:amd64', 'libngs-sdk2:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenmpi3t64:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpicard-java', 'libpixman-1-0:amd64', 'libplexus-archiver-java', 'libplexus-cipher-java', 'libplexus-classworlds-java', 'libplexus-component-annotations-java', 'libplexus-interpolation-java', 'libplexus-io-java', 'libplexus-sec-dispatcher-java', 'libplexus-utils2-java', 'libpmix2t64:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1t64:amd64', 'libreadline8t64:amd64', 'librelaxng-datatype-java', 'librhino-java', 'librngom-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsisu-inject-java', 'libsisu-plexus-java', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstax-ex-java', 'libstreambuffer-java', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libtxw2-java', 'libucx0:amd64', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwagon-http-java', 'libwagon-provider-api-java', 'libwebp6: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', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxsom-java', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libxz-java', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'ncbi-vdb-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'perl-modules-5.32', 'phylip', 'picard-tools', 'python3', 'python3-coloredlogs', 'python3-configargparse', 'python3-humanfriendly', 'python3-minimal', 'python3-pysam', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib:amd64', 'python3-setproctitle:amd64', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-cran-assertthat', 'r-cran-brio', 'r-cran-callr', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-fs', 'r-cran-gam', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-inline', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-jsonlite', '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-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-ps', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcppgsl', 'r-cran-rematch2', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-testthat', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-waldo', 'r-cran-withr', 'radiant', 'raxml', 'readline-common', 'samtools', 'sensible-utils', 'seqtk', 'shared-mime-info', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'paleomix'] 3m2.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adapterremoval adwaita-icon-theme ant ant-optional at-spi2-common bcftools bedtools bowtie2 bwa ca-certificates ca-certificates-java default-jre default-jre-headless examl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme ibverbs-providers java-common libactivation-java libamd-comgr2 libamdhip64-5 libaopalliance-java libapache-pom-java libargs4j-java libasound2-data libasound2t64 libatinject-jsr330-api-java libatk1.0-0t64 libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libbrotli1 libbsd0 libcairo2 libcbor0 libcbor0.10 libcdi-api-java libcodemodel-java libcommons-cli-java libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdeflate0 libdom4j-java libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdtd-parser-java libedit2 libelf1t64 liberror-prone-java libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfastinfoset-java libfido2-1 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libgatk-native-bindings-java libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libgfortran5 libgif7 libgkl-java libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgoogle-gson-java libgraphite2-3 libgsl-dev libgsl27 libgslcblas0 libgtk2.0-0t64 libgtk2.0-common libguava-java libguice-java libharfbuzz0b libhsa-runtime64-1 libhsakmt1 libhts3t64 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibverbs1 libice6 libicu67 libicu72 libistack-commons-java libjaxb-api-java libjaxb-java libjaxen-java libjbig0 libjoptsimple-java libjpeg62-turbo libjsoup-java libjsr305-java liblapack3 liblcms2-2 libldap-2.4-2 libldap-2.5-0 liblerc4 liblightcouch-java libllvm11 libllvm17t64 liblog4j2-java libmaven-file-management-java libmaven-parent-java libmaven-resolver-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmjson-java libmongodb-java libmpdec3 libmunge2 libncbi-ngs3 libncbi-vdb3 libncurses6 libncursesw6 libnghttp2-14 libngs-java libngs-jni libngs-sdk-dev libngs-sdk2 libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenmpi3t64 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.32 libpicard-java libpixman-1-0 libplexus-archiver-java libplexus-cipher-java libplexus-classworlds-java libplexus-component-annotations-java libplexus-interpolation-java libplexus-io-java libplexus-sec-dispatcher-java libplexus-utils2-java libpmix2t64 libpng16-16t64 libpsl5t64 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 librdmacm1t64 libreadline8t64 librelaxng-datatype-java librhino-java librngom-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libsisu-inject-java libsisu-plexus-java libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsqlite3-0 libssh2-1t64 libstax-ex-java libstreambuffer-java libtbb2 libtcl8.6 libthai-data libthai0 libtiff5 libtiff6 libtk8.6 libtxw2-java libucx0 libuv1t64 libvulkan1 libwagon-http-java libwagon-provider-api-java libwebp6 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 libxml-commons-resolver1.1-java libxml2 libxnvctrl0 libxrandr2 libxrender1 libxshmfence1 libxsom-java libxss1 libxt6t64 libxtst6 libxxf86vm1 libxz-java libz3-4 littler mafft mapdamage media-types ncbi-vdb-data netbase ocl-icd-libopencl1 openjdk-11-jre openjdk-11-jre-headless openjdk-17-jre openjdk-17-jre-headless openmpi-bin openmpi-common openssh-client openssl paleomix perl-modules-5.32 phylip picard-tools python3 python3-coloredlogs python3-configargparse python3-humanfriendly python3-minimal python3-pysam python3-ruamel.yaml python3-ruamel.yaml.clib python3-setproctitle python3.11 python3.11-minimal python3.9 python3.9-minimal r-base-core r-cran-assertthat r-cran-brio r-cran-callr r-cran-cli r-cran-codetools r-cran-colorspace r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-foreach r-cran-fs r-cran-gam r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-inline r-cran-isoband r-cran-iterators r-cran-jsonlite 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-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppgsl r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo 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, 377 to remove and 0 not upgraded. After this operation, 1420 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 ... 28382 files and directories currently installed.) Removing paleomix (1.3.8-1) ... Removing adapterremoval (2.3.3-2) ... Removing picard-tools (3.1.1+dfsg-1) ... Removing default-jre (2:1.17-75) ... Removing openjdk-17-jre:amd64 (17.0.11~7ea-1+b1) ... Removing libgtk2.0-0t64:amd64 (2.24.33-4) ... Removing adwaita-icon-theme (46.0-1) ... Removing libjaxb-java (2.3.0.1-10.1) ... Removing libtxw2-java (2.3.0.1-10.1) ... Removing libatk1.0-0t64:amd64 (2.52.0-1) ... Removing at-spi2-common (2.52.0-1) ... Removing bcftools (1.19-1+b1) ... Removing bedtools (2.31.1+dfsg-2) ... Removing bowtie2 (2.5.2-1) ... Removing bwa (0.7.17-7+b3) ... Removing mapdamage (2.2.1+dfsg-3) ... Removing r-cran-ggplot2 (3.4.4+dfsg-1) ... Removing r-cran-scales (1.3.0-1) ... Removing r-cran-rcolorbrewer (1.1-3-1) ... Removing r-cran-mgcv (1.9-1-1) ... Removing r-cran-matrix (1.6-5-1) ... Removing r-cran-viridislite (0.4.2-2) ... Removing r-cran-rcppgsl (0.3.13-1) ... Removing r-cran-rcpp (1.0.12-1) ... Removing openjdk-11-jre:amd64 (11.0.23~7ea-1) ... Removing openjdk-11-jre-headless:amd64 (11.0.23~7ea-1) ... Removing default-jre-headless (2:1.17-75) ... Removing examl (3.0.22-5) ... Removing gtk-update-icon-cache (3.24.41-4) ... Removing hicolor-icon-theme (0.17-2) ... Removing openmpi-bin (4.1.6-9) ... Removing libopenmpi3t64:amd64 (4.1.6-9) ... Removing libucx0:amd64 (1.16.0+ds-5) ... Removing libfabric1:amd64 (1.17.0-3+b1) ... Removing ibverbs-providers:amd64 (50.0-2+b1) ... Removing libfastinfoset-java (1.2.12-3) ... Removing libstreambuffer-java (1.5.4-1.1) ... Removing libstax-ex-java (1.7.8-3) ... Removing libjaxb-api-java (2.3.1-1) ... Removing libamdhip64-5 (5.7.1-3) ... Removing libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Removing libpicard-java (3.1.1+dfsg-1) ... Removing libasound2t64:amd64 (1.2.11-1+b1) ... Removing libasound2-data (1.2.11-1) ... Removing libatomic1:amd64 (14-20240330-1) ... Removing libcups2t64:amd64 (2.4.7-1.2+b1) ... Removing libavahi-client3:amd64 (0.8-13+b2) ... Removing libavahi-common3:amd64 (0.8-13+b2) ... Removing libavahi-common-data:amd64 (0.8-13+b2) ... Removing libbarclay-java (5.0.0+dfsg-1) ... Removing r-cran-gam (1.22-3-1) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing libgl1:amd64 (1.7.0-1) ... Removing libglx0:amd64 (1.7.0-1) ... Removing libglx-mesa0:amd64 (24.0.5-1) ... Removing libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Removing libcbor0:amd64 (0.5.0+dfsg-2) ... Removing openssh-client (1:9.7p1-4) ... Removing libfido2-1:amd64 (1.14.0-1+b2) ... Removing libcbor0.10:amd64 (0.10.2-1.2) ... Removing libgkl-java (0.8.11+dfsg-2) ... Removing liblog4j2-java (2.19.0-2) ... Removing liblightcouch-java (0.2.0-1) ... Removing libcommons-math3-java (3.6.1-3) ... Removing samtools (1.19.2-1+b1) ... Removing python3-pysam (0.22.0+ds-1+b2) ... Removing libhts3t64:amd64 (1.19+ds-1.1+b1) ... Removing libcurl3t64-gnutls:amd64 (8.7.1-2) ... Removing libdbus-1-3:amd64 (1.14.10-4+b1) ... Removing libtiff5:amd64 (4.2.0-1+deb11u5) ... Removing libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b2) ... Removing libhsa-runtime64-1 (5.7.1-2) ... Removing libhsakmt1:amd64 (5.7.0-1) ... Removing libgl1-mesa-dri:amd64 (24.0.5-1) ... Removing libdrm-amdgpu1:amd64 (2.4.120-2) ... Removing libdrm-radeon1:amd64 (2.4.120-2) ... Removing libdrm-intel1:amd64 (2.4.120-2) ... Removing libdrm-nouveau2:amd64 (2.4.120-2) ... Removing libdtd-parser-java (1.2-1) ... Removing libllvm11:amd64 (1:11.0.1-2) ... Removing libllvm17t64:amd64 (1:17.0.6-9+b2) ... Removing libedit2:amd64 (3.1-20230828-1) ... Removing libelf1t64:amd64 (0.191-1+b1) ... Removing libpmix2t64:amd64 (5.0.2-3) ... Removing libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Removing libevent-core-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing python3-ruamel.yaml (0.17.21-1) ... Removing python3-ruamel.yaml.clib:amd64 (0.2.8-1) ... Removing python3-setproctitle:amd64 (1.3.3-1+b1) ... Removing python3-coloredlogs (15.0.1-1) ... Removing python3-humanfriendly (10.0-5) ... Removing libfreemarker-java (2.3.32-2) ... Removing libgatk-native-bindings-java (1.0.0+dfsg-2) ... Removing libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Removing libopenblas-dev:amd64 (0.3.27+ds-1) ... Removing libopenblas-pthread-dev:amd64 (0.3.27+ds-1) ... Removing libopenblas0:amd64 (0.3.27+ds-1) ... Removing libgif7:amd64 (5.2.2-1) ... Removing libglapi-mesa:amd64 (24.0.5-1) ... Removing libglib2.0-0:amd64 (2.78.4-6) ... Removing shared-mime-info (2.4-4) ... Removing libglvnd0:amd64 (1.7.0-1) ... Removing libgoogle-gson-java (2.10.1-1) ... Removing libgsl-dev (2.7.1+dfsg-6+b1) ... Removing libgsl27:amd64 (2.7.1+dfsg-6+b1) ... Removing libgslcblas0:amd64 (2.7.1+dfsg-6+b1) ... Removing libgtk2.0-common (2.24.33-4) ... Removing libhtscodecs2:amd64 (1.6.0-1+b1) ... Removing libhwloc-plugins:amd64 (2.10.0-1+b1) ... Removing libhwloc15:amd64 (2.10.0-1+b1) ... Removing librdmacm1t64:amd64 (50.0-2+b1) ... Removing libibverbs1:amd64 (50.0-2+b1) ... Removing libicu67:amd64 (67.1-7) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Removing libjoptsimple-java (5.0.4-4) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing libmongodb-java (3.6.3-2) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... Removing libmpdec3:amd64 (2.5.1-1) ... Removing libmunge2:amd64 (0.5.15-4) ... Removing libncurses6:amd64 (6.4+20240113-1) ... Removing libngs-sdk-dev:amd64 (2.10.9-1) ... Removing libngs-sdk2:amd64 (2.10.9-1) ... Removing libnl-route-3-200:amd64 (3.7.0-0.3) ... Removing libnl-3-200:amd64 (3.7.0-0.3) ... Removing libpsm2-2 (11.2.185-2) ... Removing libnuma1:amd64 (2.0.18-1) ... Removing libpciaccess0:amd64 (0.17-3) ... Removing libperl5.32:amd64 (5.32.1-4+deb11u3) ... Removing libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: warning: alternative /usr/lib/libpsm1/libpsm_infinipath.so.1.16 (part of link group libpsm_infinipath.so.1) doesn't exist; removing from list of alternatives update-alternatives: warning: /etc/alternatives/libpsm_infinipath.so.1 is dangling; it will be updated with best choice Removing libpython3.9-minimal:amd64 (3.9.2-1) ... Removing libquadmath0:amd64 (14-20240330-1) ... Removing libxsom-java (2.3.0.1-10.1) ... Removing librngom-java (2.3.0.1-10.1) ... Removing librelaxng-datatype-java (1.0+ds1-3.1) ... Removing libsensors5:amd64 (1:3.6.0-9) ... Removing libsensors-config (1:3.6.0-9) ... Removing libtbb2:amd64 (2020.3-1) ... Removing r-cran-testthat (3.2.1-1) ... Removing r-cran-pkgload (1.3.4-1) ... Removing r-cran-fs (1.6.3+dfsg-1+b1) ... Removing libuv1t64:amd64 (1.48.0-1.1) ... Removing libvulkan1:amd64 (1.3.275.0-1) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libx11-xcb1:amd64 (2:1.8.7-1) ... Removing libxcb-dri2-0:amd64 (1.15-1) ... Removing libxcb-dri3-0:amd64 (1.15-1) ... Removing libxcb-glx0:amd64 (1.15-1) ... Removing libxcb-present0:amd64 (1.15-1) ... Removing libxcb-randr0:amd64 (1.15-1) ... Removing libxcb-sync1:amd64 (1.15-1) ... Removing libxcb-xfixes0:amd64 (1.15-1) ... Removing libxcomposite1:amd64 (1:0.4.5-1) ... Removing libxcursor1:amd64 (1:1.2.1-1) ... Removing libxdamage1:amd64 (1:1.1.6-1) ... Removing libxtst6:amd64 (2:1.2.3-1.1) ... Removing libxfixes3:amd64 (1:6.0.0-2) ... Removing libxi6:amd64 (2:1.8.1-1) ... Removing libxinerama1:amd64 (2:1.1.4-3) ... Removing libxml-commons-resolver1.1-java (1.2-11) ... Removing libxnvctrl0:amd64 (535.171.04-1) ... Removing libxrandr2:amd64 (2:1.5.4-1) ... Removing libxshmfence1:amd64 (1.3-1) ... Removing libz3-4:amd64 (4.8.12-3.1+b2) ... Removing littler (0.3.20-1) ... Removing mafft (7.505-1) ... Removing ocl-icd-libopencl1:amd64 (2.3.2-1+b1) ... Removing openmpi-common (4.1.6-9) ... Removing perl-modules-5.32 (5.32.1-4+deb11u3) ... Removing phylip (1:3.697+dfsg-4) ... Removing python3-configargparse (1.7-1) ... Removing r-cran-assertthat (0.2.1-2) ... Removing r-cran-brio (1.1.4-1) ... Removing r-cran-pkgbuild (1.4.3-1) ... Removing r-cran-callr (3.7.5-1) ... Removing r-cran-waldo (0.5.2-1) ... Removing r-cran-rematch2 (2.1.2-2) ... Removing r-cran-tibble (3.2.1+dfsg-2) ... Removing r-cran-foreach (1.5.2-1) ... Removing r-cran-codetools (0.2-20-1) ... Removing r-cran-munsell (0.5.0-2) ... Removing r-cran-colorspace (2.1-0+dfsg-1) ... Removing r-cran-diffobj (0.3.5-1+b1) ... Removing r-cran-crayon (1.5.2-1) ... Removing r-cran-desc (1.4.3-1) ... Removing r-cran-digest (0.6.35-1) ... Removing r-cran-ellipsis (0.3.2-2) ... Removing r-cran-evaluate (0.23-1) ... Removing r-cran-pillar (1.9.0+dfsg-1) ... Removing r-cran-fansi (1.0.5-1) ... Removing r-cran-farver (2.1.1-2) ... Removing r-cran-gtable (0.3.4+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-jsonlite (1.8.8+dfsg-1) ... Removing r-cran-labeling (0.4.3-1) ... Removing r-cran-nlme (3.1.164-1) ... Removing r-cran-lattice (0.22-6-1) ... Removing r-cran-littler (0.3.20-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-60.0.1-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-pkgkitten (0.2.3-1) ... Removing r-cran-praise (1.0.0-4) ... Removing r-cran-prettyunits (1.2.0-1) ... Removing r-cran-processx (3.8.3-1) ... Removing r-cran-ps (1.7.6-1) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rprojroot (2.0.4-1) ... Removing r-cran-rstudioapi (0.16.0-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing r-cran-withr (3.0.0+dfsg-1) ... Removing radiant (2.8.1+dfsg-2) ... Removing raxml (8.2.13+dfsg-1) ... Removing seqtk (1.4-2) ... Removing libhtsjdk-java (4.1.0+dfsg-1) ... Removing libcommons-jexl2-java (2.1.1-6) ... Removing libdrm2:amd64 (2.4.120-2) ... Removing libdrm-common (2.4.120-2) ... Removing python3 (3.11.8-1) ... Removing python3.11 (3.11.9-1) ... Removing libngs-java:amd64 (3.0.3+dfsg-6+b1) ... Removing libngs-jni:amd64 (3.0.3+dfsg-6+b1) ... Removing libncbi-ngs3:amd64 (3.0.3+dfsg-6+b1) ... Removing libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Removing libmbedtls14t64:amd64 (2.28.8-1) ... Removing libmbedx509-1t64:amd64 (2.28.8-1) ... Removing libmbedcrypto7t64:amd64 (2.28.8-1) ... Removing libmjson-java (1.4.0-3) ... Removing libpython3-stdlib:amd64 (3.11.8-1) ... Removing libpython3.11-stdlib:amd64 (3.11.9-1) ... find: '/usr/lib/python3': No such file or directory Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing python3-minimal (3.11.8-1) ... Removing librhino-java (1.7.14-2.1) ... Removing media-types (10.1.0) ... Removing ncbi-vdb-data (3.0.2+dfsg-2) ... Removing netbase (6.4) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-glue (1.7.0-1) ... Removing r-cran-rlang (1.1.3-1) ... Removing python3.11-minimal (3.11.9-1) ... Removing libpython3.11-minimal:amd64 (3.11.9-1) ... find: '/usr/lib/python3': No such file or directory Removing r-cran-cli (3.6.2-1) ... Removing r-base-core (4.3.3-3+b1) ... Removing libpangocairo-1.0-0:amd64 (1.52.1+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.52.1+ds-1) ... Removing libpango-1.0-0:amd64 (1.52.1+ds-1) ... Removing fontconfig (2.15.0-1.1) ... Removing libtk8.6:amd64 (8.6.14-1) ... Removing libxft2:amd64 (2.3.6-1+b1) ... Removing libcairo2:amd64 (1.18.0-3) ... Removing libfontconfig1:amd64 (2.15.0-1.1) ... Removing fontconfig-config (2.15.0-1.1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libharfbuzz0b:amd64 (8.3.0-2+b1) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b3) ... Removing libcurl4t64:amd64 (8.7.1-2) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libxt6t64:amd64 (1:1.2.1-1.2) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.20-1) ... Removing libexpat1:amd64 (2.6.2-1) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing libopenblas0-pthread:amd64 (0.3.27+ds-1) ... Removing libgfortran5:amd64 (14-20240330-1) ... Removing libglib2.0-0t64:amd64 (2.78.4-6) ... Removing libgomp1:amd64 (14-20240330-1) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libicu72:amd64 (72.1-4+b1) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing libnghttp2-14:amd64 (1.61.0-1) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libpng16-16t64:amd64 (1.6.43-5) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing libreadline8t64:amd64 (8.2-4) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Removing libwebp7:amd64 (1.3.2-0.4+b1) ... Removing libsharpyuv0:amd64 (1.3.2-0.4+b1) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Removing libtcl8.6:amd64 (8.6.14+dfsg-1) ... Removing libthai-data (0.1.29-2) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing readline-common (8.2-4) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.22) ... Removing unzip (6.0-28) ... Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-13) ... Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libbsd0:amd64 (0.12.2-1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libistack-commons-java (3.0.6-5) ... Removing ant-optional (1.10.14-1) ... Removing ant (1.10.14-1) ... Removing openjdk-17-jre-headless:amd64 (17.0.11~7ea-1+b1) ... Removing java-common (0.75) ... Removing libactivation-java (1.2.0-2) ... Removing libmaven-file-management-java (3.0.0-1) ... Removing libmaven-shared-io-java (3.0.0-4) ... Removing libmaven3-core-java (3.8.7-2) ... Removing libguice-java (4.2.3-2) ... Removing libaopalliance-java (20070526-7) ... Removing libmaven-parent-java (35-1) ... Removing libargs4j-java (2.33-2) ... Removing libplexus-sec-dispatcher-java (2.0-3) ... Removing libplexus-cipher-java (2.0-1) ... Removing libsisu-plexus-java (0.3.4-3) ... Removing libsisu-inject-java (0.3.4-2) ... Removing libcdi-api-java (1.2-3) ... Removing libcommons-cli-java (1.6.0-1) ... Removing libwagon-http-java (3.5.3-1) ... Removing libhttpclient-java (4.5.14-1) ... Removing libcommons-codec-java (1.16.0-1) ... Removing libplexus-archiver-java (4.6.1-1) ... Removing libcommons-compress-java (1.25.0-1) ... Removing libplexus-io-java (3.3.1-2) ... Removing libmaven-shared-utils-java (3.3.4-1) ... Removing libcommons-io-java (2.16.0-1) ... Removing libmaven-resolver-java (1.6.3-1) ... Removing libcommons-lang3-java (3.14.0-1) ... Removing libdom4j-java (2.1.4-1) ... Removing liberror-prone-java (2.18.0-1) ... Removing libguava-java (32.0.1-1) ... Removing libgeronimo-annotation-1.3-spec-java (1.3-1) ... Removing libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Removing libhttpcore-java (4.4.16-1) ... Removing libjaxen-java (1.1.6-4) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing libjsoup-java (1.15.3-1) ... Removing libjsr305-java (0.1~+svn49-11) ... Removing liblcms2-2:amd64 (2.14-2+b1) ... Removing libnss3:amd64 (2:3.99-1) ... Removing libnspr4:amd64 (2:4.35-1.1+b1) ... Removing libpcsclite1:amd64 (2.0.3-1) ... Removing libplexus-classworlds-java (2.7.0-1) ... Removing libplexus-component-annotations-java (2.1.1-1) ... Removing libplexus-interpolation-java (1.26-1) ... Removing libwagon-provider-api-java (3.5.3-1) ... Removing libplexus-utils2-java (3.4.2-1) ... Removing libslf4j-java (1.7.32-1) ... Removing libsnappy-java (1.1.10.5-2) ... Removing libsnappy-jni (1.1.10.5-2) ... Removing libsnappy1v5:amd64 (1.1.10-1+b1) ... Removing libsqlite3-0:amd64 (3.45.2-1) ... Removing libxz-java (1.9-1) ... Removing libcodemodel-java (2.6+jaxb2.3.0.1-10.1) ... Removing ca-certificates-java (20240118) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libcommons-logging-java (1.3.0-1) ... Removing libcommons-parent-java (56-1) ... Removing libapache-pom-java (29-2) ... Removing libatinject-jsr330-api-java (1.0+ds1-5) ... Removing openssl (3.2.1-3) ... Processing triggers for libc-bin (2.37-17) ... 3m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', 'remove', 'adapterremoval', 'adwaita-icon-theme', 'ant', 'ant-optional', 'at-spi2-common', 'bcftools', 'bedtools', 'bowtie2', 'bwa', 'ca-certificates', 'ca-certificates-java', 'default-jre', 'default-jre-headless', 'examl', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'ibverbs-providers:amd64', 'java-common', 'libactivation-java', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libaopalliance-java', 'libapache-pom-java', 'libargs4j-java', 'libasound2-data', 'libasound2t64:amd64', 'libatinject-jsr330-api-java', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcbor0:amd64', 'libcbor0.10:amd64', 'libcdi-api-java', 'libcodemodel-java', 'libcommons-cli-java', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdom4j-java', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libdtd-parser-java', 'libedit2:amd64', 'libelf1t64:amd64', 'liberror-prone-java', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfastinfoset-java', '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', 'libgeronimo-annotation-1.3-spec-java', 'libgeronimo-interceptor-3.0-spec-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgkl-java', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgtk2.0-0t64:amd64', 'libgtk2.0-common', 'libguava-java', 'libguice-java', 'libharfbuzz0b:amd64', 'libhsa-runtime64-1', 'libhsakmt1:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libistack-commons-java', 'libjaxb-api-java', 'libjaxb-java', 'libjaxen-java', 'libjbig0:amd64', 'libjoptsimple-java', 'libjpeg62-turbo:amd64', 'libjsoup-java', 'libjsr305-java', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblightcouch-java', 'libllvm11:amd64', 'libllvm17t64:amd64', 'liblog4j2-java', 'libmaven-file-management-java', 'libmaven-parent-java', 'libmaven-resolver-java', 'libmaven-shared-io-java', 'libmaven-shared-utils-java', 'libmaven3-core-java', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedx509-1t64:amd64', 'libmjson-java', 'libmongodb-java', 'libmpdec3:amd64', 'libmunge2:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngs-sdk-dev:amd64', 'libngs-sdk2:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenmpi3t64:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpicard-java', 'libpixman-1-0:amd64', 'libplexus-archiver-java', 'libplexus-cipher-java', 'libplexus-classworlds-java', 'libplexus-component-annotations-java', 'libplexus-interpolation-java', 'libplexus-io-java', 'libplexus-sec-dispatcher-java', 'libplexus-utils2-java', 'libpmix2t64:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1t64:amd64', 'libreadline8t64:amd64', 'librelaxng-datatype-java', 'librhino-java', 'librngom-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsisu-inject-java', 'libsisu-plexus-java', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstax-ex-java', 'libstreambuffer-java', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libtxw2-java', 'libucx0:amd64', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwagon-http-java', 'libwagon-provider-api-java', 'libwebp6: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', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxsom-java', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libxz-java', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'ncbi-vdb-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'perl-modules-5.32', 'phylip', 'picard-tools', 'python3', 'python3-coloredlogs', 'python3-configargparse', 'python3-humanfriendly', 'python3-minimal', 'python3-pysam', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib:amd64', 'python3-setproctitle:amd64', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-cran-assertthat', 'r-cran-brio', 'r-cran-callr', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-fs', 'r-cran-gam', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-inline', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-jsonlite', '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-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-ps', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcppgsl', 'r-cran-rematch2', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-testthat', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-waldo', 'r-cran-withr', 'radiant', 'raxml', 'readline-common', 'samtools', 'sensible-utils', 'seqtk', 'shared-mime-info', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'paleomix'] 3m2.5s INFO: Running scripts post_remove 3m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_remove_exceptions'] 3m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_remove_exceptions'] 3m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg', '--purge', 'adapterremoval', 'adwaita-icon-theme', 'ant', 'ant-optional', 'at-spi2-common', 'bcftools', 'bedtools', 'bowtie2', 'bwa', 'ca-certificates', 'ca-certificates-java', 'default-jre', 'default-jre-headless', 'examl', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'ibverbs-providers:amd64', 'java-common', 'libactivation-java', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libaopalliance-java', 'libapache-pom-java', 'libargs4j-java', 'libasound2-data', 'libasound2t64:amd64', 'libatinject-jsr330-api-java', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcbor0:amd64', 'libcbor0.10:amd64', 'libcdi-api-java', 'libcodemodel-java', 'libcommons-cli-java', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdom4j-java', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libdtd-parser-java', 'libedit2:amd64', 'libelf1t64:amd64', 'liberror-prone-java', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfastinfoset-java', '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', 'libgeronimo-annotation-1.3-spec-java', 'libgeronimo-interceptor-3.0-spec-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgkl-java', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgtk2.0-0t64:amd64', 'libgtk2.0-common', 'libguava-java', 'libguice-java', 'libharfbuzz0b:amd64', 'libhsa-runtime64-1', 'libhsakmt1:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libistack-commons-java', 'libjaxb-api-java', 'libjaxb-java', 'libjaxen-java', 'libjbig0:amd64', 'libjoptsimple-java', 'libjpeg62-turbo:amd64', 'libjsoup-java', 'libjsr305-java', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblightcouch-java', 'libllvm11:amd64', 'libllvm17t64:amd64', 'liblog4j2-java', 'libmaven-file-management-java', 'libmaven-parent-java', 'libmaven-resolver-java', 'libmaven-shared-io-java', 'libmaven-shared-utils-java', 'libmaven3-core-java', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedx509-1t64:amd64', 'libmjson-java', 'libmongodb-java', 'libmpdec3:amd64', 'libmunge2:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngs-sdk-dev:amd64', 'libngs-sdk2:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenmpi3t64:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpicard-java', 'libpixman-1-0:amd64', 'libplexus-archiver-java', 'libplexus-cipher-java', 'libplexus-classworlds-java', 'libplexus-component-annotations-java', 'libplexus-interpolation-java', 'libplexus-io-java', 'libplexus-sec-dispatcher-java', 'libplexus-utils2-java', 'libpmix2t64:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1t64:amd64', 'libreadline8t64:amd64', 'librelaxng-datatype-java', 'librhino-java', 'librngom-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsisu-inject-java', 'libsisu-plexus-java', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstax-ex-java', 'libstreambuffer-java', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libtxw2-java', 'libucx0:amd64', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwagon-http-java', 'libwagon-provider-api-java', 'libwebp6: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', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxsom-java', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libxz-java', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'ncbi-vdb-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'perl-modules-5.32', 'phylip', 'picard-tools', 'python3', 'python3-coloredlogs', 'python3-configargparse', 'python3-humanfriendly', 'python3-minimal', 'python3-pysam', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib:amd64', 'python3-setproctitle:amd64', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-cran-assertthat', 'r-cran-brio', 'r-cran-callr', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-fs', 'r-cran-gam', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-inline', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-jsonlite', '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-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-ps', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcppgsl', 'r-cran-rematch2', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-testthat', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-waldo', 'r-cran-withr', 'radiant', 'raxml', 'readline-common', 'samtools', 'sensible-utils', 'seqtk', 'shared-mime-info', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip'] 3m3.4s DUMP: dpkg: warning: ignoring request to remove adapterremoval which isn't installed (Reading database ... 7617 files and directories currently installed.) Purging configuration files for adwaita-icon-theme (46.0-1) ... dpkg: warning: ignoring request to remove ant which isn't installed dpkg: warning: ignoring request to remove ant-optional which isn't installed dpkg: warning: ignoring request to remove at-spi2-common which isn't installed dpkg: warning: ignoring request to remove bcftools which isn't installed dpkg: warning: ignoring request to remove bedtools which isn't installed dpkg: warning: ignoring request to remove bowtie2 which isn't installed dpkg: warning: ignoring request to remove bwa which isn't installed Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20240118) ... dpkg: warning: ignoring request to remove default-jre which isn't installed dpkg: warning: ignoring request to remove default-jre-headless which isn't installed dpkg: warning: ignoring request to remove examl which isn't installed Purging configuration files for fontconfig (2.15.0-1.1) ... Purging configuration files for fontconfig-config (2.15.0-1.1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/usr/share/fonts/truetype/dejavu' not empty so not removed dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed 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 (50.0-2+b1) ... Purging configuration files for java-common (0.75) ... dpkg: warning: ignoring request to remove libactivation-java which isn't installed dpkg: warning: ignoring request to remove libamd-comgr2 which isn't installed dpkg: warning: ignoring request to remove libamdhip64-5 which isn't installed dpkg: warning: ignoring request to remove libaopalliance-java which isn't installed dpkg: warning: ignoring request to remove libapache-pom-java which isn't installed dpkg: warning: ignoring request to remove libargs4j-java which isn't installed dpkg: warning: ignoring request to remove libasound2-data which isn't installed dpkg: warning: ignoring request to remove libasound2t64 which isn't installed dpkg: warning: ignoring request to remove libatinject-jsr330-api-java which isn't installed dpkg: warning: ignoring request to remove libatk1.0-0t64 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 which isn't installed dpkg: warning: ignoring request to remove libcbor0.10 which isn't installed dpkg: warning: ignoring request to remove libcdi-api-java which isn't installed dpkg: warning: ignoring request to remove libcodemodel-java which isn't installed dpkg: warning: ignoring request to remove libcommons-cli-java 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 libcups2t64 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 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 libdom4j-java 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 libdtd-parser-java which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libelf1t64 which isn't installed dpkg: warning: ignoring request to remove liberror-prone-java which isn't installed dpkg: warning: ignoring request to remove libevent-core-2.1-7t64 which isn't installed dpkg: warning: ignoring request to remove libevent-pthreads-2.1-7t64 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 libfastinfoset-java 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-3+b2) ... dpkg: warning: ignoring request to remove libgdk-pixbuf2.0-common which isn't installed dpkg: warning: ignoring request to remove libgeronimo-annotation-1.3-spec-java which isn't installed dpkg: warning: ignoring request to remove libgeronimo-interceptor-3.0-spec-java which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgif7 which isn't installed dpkg: warning: ignoring request to remove libgkl-java which isn't installed dpkg: warning: ignoring request to remove libgl1 which isn't installed Purging configuration files for libgl1-mesa-dri:amd64 (24.0.5-1) ... dpkg: warning: ignoring request to remove libglapi-mesa which isn't installed dpkg: warning: ignoring request to remove libglib2.0-0 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.78.4-6) ... dpkg: warning: ignoring request to remove libglvnd0 which isn't installed dpkg: warning: ignoring request to remove libglx-mesa0 which isn't 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Purging configuration files for libgtk2.0-common (2.24.33-4) ... dpkg: warning: ignoring request to remove libguava-java which isn't installed dpkg: warning: ignoring request to remove libguice-java which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhsa-runtime64-1 which isn't installed dpkg: warning: ignoring request to remove libhsakmt1 which isn't installed dpkg: warning: ignoring request to remove libhts3t64 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 libicu67 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libistack-commons-java which isn't installed dpkg: warning: ignoring request to remove libjaxb-api-java which isn't installed dpkg: warning: ignoring request to remove libjaxb-java which isn't installed dpkg: warning: ignoring request to remove libjaxen-java 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 libjsoup-java which isn't installed dpkg: warning: ignoring request to remove libjsr305-java 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-2.4-2 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 libllvm11 which isn't installed dpkg: warning: ignoring request to remove libllvm17t64 which isn't installed dpkg: warning: ignoring request to remove liblog4j2-java which isn't installed dpkg: warning: ignoring request to remove libmaven-file-management-java which isn't installed dpkg: warning: ignoring request to remove libmaven-parent-java which isn't installed dpkg: warning: ignoring request to remove libmaven-resolver-java which isn't installed dpkg: warning: ignoring request to remove libmaven-shared-io-java which isn't installed dpkg: warning: ignoring request to remove libmaven-shared-utils-java which isn't installed dpkg: warning: ignoring request to remove libmaven3-core-java which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7t64 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14t64 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1t64 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 libmpdec3 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 dpkg: warning: ignoring request to remove libngs-sdk-dev which isn't installed dpkg: warning: ignoring request to remove libngs-sdk2 which isn't installed Purging configuration files for libnl-3-200:amd64 (3.7.0-0.3) ... dpkg: warning: ignoring request to remove libnl-route-3-200 which isn't installed dpkg: warning: ignoring request to remove 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 libopenmpi3t64 which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.29) ... dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpcsclite1 which isn't installed dpkg: warning: ignoring request to remove libperl5.32 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 libplexus-archiver-java which isn't installed dpkg: warning: ignoring request to remove libplexus-cipher-java which isn't installed dpkg: warning: ignoring request to remove libplexus-classworlds-java which isn't installed dpkg: warning: ignoring request to remove libplexus-component-annotations-java which isn't installed dpkg: warning: ignoring request to remove libplexus-interpolation-java which isn't installed dpkg: warning: ignoring request to remove libplexus-io-java which isn't installed dpkg: warning: ignoring request to remove libplexus-sec-dispatcher-java which isn't installed dpkg: warning: ignoring request to remove libplexus-utils2-java which isn't installed dpkg: warning: ignoring request to remove libpmix2t64 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed Purging configuration files for libpsm-infinipath1 (3.3+20.604758e7-6.3) ... dpkg: warning: ignoring request to remove libpsm2-2 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.9-1) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove librdmacm1t64 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-4) ... dpkg: warning: ignoring request to remove librelaxng-datatype-java which isn't installed dpkg: warning: ignoring request to remove librhino-java which isn't installed dpkg: warning: ignoring request to remove librngom-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 (1:3.6.0-9) ... dpkg: warning: ignoring request to remove libsensors5 which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsisu-inject-java which isn't installed dpkg: warning: ignoring request to remove libsisu-plexus-java 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 libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libstax-ex-java which isn't installed dpkg: warning: ignoring request to remove libstreambuffer-java which isn't installed dpkg: warning: ignoring request to remove libtbb2 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 libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtxw2-java which isn't installed dpkg: warning: ignoring request to remove libucx0 which isn't installed dpkg: warning: ignoring request to remove libuv1t64 which isn't installed dpkg: warning: ignoring request to remove libvulkan1 which isn't installed dpkg: warning: ignoring request to remove libwagon-http-java which isn't installed dpkg: warning: ignoring request to remove libwagon-provider-api-java which isn't installed dpkg: warning: ignoring request to remove libwebp6 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 Purging configuration files for libxml-commons-resolver1.1-java (1.2-11) ... dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxnvctrl0 which isn't installed dpkg: warning: ignoring request to remove 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 libxsom-java which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6t64 which isn't installed dpkg: warning: ignoring request to remove libxtst6 which isn't installed dpkg: warning: ignoring request to remove libxxf86vm1 which isn't installed dpkg: warning: ignoring request to remove libxz-java which isn't installed dpkg: warning: ignoring request to remove libz3-4 which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed dpkg: warning: ignoring request to remove mafft which isn't installed dpkg: warning: ignoring request to remove mapdamage which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove ncbi-vdb-data which isn't installed Purging configuration files for netbase (6.4) ... dpkg: warning: ignoring request to remove ocl-icd-libopencl1 which isn't installed dpkg: warning: ignoring request to remove openjdk-11-jre which isn't installed Purging configuration files for openjdk-11-jre-headless:amd64 (11.0.23~7ea-1) ... dpkg: warning: ignoring request to remove openjdk-17-jre which isn't installed Purging configuration files for openjdk-17-jre-headless:amd64 (17.0.11~7ea-1+b1) ... Purging configuration files for openmpi-bin (4.1.6-9) ... dpkg: warning: ignoring request to remove openmpi-common which isn't installed Purging configuration files for openssh-client (1:9.7p1-4) ... warn: The group `ssh' does not exist. Purging configuration files for openssl (3.2.1-3) ... dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed dpkg: warning: ignoring request to remove phylip which isn't installed dpkg: warning: ignoring request to remove picard-tools which isn't installed Purging configuration files for python3 (3.11.8-1) ... dpkg: warning: ignoring request to remove python3-coloredlogs which isn't installed dpkg: warning: ignoring request to remove python3-configargparse which isn't installed dpkg: warning: ignoring request to remove python3-humanfriendly which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-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 (3.11.9-1) ... dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for r-base-core (4.3.3-3+b1) ... dpkg: warning: ignoring request to remove r-cran-assertthat which isn't installed dpkg: warning: ignoring request to remove r-cran-brio which isn't installed dpkg: warning: ignoring request to remove r-cran-callr which isn't installed 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-crayon which isn't installed dpkg: warning: ignoring request to remove r-cran-desc which isn't installed dpkg: warning: ignoring request to remove r-cran-diffobj which isn't installed dpkg: warning: ignoring request to remove r-cran-digest which isn't installed dpkg: warning: ignoring request to remove r-cran-ellipsis which isn't installed dpkg: warning: ignoring request to remove r-cran-evaluate 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-fs 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-jsonlite 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-pkgbuild 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-pkgload which isn't installed dpkg: warning: ignoring request to remove r-cran-praise which isn't installed dpkg: warning: ignoring request to remove r-cran-prettyunits which isn't installed dpkg: warning: ignoring request to remove r-cran-processx which isn't installed dpkg: warning: ignoring request to remove r-cran-ps 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-rematch2 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-rprojroot which isn't installed dpkg: warning: ignoring request to remove r-cran-rstudioapi 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-testthat 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-waldo 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 (8.2-4) ... dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed dpkg: warning: ignoring request to remove seqtk which isn't installed Purging configuration files for shared-mime-info (2.4-4) ... 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: while removing x11-common, directory '/etc/init.d' not empty so not removed dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 3m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg', '--purge', 'adapterremoval', 'adwaita-icon-theme', 'ant', 'ant-optional', 'at-spi2-common', 'bcftools', 'bedtools', 'bowtie2', 'bwa', 'ca-certificates', 'ca-certificates-java', 'default-jre', 'default-jre-headless', 'examl', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'ibverbs-providers:amd64', 'java-common', 'libactivation-java', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libaopalliance-java', 'libapache-pom-java', 'libargs4j-java', 'libasound2-data', 'libasound2t64:amd64', 'libatinject-jsr330-api-java', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcbor0:amd64', 'libcbor0.10:amd64', 'libcdi-api-java', 'libcodemodel-java', 'libcommons-cli-java', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdom4j-java', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libdtd-parser-java', 'libedit2:amd64', 'libelf1t64:amd64', 'liberror-prone-java', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfastinfoset-java', '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', 'libgeronimo-annotation-1.3-spec-java', 'libgeronimo-interceptor-3.0-spec-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgkl-java', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgtk2.0-0t64:amd64', 'libgtk2.0-common', 'libguava-java', 'libguice-java', 'libharfbuzz0b:amd64', 'libhsa-runtime64-1', 'libhsakmt1:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libistack-commons-java', 'libjaxb-api-java', 'libjaxb-java', 'libjaxen-java', 'libjbig0:amd64', 'libjoptsimple-java', 'libjpeg62-turbo:amd64', 'libjsoup-java', 'libjsr305-java', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblightcouch-java', 'libllvm11:amd64', 'libllvm17t64:amd64', 'liblog4j2-java', 'libmaven-file-management-java', 'libmaven-parent-java', 'libmaven-resolver-java', 'libmaven-shared-io-java', 'libmaven-shared-utils-java', 'libmaven3-core-java', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedx509-1t64:amd64', 'libmjson-java', 'libmongodb-java', 'libmpdec3:amd64', 'libmunge2:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngs-sdk-dev:amd64', 'libngs-sdk2:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenmpi3t64:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpicard-java', 'libpixman-1-0:amd64', 'libplexus-archiver-java', 'libplexus-cipher-java', 'libplexus-classworlds-java', 'libplexus-component-annotations-java', 'libplexus-interpolation-java', 'libplexus-io-java', 'libplexus-sec-dispatcher-java', 'libplexus-utils2-java', 'libpmix2t64:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1t64:amd64', 'libreadline8t64:amd64', 'librelaxng-datatype-java', 'librhino-java', 'librngom-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsisu-inject-java', 'libsisu-plexus-java', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstax-ex-java', 'libstreambuffer-java', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libtxw2-java', 'libucx0:amd64', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwagon-http-java', 'libwagon-provider-api-java', 'libwebp6: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', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxsom-java', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libxz-java', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'ncbi-vdb-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'perl-modules-5.32', 'phylip', 'picard-tools', 'python3', 'python3-coloredlogs', 'python3-configargparse', 'python3-humanfriendly', 'python3-minimal', 'python3-pysam', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib:amd64', 'python3-setproctitle:amd64', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-cran-assertthat', 'r-cran-brio', 'r-cran-callr', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-fs', 'r-cran-gam', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-inline', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-jsonlite', '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-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-ps', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcppgsl', 'r-cran-rematch2', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-testthat', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-waldo', 'r-cran-withr', 'radiant', 'raxml', 'readline-common', 'samtools', 'sensible-utils', 'seqtk', 'shared-mime-info', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip'] 3m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg', '--purge', 'paleomix'] 3m3.4s DUMP: dpkg: warning: ignoring request to remove paleomix which isn't installed 3m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg', '--purge', 'paleomix'] 3m3.4s INFO: Running scripts post_purge 3m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_purge_exceptions'] 3m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_purge_exceptions'] 3m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg', '--purge', '--pending'] 3m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg', '--purge', '--pending'] 3m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg', '--remove', '--pending'] 3m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg', '--remove', '--pending'] 3m3.5s INFO: Running scripts post_test 3m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_test_exceptions'] 3m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'tmp/scripts/post_test_exceptions'] 3m3.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 3m4.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 3m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg-divert', '--list'] 3m4.0s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64 diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64 3m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'dpkg-divert', '--list'] 3m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', 'clean'] 3m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuarkol71', 'apt-get', 'clean'] 3m4.2s DEBUG: Recording chroot state 3m5.0s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-dejavu-mono, fonts-dejavu-core /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-dejavu-mono, fonts-dejavu-core /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned /usr/lib/x86_64-linux-gnu/libmpi_usempi_ignore_tkr-gfortranso.40 -> libmpi_usempi_ignore_tkr-gfortran.so.40.30.0 not owned /usr/local/share/fonts/ not owned /usr/local/share/fonts/.uuid not owned /usr/share/fonts/ owned by: fonts-dejavu-mono, fonts-dejavu-core /usr/share/fonts/.uuid not owned /usr/share/fonts/truetype/ owned by: fonts-dejavu-mono, fonts-dejavu-core /usr/share/fonts/truetype/.uuid not owned /usr/share/fonts/truetype/dejavu/ owned by: fonts-dejavu-mono, fonts-dejavu-core /usr/share/fonts/truetype/dejavu/.uuid not owned 3m5.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/shm'] 3m5.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/shm'] 3m5.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/console'] 3m5.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/console'] 3m5.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/ptmx'] 3m5.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/ptmx'] 3m5.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/pts'] 3m5.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuarkol71/dev/pts'] 3m5.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuarkol71/proc'] 3m5.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuarkol71/proc'] 3m5.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 3m5.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpuarkol71'] 3m5.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpuarkol71 3m5.9s INFO: PASS: Upgrading between Debian distributions. 3m5.9s INFO: PASS: All tests. 3m5.9s INFO: piuparts run ends. ret=0 End: 2024-04-14 15:45:19 GMT