Start: 2024-01-22 18:26:20 GMT [bullseye] 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 [bullseye-next] 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 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 --warn-on-usr-move fail --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 bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt paleomix=1.3.2-1 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 1.2 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 --warn-on-usr-move fail --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 bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt paleomix=1.3.2-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-27-amd64 #1 SMP Debian 5.10.205-2 (2023-12-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpv68ck88f 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpv68ck88f 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m1.9s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/proc'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/proc'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/pts'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/pts'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/ptmx'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/ptmx'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/console'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/console'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/shm'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/shm'] 0m1.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m1.9s DEBUG: Created policy-rc.d and chmodded it. 0m1.9s DEBUG: Created resolv.conf. 0m1.9s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpv68ck88f/tmp/scripts/ 0m1.9s INFO: Running scripts post_chroot_unpack 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', 'update'] 0m3.0s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', 'update'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.6s DUMP: cd994be14815166bf41ad7cebd6f56fc - 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.6s INFO: Running scripts post_setup 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_setup_dummy_users'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_setup_dummy_users'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_setup_forbid_home'] 0m5.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_setup_forbid_home'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_setup_minimize'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_setup_minimize'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_setup_zz_backports'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_setup_zz_backports'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.1s 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+deb11u8 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+deb11u6 install ok installed libc6:amd64 libc6 2.31-13+deb11u6 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+deb11u3 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+deb11u2 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 install ok installed tzdata tzdata 2021a-1+deb11u10 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 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat 0m5.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 0m5.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 0m5.4s INFO: Running scripts is_testable 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/is_testable_uninstallable'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/is_testable_uninstallable'] 0m5.4s INFO: Running scripts pre_test 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_test_exceptions'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_test_exceptions'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_test_root_password'] 0m5.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_test_root_password'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'show', '--no-all-versions', 'paleomix'] 0m5.7s 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 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'show', '--no-all-versions', 'paleomix'] 0m5.7s INFO: apt-cache knows about the following packages: paleomix 0m5.7s INFO: Running scripts pre_install 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_database-server'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_database-server'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_exceptions'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_exceptions'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_extras'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_extras'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'policy'] 0m5.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.8,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'policy'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'policy', 'paleomix'] 0m5.9s 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 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'policy', 'paleomix'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', '-y', 'install', 'paleomix'] 1m22.8s 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+deb11u2 [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+deb11u2 [4106 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.32.1-4+deb11u2 [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+deb11u2 [930 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 [1370 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 11.0.20+8-1~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 [77.1 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+deb11u9 [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+deb11u1 [311 kB] Get:78 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u1 [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+deb11u1 [203 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 11.0.20+8-1~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 [552 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+deb11u9 [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+deb11u4 [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 25s (9726 kB/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 ... 6666 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.32_5.32.1-4+deb11u2_all.deb ... Unpacking perl-modules-5.32 (5.32.1-4+deb11u2) ... 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+deb11u2_amd64.deb ... Unpacking libperl5.32:amd64 (5.32.1-4+deb11u2) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.32.1-4+deb11u2_amd64.deb ... Unpacking perl (5.32.1-4+deb11u2) ... 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 ... 8931 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 ... 9369 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) ... 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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+deb11u4) ... 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+deb11u9) ... 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+deb11u2) ... 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+deb11u9) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u1) ... 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+deb11u1) ... 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+deb11u2) ... 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+deb11u2) ... 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) ... 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 (11.0.20+8-1~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 (11.0.20+8-1~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+deb11u6) ... 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. 1m22.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', '-y', 'install', 'paleomix'] 1m22.8s INFO: Running scripts post_install 1m22.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_install_exceptions'] 1m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_install_exceptions'] 1m22.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 1m23.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 1m23.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpv68ck88f to bullseye-next 1m23.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main deb http://security.debian.org bullseye-security main deb http://deb.debian.org/debian/ bullseye-updates main deb http://deb.debian.org/debian/ bullseye-proposed-updates main 1m23.9s INFO: Running scripts pre_distupgrade 1m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_distupgrade_exceptions'] 1m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_distupgrade_exceptions'] 1m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', 'update'] 1m25.9s DUMP: Get:1 http://security.debian.org bullseye-security InRelease [48.4 kB] Hit:2 http://deb.debian.org/debian bullseye InRelease Get:3 http://deb.debian.org/debian bullseye-updates InRelease [44.1 kB] Get:4 http://deb.debian.org/debian bullseye-proposed-updates InRelease [54.0 kB] Get:5 http://security.debian.org bullseye-security/main amd64 Packages [265 kB] Get:6 http://security.debian.org bullseye-security/main Translation-en [171 kB] Get:7 http://deb.debian.org/debian bullseye-updates/main amd64 Packages [18.8 kB] Get:8 http://deb.debian.org/debian bullseye-updates/main Translation-en [10.9 kB] Get:9 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages [158 kB] Get:10 http://deb.debian.org/debian bullseye-proposed-updates/main Translation-en [92.1 kB] Fetched 862 kB in 1s (853 kB/s) Reading package lists... 1m25.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', 'update'] 1m25.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', '-yf', 'dist-upgrade'] 1m38.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc6 libcurl3-gnutls libcurl4 libglib2.0-0 libgnutls30 libnghttp2-14 libperl5.32 libpmix2 libtiff5 libx11-6 libx11-data libx11-xcb1 openjdk-11-jre openjdk-11-jre-headless openssh-client perl perl-base perl-modules-5.32 tar tzdata 21 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 58.6 MB of archives. After this operation, 100 kB of additional disk space will be used. Get:1 http://security.debian.org bullseye-security/main amd64 libc6 amd64 2.31-13+deb11u7 [2823 kB] Get:2 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 libperl5.32 amd64 5.32.1-4+deb11u3 [4121 kB] Get:3 http://security.debian.org bullseye-security/main amd64 libc-bin amd64 2.31-13+deb11u7 [829 kB] Get:4 http://security.debian.org bullseye-security/main amd64 openssh-client amd64 1:8.4p1-5+deb11u3 [932 kB] Get:5 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 perl amd64 5.32.1-4+deb11u3 [293 kB] Get:6 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 perl-base amd64 5.32.1-4+deb11u3 [1628 kB] Get:7 http://security.debian.org bullseye-security/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u1 [77.2 kB] Get:8 http://security.debian.org bullseye-security/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u11 [344 kB] Get:9 http://security.debian.org bullseye-security/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u11 [347 kB] Get:10 http://security.debian.org bullseye-security/main amd64 libpmix2 amd64 4.0.0-4.1+deb11u1 [553 kB] Get:11 http://security.debian.org bullseye-security/main amd64 libtiff5 amd64 4.2.0-1+deb11u5 [290 kB] Get:12 http://security.debian.org bullseye-security/main amd64 libx11-data all 2:1.7.2-1+deb11u2 [311 kB] Get:13 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 perl-modules-5.32 all 5.32.1-4+deb11u3 [2823 kB] Get:14 http://security.debian.org bullseye-security/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u2 [772 kB] Get:15 http://security.debian.org bullseye-security/main amd64 libx11-xcb1 amd64 2:1.7.2-1+deb11u2 [204 kB] Get:16 http://security.debian.org bullseye-security/main amd64 openjdk-11-jre amd64 11.0.21+9-1~deb11u1 [194 kB] Get:17 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 tar amd64 1.34+dfsg-1+deb11u1 [847 kB] Get:18 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 libgnutls30 amd64 3.7.1-5+deb11u4 [1340 kB] Get:19 http://deb.debian.org/debian bullseye-updates/main amd64 tzdata all 2021a-1+deb11u11 [287 kB] Get:20 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 libglib2.0-0 amd64 2.66.8-1+deb11u1 [1374 kB] Get:21 http://security.debian.org bullseye-security/main amd64 openjdk-11-jre-headless amd64 11.0.21+9-1~deb11u1 [38.2 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 58.6 MB in 2s (24.8 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23207 files and directories currently installed.) Preparing to unpack .../libperl5.32_5.32.1-4+deb11u3_amd64.deb ... Unpacking libperl5.32:amd64 (5.32.1-4+deb11u3) over (5.32.1-4+deb11u2) ... Preparing to unpack .../perl_5.32.1-4+deb11u3_amd64.deb ... Unpacking perl (5.32.1-4+deb11u3) over (5.32.1-4+deb11u2) ... Preparing to unpack .../perl-base_5.32.1-4+deb11u3_amd64.deb ... Unpacking perl-base (5.32.1-4+deb11u3) over (5.32.1-4+deb11u2) ... Setting up perl-base (5.32.1-4+deb11u3) ... (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 ... 23207 files and directories currently installed.) Preparing to unpack .../perl-modules-5.32_5.32.1-4+deb11u3_all.deb ... Unpacking perl-modules-5.32 (5.32.1-4+deb11u3) over (5.32.1-4+deb11u2) ... Preparing to unpack .../libc6_2.31-13+deb11u7_amd64.deb ... Unpacking libc6:amd64 (2.31-13+deb11u7) over (2.31-13+deb11u6) ... Setting up libc6:amd64 (2.31-13+deb11u7) ... (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 ... 23207 files and directories currently installed.) Preparing to unpack .../tar_1.34+dfsg-1+deb11u1_amd64.deb ... Unpacking tar (1.34+dfsg-1+deb11u1) over (1.34+dfsg-1) ... Setting up tar (1.34+dfsg-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 ... 23207 files and directories currently installed.) Preparing to unpack .../libc-bin_2.31-13+deb11u7_amd64.deb ... Unpacking libc-bin (2.31-13+deb11u7) over (2.31-13+deb11u6) ... Setting up libc-bin (2.31-13+deb11u7) ... (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 ... 23207 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.1-5+deb11u4_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.1-5+deb11u4) over (3.7.1-5+deb11u3) ... Setting up libgnutls30:amd64 (3.7.1-5+deb11u4) ... (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 ... 23207 files and directories currently installed.) Preparing to unpack .../00-tzdata_2021a-1+deb11u11_all.deb ... Unpacking tzdata (2021a-1+deb11u11) over (2021a-1+deb11u10) ... Preparing to unpack .../01-openssh-client_1%3a8.4p1-5+deb11u3_amd64.deb ... Unpacking openssh-client (1:8.4p1-5+deb11u3) over (1:8.4p1-5+deb11u2) ... Preparing to unpack .../02-libnghttp2-14_1.43.0-1+deb11u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.43.0-1+deb11u1) over (1.43.0-1) ... Preparing to unpack .../03-libcurl3-gnutls_7.74.0-1.3+deb11u11_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u11) over (7.74.0-1.3+deb11u9) ... Preparing to unpack .../04-libcurl4_7.74.0-1.3+deb11u11_amd64.deb ... Unpacking libcurl4:amd64 (7.74.0-1.3+deb11u11) over (7.74.0-1.3+deb11u9) ... Preparing to unpack .../05-libglib2.0-0_2.66.8-1+deb11u1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.66.8-1+deb11u1) over (2.66.8-1) ... Preparing to unpack .../06-libpmix2_4.0.0-4.1+deb11u1_amd64.deb ... Unpacking libpmix2:amd64 (4.0.0-4.1+deb11u1) over (4.0.0-4.1) ... Preparing to unpack .../07-libtiff5_4.2.0-1+deb11u5_amd64.deb ... Unpacking libtiff5:amd64 (4.2.0-1+deb11u5) over (4.2.0-1+deb11u4) ... Preparing to unpack .../08-libx11-data_2%3a1.7.2-1+deb11u2_all.deb ... Unpacking libx11-data (2:1.7.2-1+deb11u2) over (2:1.7.2-1+deb11u1) ... Preparing to unpack .../09-libx11-6_2%3a1.7.2-1+deb11u2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.7.2-1+deb11u2) over (2:1.7.2-1+deb11u1) ... Preparing to unpack .../10-libx11-xcb1_2%3a1.7.2-1+deb11u2_amd64.deb ... Unpacking libx11-xcb1:amd64 (2:1.7.2-1+deb11u2) over (2:1.7.2-1+deb11u1) ... Preparing to unpack .../11-openjdk-11-jre_11.0.21+9-1~deb11u1_amd64.deb ... Unpacking openjdk-11-jre:amd64 (11.0.21+9-1~deb11u1) over (11.0.20+8-1~deb11u1) ... Preparing to unpack .../12-openjdk-11-jre-headless_11.0.21+9-1~deb11u1_amd64.deb ... Unpacking openjdk-11-jre-headless:amd64 (11.0.21+9-1~deb11u1) over (11.0.20+8-1~deb11u1) ... Setting up libpmix2:amd64 (4.0.0-4.1+deb11u1) ... Setting up libglib2.0-0:amd64 (2.66.8-1+deb11u1) ... No schema files found: doing nothing. Setting up openssh-client (1:8.4p1-5+deb11u3) ... Setting up perl-modules-5.32 (5.32.1-4+deb11u3) ... Setting up openjdk-11-jre-headless:amd64 (11.0.21+9-1~deb11u1) ... 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 libnghttp2-14:amd64 (1.43.0-1+deb11u1) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u11) ... Setting up tzdata (2021a-1+deb11u11) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jan 22 18:27:59 UTC 2024. Universal Time is now: Mon Jan 22 18:27:59 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libx11-data (2:1.7.2-1+deb11u2) ... Setting up libperl5.32:amd64 (5.32.1-4+deb11u3) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u11) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u2) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u5) ... Setting up libx11-xcb1:amd64 (2:1.7.2-1+deb11u2) ... Setting up openjdk-11-jre:amd64 (11.0.21+9-1~deb11u1) ... Setting up perl (5.32.1-4+deb11u3) ... Processing triggers for libc-bin (2.31-13+deb11u7) ... 1m38.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', '-yf', 'dist-upgrade'] 1m38.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m38.8s DUMP: 82086c2cf5080a75221814dcfc39b889 - 1m38.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m38.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'show', '--no-all-versions', 'paleomix'] 1m39.1s 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 1m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'show', '--no-all-versions', 'paleomix'] 1m39.1s INFO: apt-cache knows about the following packages: paleomix 1m39.1s INFO: Running scripts pre_install 1m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_database-server'] 1m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_database-server'] 1m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_exceptions'] 1m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_exceptions'] 1m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_extras'] 1m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_extras'] 1m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_foreign_architecture'] 1m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_foreign_architecture'] 1m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'policy'] 1m39.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.8,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'policy'] 1m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'policy', 'paleomix'] 1m39.2s DUMP: paleomix: Installed: 1.3.2-1 Candidate: 1.3.2-1 Version table: *** 1.3.2-1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 1m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'policy', 'paleomix'] 1m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', '-y', 'install', 'paleomix'] 1m39.8s DUMP: Reading package lists... Building dependency tree... Reading state information... paleomix is already the newest version (1.3.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', '-y', 'install', 'paleomix'] 1m39.8s INFO: Running scripts post_install 1m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_install_exceptions'] 1m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_install_exceptions'] 1m39.8s INFO: Running scripts post_distupgrade 1m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_distupgrade_exceptions'] 1m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_distupgrade_exceptions'] 1m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_distupgrade_zz_backports'] 1m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_distupgrade_zz_backports'] 1m39.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 1m40.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 1m40.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 1m41.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 1m41.7s INFO: Running scripts pre_install 1m41.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_database-server'] 1m41.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_database-server'] 1m41.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_exceptions'] 1m41.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_exceptions'] 1m41.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_extras'] 1m41.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_extras'] 1m41.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_foreign_architecture'] 1m41.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_foreign_architecture'] 1m41.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m41.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m41.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'policy'] 1m41.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.8,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m41.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'policy'] 1m41.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'policy', 'paleomix'] 1m41.8s DUMP: paleomix: Installed: 1.3.2-1 Candidate: 1.3.2-1 Version table: *** 1.3.2-1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 1m41.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-cache', 'policy', 'paleomix'] 1m41.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', '-y', 'install', 'paleomix=1.3.2-1'] 1m42.3s DUMP: Reading package lists... Building dependency tree... Reading state information... paleomix is already the newest version (1.3.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', '-y', 'install', 'paleomix=1.3.2-1'] 1m42.3s INFO: Running scripts post_install 1m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_install_exceptions'] 1m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_install_exceptions'] 1m42.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 1m43.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 1m43.5s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 1m43.6s INFO: /bin converted to /usr/bin by /usr merge 1m43.6s INFO: /lib converted to /usr/lib by /usr merge 1m43.6s INFO: /lib/init converted to /usr/lib/init by /usr merge 1m43.6s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 1m43.6s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 1m43.6s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 1m43.6s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 1m43.6s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 1m43.6s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 1m43.6s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 1m43.6s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 1m43.6s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 1m43.6s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 1m43.6s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 1m43.6s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 1m43.6s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 1m43.6s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 1m43.6s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 1m43.6s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 1m43.6s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 1m43.6s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 1m43.6s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 1m43.6s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 1m43.6s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 1m43.6s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 1m43.6s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 1m43.6s INFO: /lib64 converted to /usr/lib64 by /usr merge 1m43.6s INFO: /sbin converted to /usr/sbin by /usr merge 1m44.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', '-ac', '--ignore-obsolete'] 1m48.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', '-ac', '--ignore-obsolete'] 1m48.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m48.8s DUMP: 0.15.6 1m48.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m48.8s INFO: Running adequate version 0.15.6 now. 1m48.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'paleomix'] 1m49.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'paleomix'] 1m49.0s INFO: Running scripts pre_remove 1m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m49.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m49.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m59.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m59.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m59.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m59.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m59.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m59.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_remove_exceptions'] 1m59.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/pre_remove_exceptions'] 1m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m59.5s DUMP: install ok installed adapterremoval adapterremoval 2.3.1-3 install ok installed adduser adduser 3.118+deb11u1 install ok installed ant ant 1.10.9-4 install ok installed ant-optional ant-optional 1.10.9-4 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u8 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bcftools bcftools 1.11-1 install ok installed bedtools bedtools 2.30.0+dfsg-1 install ok installed bowtie2 bowtie2 2.4.2-2+b3 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed bwa bwa 0.7.17-6+b1 install ok installed ca-certificates ca-certificates 20210119 install ok installed ca-certificates-java ca-certificates-java 20190909+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 default-jre default-jre 2:1.11-72 install ok installed default-jre-headless default-jre-headless 2:1.11-72 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 examl examl 3.0.22-1+b4 install ok installed findutils findutils 4.8.0-1 install ok installed fontconfig fontconfig 2.13.1-4.2 install ok installed fontconfig-config fontconfig-config 2.13.1-4.2 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-2 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 ibverbs-providers:amd64 ibverbs-providers 33.2-1 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed java-common java-common 0.72 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libactivation-java libactivation-java 1.2.0-2 install ok installed libaopalliance-java libaopalliance-java 20070526-6 install ok installed libapache-pom-java libapache-pom-java 18-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libargs4j-java libargs4j-java 2.33-1.1 install ok installed libasound2:amd64 libasound2 1.2.4-1.1 install ok installed libasound2-data libasound2-data 1.2.4-1.1 install ok installed libatinject-jsr330-api-java libatinject-jsr330-api-java 1.0+ds1-5 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 libavahi-client3:amd64 libavahi-client3 0.8-5+deb11u2 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-5+deb11u2 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-5+deb11u2 install ok installed libbarclay-java libbarclay-java 2.1.0-3.1 install ok installed libblas3:amd64 libblas3 3.9.0-3+deb11u1 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b2 install ok installed libbsd0:amd64 libbsd0 0.11.3-1+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+deb11u7 install ok installed libc6:amd64 libc6 2.31-13+deb11u7 install ok installed libcairo2:amd64 libcairo2 1.16.0-5 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcbor0:amd64 libcbor0 0.5.0+dfsg-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 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcommons-cli-java libcommons-cli-java 1.4-2 install ok installed libcommons-codec-java libcommons-codec-java 1.15-1 install ok installed libcommons-compress-java libcommons-compress-java 1.20-1 install ok installed libcommons-io-java libcommons-io-java 2.8.0-1 install ok installed libcommons-jexl2-java libcommons-jexl2-java 2.1.1-5 install ok installed libcommons-lang3-java libcommons-lang3-java 3.11-1 install ok installed libcommons-logging-java libcommons-logging-java 1.2-2 install ok installed libcommons-math3-java libcommons-math3-java 3.6.1-3 install ok installed libcommons-parent-java libcommons-parent-java 43-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libcups2:amd64 libcups2 2.3.3op2-3+deb11u6 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.74.0-1.3+deb11u11 install ok installed libcurl4:amd64 libcurl4 7.74.0-1.3+deb11u11 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.12.28-0+deb11u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libdeflate0:amd64 libdeflate0 1.7-1 install ok installed libdom4j-java libdom4j-java 2.1.3-1 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.104-1 install ok installed libdrm-common libdrm-common 2.4.104-1 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.104-1 install ok installed libdrm-nouveau2:amd64 libdrm-nouveau2 2.4.104-1 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.104-1 install ok installed libdrm2:amd64 libdrm2 2.4.104-1 install ok installed libdtd-parser-java libdtd-parser-java 1.2-1 install ok installed libedit2:amd64 libedit2 3.1-20191231-2+b1 install ok installed libelf1:amd64 libelf1 0.183-1 install ok installed libevent-core-2.1-7:amd64 libevent-core-2.1-7 2.1.12-stable-1 install ok installed libevent-pthreads-2.1-7:amd64 libevent-pthreads-2.1-7 2.1.12-stable-1 install ok installed libexpat1:amd64 libexpat1 2.2.10-2+deb11u5 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libfabric1 libfabric1 1.11.0-2 install ok installed libfastinfoset-java libfastinfoset-java 1.2.12-3 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libfido2-1:amd64 libfido2-1 1.6.0-2 install ok installed libfontconfig1:amd64 libfontconfig1 2.13.1-4.2 install ok installed libfreemarker-java libfreemarker-java 2.3.23-11 install ok installed libfreetype6:amd64 libfreetype6 2.10.4+dfsg-1+deb11u1 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2+deb11u1 install ok installed libgatk-native-bindings-java libgatk-native-bindings-java 1.0.0-2.1 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 libgdbm-compat4:amd64 libgdbm-compat4 1.19-2 install ok installed libgdbm6:amd64 libgdbm6 1.19-2 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 10.2.1-6 install ok installed libgif7:amd64 libgif7 5.1.9-2 install ok installed libgkl-java libgkl-java 0.8.7+dfsg-1 install ok installed libgl1:amd64 libgl1 1.3.2-1 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 20.3.5-1 install ok installed libglapi-mesa:amd64 libglapi-mesa 20.3.5-1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.66.8-1+deb11u1 install ok installed libglvnd0:amd64 libglvnd0 1.3.2-1 install ok installed libglx-mesa0:amd64 libglx-mesa0 20.3.5-1 install ok installed libglx0:amd64 libglx0 1.3.2-1 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 libgomp1:amd64 libgomp1 10.2.1-6 install ok installed libgoogle-gson-java libgoogle-gson-java 2.8.6-1+deb11u1 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgsl-dev libgsl-dev 2.6+dfsg-2 install ok installed libgsl25:amd64 libgsl25 2.6+dfsg-2 install ok installed libgslcblas0:amd64 libgslcblas0 2.6+dfsg-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libguava-java libguava-java 29.0-6 install ok installed libguice-java libguice-java 4.2.3-2 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 2.7.4-1 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libhts3:amd64 libhts3 1.11-4 install ok installed libhtsjdk-java libhtsjdk-java 2.23.0+dfsg-2 install ok installed libhttpclient-java libhttpclient-java 4.5.13-2 install ok installed libhttpcore-java libhttpcore-java 4.4.14-1 install ok installed libhwloc-plugins:amd64 libhwloc-plugins 2.4.1+dfsg-1 install ok installed libhwloc15:amd64 libhwloc15 2.4.1+dfsg-1 install ok installed libibverbs1:amd64 libibverbs1 33.2-1 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 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 install ok installed libjaxen-java libjaxen-java 1.1.6-4 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjoptsimple-java libjoptsimple-java 5.0.4-4 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.0.6-4 install ok installed libjsoup-java libjsoup-java 1.10.2-2 install ok installed libjsr305-java libjsr305-java 0.1~+svn49-11 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 liblapack3:amd64 liblapack3 3.9.0-3+deb11u1 install ok installed liblcms2-2:amd64 liblcms2-2 2.12~rc1-2 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 install ok installed liblightcouch-java liblightcouch-java 0.0.6-1.1 install ok installed libllvm11:amd64 libllvm11 1:11.0.1-2 install ok installed liblog4j2-java liblog4j2-java 2.17.1-1~deb11u1 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 libmaven-file-management-java libmaven-file-management-java 3.0.0-1 install ok installed libmaven-parent-java libmaven-parent-java 31-2 install ok installed libmaven-resolver-java libmaven-resolver-java 1.4.2-3 install ok installed libmaven-shared-io-java libmaven-shared-io-java 3.0.0-3 install ok installed libmaven-shared-utils-java libmaven-shared-utils-java 3.3.0-1+deb11u1 install ok installed libmaven3-core-java libmaven3-core-java 3.6.3-5 install ok installed libmd0:amd64 libmd0 1.0.3-3 install ok installed libmongodb-java libmongodb-java 3.6.3-2 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-1 install ok installed libncurses6:amd64 libncurses6 6.2+20201114-2+deb11u2 install ok installed libncursesw6:amd64 libncursesw6 6.2+20201114-2+deb11u2 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.43.0-1+deb11u1 install ok installed libngs-java:amd64 libngs-java 2.10.9-1 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 3.4.0-1+b1 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.4.0-1+b1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libnspr4:amd64 libnspr4 2:4.29-1 install ok installed libnss3:amd64 libnss3 2:3.61-1+deb11u3 install ok installed libnuma1:amd64 libnuma1 2.0.12-1+b1 install ok installed libopenblas-dev:amd64 libopenblas-dev 0.3.13+ds-3+deb11u1 install ok installed libopenblas-pthread-dev:amd64 libopenblas-pthread-dev 0.3.13+ds-3+deb11u1 install ok installed libopenblas0:amd64 libopenblas0 0.3.13+ds-3+deb11u1 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.13+ds-3+deb11u1 install ok installed libopenmpi3:amd64 libopenmpi3 4.1.0-10 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 libpango-1.0-0:amd64 libpango-1.0-0 1.46.2-3 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.46.2-3 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.46.2-3 install ok installed libpaper-utils libpaper-utils 1.1.28+b1 install ok installed libpaper1:amd64 libpaper1 1.1.28+b1 install ok installed libpciaccess0:amd64 libpciaccess0 0.16-1 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 libpcsclite1:amd64 libpcsclite1 1.9.1-1 install ok installed libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u3 install ok installed libpicard-java libpicard-java 2.24.1+dfsg-1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.40.0-1.1~deb11u1 install ok installed libplexus-archiver-java libplexus-archiver-java 3.6.0-2 install ok installed libplexus-cipher-java libplexus-cipher-java 1.8-2 install ok installed libplexus-classworlds-java libplexus-classworlds-java 2.6.0-1 install ok installed libplexus-component-annotations-java libplexus-component-annotations-java 2.1.0-1 install ok installed libplexus-interpolation-java libplexus-interpolation-java 1.26-1 install ok installed libplexus-io-java libplexus-io-java 3.2.0-1.1 install ok installed libplexus-sec-dispatcher-java libplexus-sec-dispatcher-java 1.4-4 install ok installed libplexus-utils2-java libplexus-utils2-java 3.3.0-1 install ok installed libpmix2:amd64 libpmix2 4.0.0-4.1+deb11u1 install ok installed libpng16-16:amd64 libpng16-16 1.6.37-3 install ok installed libpsl5:amd64 libpsl5 0.21.0-1.2 install ok installed libpsm-infinipath1 libpsm-infinipath1 3.3+20.604758e7-6.1 install ok installed libpsm2-2 libpsm2-2 11.2.185-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.9.2-3 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 10.2.1-6 install ok installed librdmacm1:amd64 librdmacm1 33.2-1 install ok installed libreadline8:amd64 libreadline8 8.1-1 install ok installed librelaxng-datatype-java librelaxng-datatype-java 1.0+ds1-3.1 install ok installed librngom-java librngom-java 2.3.0.1-10 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-2.1+deb11u1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-2.1+deb11u1 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 libsensors-config libsensors-config 1:3.6.0-7 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-7 install ok installed libsepol1:amd64 libsepol1 3.1-1 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 1.7.30-1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libsnappy-java libsnappy-java 1.1.8.3-1 install ok installed libsnappy-jni libsnappy-jni 1.1.8.3-1 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.1.8-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.34.1-3 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssh2-1:amd64 libssh2-1 1.9.0-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstax-ex-java libstax-ex-java 1.7.8-3 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libstreambuffer-java libstreambuffer-java 1.5.4-1.1 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 libtbb2:amd64 libtbb2 2020.3-1 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.11+dfsg-1 install ok installed libthai-data libthai-data 0.1.28-3 install ok installed libthai0:amd64 libthai0 0.1.28-3 install ok installed libtiff5:amd64 libtiff5 4.2.0-1+deb11u5 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 libtk8.6:amd64 libtk8.6 8.6.11-2 install ok installed libtxw2-java libtxw2-java 2.3.0.1-10 install ok installed libucx0:amd64 libucx0 1.10.1~rc1+really.1.10.0-1 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 libvulkan1:amd64 libvulkan1 1.2.162.0-1 install ok installed libwagon-http-java libwagon-http-java 3.3.4-1 install ok installed libwagon-provider-api-java libwagon-provider-api-java 3.3.4-1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2.1+deb11u2 install ok installed libx11-6:amd64 libx11-6 2:1.7.2-1+deb11u2 install ok installed libx11-data libx11-data 2:1.7.2-1+deb11u2 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.7.2-1+deb11u2 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-dri2-0:amd64 libxcb-dri2-0 1.14-3 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.14-3 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.14-3 install ok installed libxcb-present0:amd64 libxcb-present0 1.14-3 install ok installed libxcb-render0:amd64 libxcb-render0 1.14-3 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.14-3 install ok installed libxcb-sync1:amd64 libxcb-sync1 1.14-3 install ok installed libxcb-xfixes0:amd64 libxcb-xfixes0 1.14-3 install ok installed libxcb1:amd64 libxcb1 1.14-3 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.5-2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.3-1.1 install ok installed libxfixes3:amd64 libxfixes3 1:5.0.3-2 install ok installed libxft2:amd64 libxft2 2.3.2-2 install ok installed libxi6:amd64 libxi6 2:1.7.10-1 install ok installed libxml-commons-resolver1.1-java libxml-commons-resolver1.1-java 1.2-11 install ok installed libxml2:amd64 libxml2 2.9.10+dfsg-6.7+deb11u4 install ok installed libxnvctrl0:amd64 libxnvctrl0 470.141.03-1~deb11u1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1 install ok installed libxshmfence1:amd64 libxshmfence1 1.3-1 install ok installed libxsom-java libxsom-java 2.3.0.1-10 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6:amd64 libxt6 1:1.2.0-1 install ok installed libxtst6:amd64 libxtst6 2:1.2.3-1 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libxz-java libxz-java 1.8-2 install ok installed libz3-4:amd64 libz3-4 4.8.10-1 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed littler littler 0.3.12-1 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 mafft mafft 7.475-1 install ok installed mapdamage mapdamage 2.2.1+dfsg-1 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed media-types media-types 4.0.0 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 ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.2.14-2 install ok installed openjdk-11-jre:amd64 openjdk-11-jre 11.0.21+9-1~deb11u1 install ok installed openjdk-11-jre-headless:amd64 openjdk-11-jre-headless 11.0.21+9-1~deb11u1 install ok installed openmpi-bin openmpi-bin 4.1.0-10 install ok installed openmpi-common openmpi-common 4.1.0-10 install ok installed openssh-client openssh-client 1:8.4p1-5+deb11u3 install ok installed openssl openssl 1.1.1w-0+deb11u1 install ok installed paleomix paleomix 1.3.2-1 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl perl 5.32.1-4+deb11u3 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.1-4+deb11u3 install ok installed phylip phylip 1:3.697+dfsg-2 install ok installed picard-tools picard-tools 2.24.1+dfsg-1 install ok installed python3 python3 3.9.2-3 install ok installed python3-coloredlogs python3-coloredlogs 7.3-2 install ok installed python3-configargparse python3-configargparse 1.2.3-1 install ok installed python3-humanfriendly python3-humanfriendly 9.1-1 install ok installed python3-minimal python3-minimal 3.9.2-3 install ok installed python3-pysam python3-pysam 0.15.4+ds-3+b2 install ok installed python3-ruamel.yaml python3-ruamel.yaml 0.16.12-2 install ok installed python3-ruamel.yaml.clib:amd64 python3-ruamel.yaml.clib 0.2.2-1+b2 install ok installed python3-setproctitle:amd64 python3-setproctitle 1.2.1-1+b1 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 4.0.4-1 install ok installed r-cran-assertthat r-cran-assertthat 0.2.1-2 install ok installed r-cran-brio r-cran-brio 1.1.1-1 install ok installed r-cran-callr r-cran-callr 3.5.1-1 install ok installed r-cran-cli r-cran-cli 2.3.0-1 install ok installed r-cran-codetools r-cran-codetools 0.2-18-1 install ok installed r-cran-colorspace r-cran-colorspace 2.0-0+dfsg-1 install ok installed r-cran-crayon r-cran-crayon 1.4.0-1 install ok installed r-cran-desc r-cran-desc 1.2.0-3 install ok installed r-cran-diffobj r-cran-diffobj 0.3.2-1 install ok installed r-cran-digest r-cran-digest 0.6.27-1 install ok installed r-cran-ellipsis r-cran-ellipsis 0.3.1-1 install ok installed r-cran-evaluate r-cran-evaluate 0.14-2 install ok installed r-cran-fansi r-cran-fansi 0.4.2-1 install ok installed r-cran-farver r-cran-farver 2.0.3-1+b1 install ok installed r-cran-foreach r-cran-foreach 1.5.1-1 install ok installed r-cran-gam r-cran-gam 1.20-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.3.3+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.4.2-1 install ok installed r-cran-gtable r-cran-gtable 0.3.0+dfsg-2 install ok installed r-cran-inline r-cran-inline 0.3.17-1 install ok installed r-cran-isoband r-cran-isoband 0.2.3-2 install ok installed r-cran-iterators r-cran-iterators 1.0.13-1 install ok installed r-cran-jsonlite r-cran-jsonlite 1.7.2+dfsg-1 install ok installed r-cran-labeling r-cran-labeling 0.4.2-1 install ok installed r-cran-lattice r-cran-lattice 0.20-41-1+b1 install ok installed r-cran-lifecycle r-cran-lifecycle 0.2.0-2 install ok installed r-cran-littler r-cran-littler 0.3.12-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.1-1 install ok installed r-cran-mass r-cran-mass 7.3-53.1-1 install ok installed r-cran-matrix r-cran-matrix 1.3-2-1 install ok installed r-cran-mgcv r-cran-mgcv 1.8-34-1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-2 install ok installed r-cran-nlme r-cran-nlme 3.1.152-1 install ok installed r-cran-pillar r-cran-pillar 1.4.7-1 install ok installed r-cran-pkgbuild r-cran-pkgbuild 1.2.0-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.1-1 install ok installed r-cran-pkgload r-cran-pkgload 1.1.0-1 install ok installed r-cran-praise r-cran-praise 1.0.0-4 install ok installed r-cran-prettyunits r-cran-prettyunits 1.1.1-2 install ok installed r-cran-processx r-cran-processx 3.4.5-1 install ok installed r-cran-ps r-cran-ps 1.5.0-1 install ok installed r-cran-r6 r-cran-r6 2.5.0-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-2-3 install ok installed r-cran-rcpp r-cran-rcpp 1.0.6-1 install ok installed r-cran-rcppgsl r-cran-rcppgsl 0.3.8-1 install ok installed r-cran-rematch2 r-cran-rematch2 2.1.2-2 install ok installed r-cran-rlang r-cran-rlang 0.4.10-1 install ok installed r-cran-rprojroot r-cran-rprojroot 2.0.2-1 install ok installed r-cran-rstudioapi r-cran-rstudioapi 0.13-1 install ok installed r-cran-scales r-cran-scales 1.1.1-1 install ok installed r-cran-testthat r-cran-testthat 3.0.1-1 install ok installed r-cran-tibble r-cran-tibble 3.0.6+dfsg-1 install ok installed r-cran-utf8 r-cran-utf8 1.1.4-2 install ok installed r-cran-vctrs r-cran-vctrs 0.3.6-1 install ok installed r-cran-viridislite r-cran-viridislite 0.3.0-4 install ok installed r-cran-waldo r-cran-waldo 0.2.3-2 install ok installed r-cran-withr r-cran-withr 2.4.1-1 install ok installed radiant radiant 2.7.1+dfsg-4 install ok installed raxml raxml 8.2.12+dfsg-6+b4 install ok installed readline-common readline-common 8.1-1 install ok installed samtools samtools 1.11-1 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.14 install ok installed seqtk seqtk 1.3-2 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 2021a-1+deb11u11 install ok installed ucf ucf 3.0043 install ok installed unzip unzip 6.0-26+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed x11-common x11-common 1:7.7+22 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-12 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 1m59.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', 'remove', '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:amd64', 'java-common', 'libactivation-java', 'libaopalliance-java', 'libapache-pom-java', 'libargs4j-java', 'libasound2:amd64', 'libasound2-data', 'libatinject-jsr330-api-java', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcbor0: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', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4: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', 'libelf1:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libexpat1:amd64', 'libfabric1', 'libfastinfoset-java', 'libfido2-1:amd64', 'libfontconfig1:amd64', 'libfreemarker-java', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgatk-native-bindings-java', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', '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', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl25:amd64', 'libgslcblas0:amd64', 'libguava-java', 'libguice-java', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu67: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', 'liblightcouch-java', 'libllvm11:amd64', 'liblog4j2-java', 'libmaven-file-management-java', 'libmaven-parent-java', 'libmaven-resolver-java', 'libmaven-shared-io-java', 'libmaven-shared-utils-java', 'libmaven3-core-java', 'libmd0:amd64', 'libmongodb-java', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java: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', 'libopenmpi3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32: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', 'libpmix2:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1:amd64', 'libreadline8:amd64', 'librelaxng-datatype-java', 'librngom-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsisu-inject-java', 'libsisu-plexus-java', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstax-ex-java', 'libstreambuffer-java', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtk8.6:amd64', 'libtxw2-java', 'libucx0:amd64', 'libvulkan1:amd64', 'libwagon-http-java', 'libwagon-provider-api-java', 'libwebp6: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-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxsom-java', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libxz-java', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'ocl-icd-libopencl1:amd64', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', '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:amd64', 'python3-setproctitle:amd64', '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', 'paleomix'] 2m4.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: 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, 0 newly installed, 330 to remove and 0 not upgraded. After this operation, 826 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 ... 23207 files and directories currently installed.) Removing paleomix (1.3.2-1) ... Removing adapterremoval (2.3.1-3) ... Removing picard-tools (2.24.1+dfsg-1) ... Removing libpicard-java (2.24.1+dfsg-1) ... Removing libhtsjdk-java (2.23.0+dfsg-2) ... Removing libjaxb-java (2.3.0.1-10) ... Removing libtxw2-java (2.3.0.1-10) ... Removing bcftools (1.11-1) ... Removing bedtools (2.30.0+dfsg-1) ... Removing bowtie2 (2.4.2-2+b3) ... Removing bwa (0.7.17-6+b1) ... Removing default-jre (2:1.11-72) ... Removing openjdk-11-jre:amd64 (11.0.21+9-1~deb11u1) ... Removing default-jre-headless (2:1.11-72) ... Removing mapdamage (2.2.1+dfsg-1) ... Removing r-cran-ggplot2 (3.3.3+dfsg-1) ... Removing r-cran-mgcv (1.8-34-1) ... Removing r-cran-matrix (1.3-2-1) ... Removing r-cran-rcppgsl (0.3.8-1) ... Removing r-cran-rcpp (1.0.6-1) ... Removing examl (3.0.22-1+b4) ... Removing openmpi-bin (4.1.0-10) ... Removing libopenmpi3:amd64 (4.1.0-10) ... Removing libucx0:amd64 (1.10.1~rc1+really.1.10.0-1) ... Removing libfabric1 (1.11.0-2) ... Removing ibverbs-providers:amd64 (33.2-1) ... 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 libcommons-jexl2-java (2.1.1-5) ... Removing libbarclay-java (2.1.0-3.1) ... Removing r-cran-gam (1.20-1) ... Removing liblapack3:amd64 (3.9.0-3+deb11u1) ... Removing libblas3:amd64 (3.9.0-3+deb11u1) ... Removing samtools (1.11-1) ... Removing libgl1:amd64 (1.3.2-1) ... Removing libglx0:amd64 (1.3.2-1) ... Removing libglx-mesa0:amd64 (20.3.5-1) ... Removing libx11-xcb1:amd64 (2:1.7.2-1+deb11u2) ... Removing libpmix2:amd64 (4.0.0-4.1+deb11u1) ... Removing libhwloc-plugins:amd64 (2.4.1+dfsg-1) ... Removing libxnvctrl0:amd64 (470.141.03-1~deb11u1) ... Removing libxcb-xfixes0:amd64 (1.14-3) ... Removing openssh-client (1:8.4p1-5+deb11u3) ... Removing libfido2-1:amd64 (1.6.0-2) ... Removing libcbor0:amd64 (0.5.0+dfsg-2) ... Removing liblog4j2-java (2.17.1-1~deb11u1) ... Removing liblightcouch-java (0.0.6-1.1) ... Removing libcommons-math3-java (3.6.1-3) ... Removing libgl1-mesa-dri:amd64 (20.3.5-1) ... Removing libdrm-amdgpu1:amd64 (2.4.104-1) ... Removing libdrm-intel1:amd64 (2.4.104-1) ... Removing libdrm-radeon1:amd64 (2.4.104-1) ... Removing libdrm-nouveau2:amd64 (2.4.104-1) ... Removing libdtd-parser-java (1.2-1) ... Removing libllvm11:amd64 (1:11.0.1-2) ... Removing libedit2:amd64 (3.1-20191231-2+b1) ... Removing libelf1:amd64 (0.183-1) ... Removing libevent-pthreads-2.1-7:amd64 (2.1.12-stable-1) ... Removing libevent-core-2.1-7:amd64 (2.1.12-stable-1) ... Removing python3-ruamel.yaml (0.16.12-2) ... Removing python3-ruamel.yaml.clib:amd64 (0.2.2-1+b2) ... Removing python3-pysam (0.15.4+ds-3+b2) ... Removing python3-setproctitle:amd64 (1.2.1-1+b1) ... Removing python3-configargparse (1.2.3-1) ... Removing libfreemarker-java (2.3.23-11) ... Removing libgatk-native-bindings-java (1.0.0-2.1) ... Removing mafft (7.475-1) ... Removing perl (5.32.1-4+deb11u3) ... Removing libperl5.32:amd64 (5.32.1-4+deb11u3) ... Removing libgdbm-compat4:amd64 (1.19-2) ... Removing libgdbm6:amd64 (1.19-2) ... Removing libopenblas-dev:amd64 (0.3.13+ds-3+deb11u1) ... Removing libopenblas-pthread-dev:amd64 (0.3.13+ds-3+deb11u1) ... Removing libopenblas0:amd64 (0.3.13+ds-3+deb11u1) ... Removing libgif7:amd64 (5.1.9-2) ... Removing libgkl-java (0.8.7+dfsg-1) ... Removing libglapi-mesa:amd64 (20.3.5-1) ... Removing libglvnd0:amd64 (1.3.2-1) ... Removing libgoogle-gson-java (2.8.6-1+deb11u1) ... Removing libgsl-dev (2.6+dfsg-2) ... Removing libgsl25:amd64 (2.6+dfsg-2) ... Removing libgslcblas0:amd64 (2.6+dfsg-2) ... Removing libhwloc15:amd64 (2.4.1+dfsg-1) ... Removing librdmacm1:amd64 (33.2-1) ... Removing libibverbs1:amd64 (33.2-1) ... Removing libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Removing libjoptsimple-java (5.0.4-4) ... Removing libmongodb-java (3.6.3-2) ... Removing libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Removing libngs-java:amd64 (2.10.9-1) ... Removing libngs-sdk-dev:amd64 (2.10.9-1) ... Removing libngs-sdk2:amd64 (2.10.9-1) ... Removing libnl-route-3-200:amd64 (3.4.0-1+b1) ... Removing libnl-3-200:amd64 (3.4.0-1+b1) ... Removing libpsm2-2 (11.2.185-1) ... Removing libnuma1:amd64 (2.0.12-1+b1) ... Removing libpciaccess0:amd64 (0.16-1) ... Removing libpsm-infinipath1 (3.3+20.604758e7-6.1) ... 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 libxsom-java (2.3.0.1-10) ... Removing librngom-java (2.3.0.1-10) ... Removing librelaxng-datatype-java (1.0+ds1-3.1) ... Removing libsensors5:amd64 (1:3.6.0-7) ... Removing libsensors-config (1:3.6.0-7) ... Removing libtbb2:amd64 (2020.3-1) ... Removing libvulkan1:amd64 (1.2.162.0-1) ... Removing libxcb-dri2-0:amd64 (1.14-3) ... Removing libxcb-dri3-0:amd64 (1.14-3) ... Removing libxcb-glx0:amd64 (1.14-3) ... Removing libxcb-present0:amd64 (1.14-3) ... Removing libxcb-sync1:amd64 (1.14-3) ... Removing libxdamage1:amd64 (1:1.1.5-2) ... Removing libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Removing libxfixes3:amd64 (1:5.0.3-2) ... Removing libxtst6:amd64 (2:1.2.3-1) ... Removing libxi6:amd64 (2:1.7.10-1) ... Removing libxml-commons-resolver1.1-java (1.2-11) ... Removing libxshmfence1:amd64 (1.3-1) ... Removing libz3-4:amd64 (4.8.10-1) ... Removing littler (0.3.12-1) ... Removing ocl-icd-libopencl1:amd64 (2.2.14-2) ... Removing openmpi-common (4.1.0-10) ... Removing perl-modules-5.32 (5.32.1-4+deb11u3) ... Removing phylip (1:3.697+dfsg-2) ... Removing python3-coloredlogs (7.3-2) ... Removing python3-humanfriendly (9.1-1) ... Removing r-cran-isoband (0.2.3-2) ... Removing r-cran-testthat (3.0.1-1) ... Removing r-cran-pkgload (1.1.0-1) ... Removing r-cran-waldo (0.2.3-2) ... Removing r-cran-brio (1.1.1-1) ... Removing r-cran-pkgbuild (1.2.0-1) ... Removing r-cran-callr (3.5.1-1) ... Removing r-cran-foreach (1.5.1-1) ... Removing r-cran-codetools (0.2-18-1) ... Removing r-cran-scales (1.1.1-1) ... Removing r-cran-munsell (0.5.0-2) ... Removing r-cran-colorspace (2.0-0+dfsg-1) ... Removing r-cran-rematch2 (2.1.2-2) ... Removing r-cran-tibble (3.0.6+dfsg-1) ... Removing r-cran-pillar (1.4.7-1) ... Removing r-cran-diffobj (0.3.2-1) ... Removing r-cran-vctrs (0.3.6-1) ... Removing r-cran-digest (0.6.27-1) ... Removing r-cran-ellipsis (0.3.1-1) ... Removing r-cran-evaluate (0.14-2) ... Removing r-cran-fansi (0.4.2-1) ... Removing r-cran-farver (2.0.3-1+b1) ... Removing r-cran-lifecycle (0.2.0-2) ... Removing r-cran-gtable (0.3.0+dfsg-2) ... Removing r-cran-inline (0.3.17-1) ... Removing r-cran-iterators (1.0.13-1) ... Removing r-cran-jsonlite (1.7.2+dfsg-1) ... Removing r-cran-labeling (0.4.2-1) ... Removing r-cran-nlme (3.1.152-1) ... Removing r-cran-lattice (0.20-41-1+b1) ... Removing r-cran-littler (0.3.12-1) ... Removing r-cran-magrittr (2.0.1-1) ... Removing r-cran-mass (7.3-53.1-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-pkgkitten (0.2.1-1) ... Removing r-cran-praise (1.0.0-4) ... Removing r-cran-prettyunits (1.1.1-2) ... Removing r-cran-processx (3.4.5-1) ... Removing r-cran-ps (1.5.0-1) ... Removing r-cran-rcolorbrewer (1.1-2-3) ... Removing r-cran-rlang (0.4.10-1) ... Removing r-cran-rstudioapi (0.13-1) ... Removing r-cran-utf8 (1.1.4-2) ... Removing r-cran-viridislite (0.3.0-4) ... Removing r-cran-withr (2.4.1-1) ... Removing radiant (2.7.1+dfsg-4) ... Removing raxml (8.2.12+dfsg-6+b4) ... Removing seqtk (1.3-2) ... Removing libhts3:amd64 (1.11-4) ... Removing libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u11) ... Removing libdrm2:amd64 (2.4.104-1) ... Removing libdrm-common (2.4.104-1) ... Removing python3 (3.9.2-3) ... Removing python3-minimal (3.9.2-3) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing libpython3-stdlib:amd64 (3.9.2-3) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec3:amd64 (2.5.1-1) ... Removing libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing media-types (4.0.0) ... Removing r-cran-desc (1.2.0-3) ... Removing r-cran-cli (2.3.0-1) ... Removing r-cran-assertthat (0.2.1-2) ... Removing r-cran-crayon (1.4.0-1) ... Removing r-cran-glue (1.4.2-1) ... Removing r-cran-r6 (2.5.0-1) ... Removing r-cran-rprojroot (2.0.2-1) ... Removing r-base-core (4.0.4-1) ... Removing libpangocairo-1.0-0:amd64 (1.46.2-3) ... Removing libpangoft2-1.0-0:amd64 (1.46.2-3) ... Removing libpango-1.0-0:amd64 (1.46.2-3) ... Removing fontconfig (2.13.1-4.2) ... Removing libtk8.6:amd64 (8.6.11-2) ... Removing libxft2:amd64 (2.3.2-2) ... Removing libcairo2:amd64 (1.16.0-5) ... Removing libcurl4:amd64 (7.74.0-1.3+deb11u11) ... Removing libxt6:amd64 (1:1.2.0-1) ... Removing libthai0:amd64 (0.1.28-3) ... Removing libdatrie1:amd64 (0.2.13-1) ... Removing libtiff5:amd64 (4.2.0-1+deb11u5) ... Removing libdeflate0:amd64 (1.7-1) ... Removing libfribidi0:amd64 (1.0.8-2+deb11u1) ... Removing libopenblas0-pthread:amd64 (0.3.13+ds-3+deb11u1) ... Removing libgfortran5:amd64 (10.2.1-6) ... Removing libgomp1:amd64 (10.2.1-6) ... Removing libicu67:amd64 (67.1-7) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing libnghttp2-14:amd64 (1.43.0-1+deb11u1) ... Removing libpaper-utils (1.1.28+b1) ... Removing libpaper1:amd64 (1.1.28+b1) ... Removing libpixman-1-0:amd64 (0.40.0-1.1~deb11u1) ... Removing libpsl5:amd64 (0.21.0-1.2) ... Removing libquadmath0:amd64 (10.2.1-6) ... Removing libreadline8:amd64 (8.1-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libssh2-1:amd64 (1.9.0-2) ... Removing libtcl8.6:amd64 (8.6.11+dfsg-1) ... Removing libthai-data (0.1.28-3) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libxcb-render0:amd64 (1.14-3) ... Removing libxcb-shm0:amd64 (1.14-3) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing readline-common (8.1-1) ... Removing unzip (6.0-26+deb11u1) ... Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-12) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libxext6:amd64 (2:1.3.3-1.1) ... Removing x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libx11-6:amd64 (2:1.7.2-1+deb11u2) ... Removing libxcb1:amd64 (1.14-3) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.3-1+deb11u1) ... Removing libmd0:amd64 (1.0.3-3) ... Removing libx11-data (2:1.7.2-1+deb11u2) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing libistack-commons-java (3.0.6-5) ... Removing ant-optional (1.10.9-4) ... Removing ant (1.10.9-4) ... Removing ca-certificates-java (20190909+deb11u1) ... Removing openjdk-11-jre-headless:amd64 (11.0.21+9-1~deb11u1) ... Removing ca-certificates (20210119) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libfontconfig1:amd64 (2.13.1-4.2) ... Removing fontconfig-config (2.13.1-4.2) ... Removing fonts-dejavu-core (2.37-2) ... Removing java-common (0.72) ... Removing libactivation-java (1.2.0-2) ... Removing libmaven-file-management-java (3.0.0-1) ... Removing libmaven-shared-io-java (3.0.0-3) ... Removing libmaven3-core-java (3.6.3-5) ... Removing libguice-java (4.2.3-2) ... Removing libaopalliance-java (20070526-6) ... Removing libmaven-parent-java (31-2) ... Removing libargs4j-java (2.33-1.1) ... Removing libasound2:amd64 (1.2.4-1.1) ... Removing libasound2-data (1.2.4-1.1) ... Removing libguava-java (29.0-6) ... Removing libsisu-plexus-java (0.3.4-3) ... Removing libsisu-inject-java (0.3.4-2) ... Removing libcdi-api-java (1.2-3) ... Removing libatinject-jsr330-api-java (1.0+ds1-5) ... Removing libcups2:amd64 (2.3.3op2-3+deb11u6) ... Removing libavahi-client3:amd64 (0.8-5+deb11u2) ... Removing libavahi-common3:amd64 (0.8-5+deb11u2) ... Removing libavahi-common-data:amd64 (0.8-5+deb11u2) ... Removing libcommons-cli-java (1.4-2) ... Removing libwagon-http-java (3.3.4-1) ... Removing libhttpclient-java (4.5.13-2) ... Removing libcommons-codec-java (1.15-1) ... Removing libplexus-archiver-java (3.6.0-2) ... Removing libcommons-compress-java (1.20-1) ... Removing libplexus-io-java (3.2.0-1.1) ... Removing libmaven-shared-utils-java (3.3.0-1+deb11u1) ... Removing libcommons-io-java (2.8.0-1) ... Removing libcommons-lang3-java (3.11-1) ... Removing libdbus-1-3:amd64 (1.12.28-0+deb11u1) ... Removing libdom4j-java (2.1.3-1) ... Removing libexpat1:amd64 (2.2.10-2+deb11u5) ... Removing libharfbuzz0b:amd64 (2.7.4-1) ... Removing libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Removing libgeronimo-annotation-1.3-spec-java (1.3-1) ... Removing libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Removing libglib2.0-0:amd64 (2.66.8-1+deb11u1) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libhttpcore-java (4.4.14-1) ... Removing libjaxen-java (1.1.6-4) ... Removing libjpeg62-turbo:amd64 (1:2.0.6-4) ... Removing libjsoup-java (1.10.2-2) ... Removing libjsr305-java (0.1~+svn49-11) ... Removing liblcms2-2:amd64 (2.12~rc1-2) ... Removing libmaven-resolver-java (1.4.2-3) ... Removing libnss3:amd64 (2:3.61-1+deb11u3) ... Removing libnspr4:amd64 (2:4.29-1) ... Removing libpcsclite1:amd64 (1.9.1-1) ... Removing libplexus-sec-dispatcher-java (1.4-4) ... Removing libplexus-cipher-java (1.8-2) ... Removing libplexus-classworlds-java (2.6.0-1) ... Removing libplexus-component-annotations-java (2.1.0-1) ... Removing libplexus-interpolation-java (1.26-1) ... Removing libwagon-provider-api-java (3.3.4-1) ... Removing libplexus-utils2-java (3.3.0-1) ... Removing libpng16-16:amd64 (1.6.37-3) ... Removing libslf4j-java (1.7.30-1) ... Removing libsnappy-java (1.1.8.3-1) ... Removing libsnappy-jni (1.1.8.3-1) ... Removing libsnappy1v5:amd64 (1.1.8-1) ... Removing libsqlite3-0:amd64 (3.34.1-3) ... Removing libxz-java (1.8-2) ... Removing openssl (1.1.1w-0+deb11u1) ... Removing ucf (3.0043) ... Removing sensible-utils (0.0.14) ... Removing libcodemodel-java (2.6+jaxb2.3.0.1-10) ... Removing libcommons-logging-java (1.2-2) ... Removing libcommons-parent-java (43-1) ... Removing libapache-pom-java (18-1) ... Removing libbrotli1:amd64 (1.0.9-2+b2) ... Processing triggers for libc-bin (2.31-13+deb11u7) ... 2m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', 'remove', '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:amd64', 'java-common', 'libactivation-java', 'libaopalliance-java', 'libapache-pom-java', 'libargs4j-java', 'libasound2:amd64', 'libasound2-data', 'libatinject-jsr330-api-java', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcbor0: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', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4: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', 'libelf1:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libexpat1:amd64', 'libfabric1', 'libfastinfoset-java', 'libfido2-1:amd64', 'libfontconfig1:amd64', 'libfreemarker-java', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgatk-native-bindings-java', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', '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', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl25:amd64', 'libgslcblas0:amd64', 'libguava-java', 'libguice-java', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu67: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', 'liblightcouch-java', 'libllvm11:amd64', 'liblog4j2-java', 'libmaven-file-management-java', 'libmaven-parent-java', 'libmaven-resolver-java', 'libmaven-shared-io-java', 'libmaven-shared-utils-java', 'libmaven3-core-java', 'libmd0:amd64', 'libmongodb-java', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java: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', 'libopenmpi3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32: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', 'libpmix2:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1:amd64', 'libreadline8:amd64', 'librelaxng-datatype-java', 'librngom-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsisu-inject-java', 'libsisu-plexus-java', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstax-ex-java', 'libstreambuffer-java', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtk8.6:amd64', 'libtxw2-java', 'libucx0:amd64', 'libvulkan1:amd64', 'libwagon-http-java', 'libwagon-provider-api-java', 'libwebp6: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-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxsom-java', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libxz-java', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'ocl-icd-libopencl1:amd64', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', '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:amd64', 'python3-setproctitle:amd64', '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', 'paleomix'] 2m4.4s INFO: Running scripts post_remove 2m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_remove_exceptions'] 2m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_remove_exceptions'] 2m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg', '--purge', '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:amd64', 'java-common', 'libactivation-java', 'libaopalliance-java', 'libapache-pom-java', 'libargs4j-java', 'libasound2:amd64', 'libasound2-data', 'libatinject-jsr330-api-java', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcbor0: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', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4: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', 'libelf1:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libexpat1:amd64', 'libfabric1', 'libfastinfoset-java', 'libfido2-1:amd64', 'libfontconfig1:amd64', 'libfreemarker-java', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgatk-native-bindings-java', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', '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', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl25:amd64', 'libgslcblas0:amd64', 'libguava-java', 'libguice-java', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu67: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', 'liblightcouch-java', 'libllvm11:amd64', 'liblog4j2-java', 'libmaven-file-management-java', 'libmaven-parent-java', 'libmaven-resolver-java', 'libmaven-shared-io-java', 'libmaven-shared-utils-java', 'libmaven3-core-java', 'libmd0:amd64', 'libmongodb-java', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java: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', 'libopenmpi3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32: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', 'libpmix2:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1:amd64', 'libreadline8:amd64', 'librelaxng-datatype-java', 'librngom-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsisu-inject-java', 'libsisu-plexus-java', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstax-ex-java', 'libstreambuffer-java', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtk8.6:amd64', 'libtxw2-java', 'libucx0:amd64', 'libvulkan1:amd64', 'libwagon-http-java', 'libwagon-provider-api-java', 'libwebp6: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-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxsom-java', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libxz-java', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'ocl-icd-libopencl1:amd64', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', '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:amd64', 'python3-setproctitle:amd64', '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'] 2m5.6s DUMP: dpkg: warning: ignoring request to remove adapterremoval which isn't installed 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 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 (Reading database ... 6789 files and directories currently installed.) Purging configuration files for ca-certificates (20210119) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20190909+deb11u1) ... 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 (2.13.1-4.2) ... Purging configuration files for fontconfig-config (2.13.1-4.2) ... Purging configuration files for fonts-dejavu-core (2.37-2) ... dpkg: warning: while removing fonts-dejavu-core, directory '/usr/share/fonts/truetype/dejavu' not empty so not removed Purging configuration files for ibverbs-providers:amd64 (33.2-1) ... Purging configuration files for java-common (0.72) ... dpkg: warning: ignoring request to remove libactivation-java 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 which isn't installed dpkg: warning: ignoring request to remove libasound2-data which isn't installed dpkg: warning: ignoring request to remove libatinject-jsr330-api-java 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 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 libcups2 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdbus-1-3 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove 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 libelf1 which isn't installed dpkg: warning: ignoring request to remove libevent-core-2.1-7 which isn't installed dpkg: warning: ignoring request to remove libevent-pthreads-2.1-7 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfabric1 which isn't installed dpkg: warning: ignoring request to remove 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 dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 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 (20.3.5-1) ... dpkg: warning: ignoring request to remove libglapi-mesa which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.66.8-1+deb11u1) ... dpkg: warning: ignoring request to remove libglvnd0 which isn't installed dpkg: warning: ignoring request to remove libglx-mesa0 which isn't installed dpkg: warning: ignoring request to remove libglx0 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgoogle-gson-java which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libgsl-dev which isn't installed dpkg: warning: ignoring request to remove libgsl25 which isn't installed dpkg: warning: ignoring request to remove libgslcblas0 which isn't installed 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 libhts3 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 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 liblightcouch-java which isn't installed dpkg: warning: ignoring request to remove libllvm11 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 libmd0 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 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-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 (3.4.0-1+b1) ... 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 libopenmpi3 which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.28+b1) ... 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 libpmix2 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed Purging configuration files for libpsm-infinipath1 (3.3+20.604758e7-6.1) ... 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 libpython3.9-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 librdmacm1 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove librelaxng-datatype-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 (1:3.6.0-7) ... dpkg: warning: ignoring request to remove libsensors5 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 libssh2-1 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 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 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 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-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 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 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 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 libxt6 which isn't installed dpkg: warning: ignoring request to remove libxtst6 which isn't installed dpkg: warning: ignoring request to remove libxxf86vm1 which isn't installed dpkg: warning: ignoring request to remove 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 (4.0.0) ... 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 (11.0.21+9-1~deb11u1) ... Purging configuration files for openmpi-bin (4.1.0-10) ... dpkg: warning: ignoring request to remove openmpi-common which isn't installed Purging configuration files for openssh-client (1:8.4p1-5+deb11u3) ... dpkg: warning: while removing openssh-client, directory '/usr/lib/systemd' not empty so not removed Purging configuration files for openssl (1.1.1w-0+deb11u1) ... Purging configuration files for perl (5.32.1-4+deb11u3) ... 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 (3.9.2-3) ... 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 python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for r-base-core (4.0.4-1) ... 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-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 (2.7.1+dfsg-4) ... dpkg: warning: ignoring request to remove raxml which isn't installed Purging configuration files for readline-common (8.1-1) ... 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 ucf (3.0043) ... Purging configuration files for unzip (6.0-26+deb11u1) ... Purging configuration files for x11-common (1:7.7+22) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 2m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg', '--purge', '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:amd64', 'java-common', 'libactivation-java', 'libaopalliance-java', 'libapache-pom-java', 'libargs4j-java', 'libasound2:amd64', 'libasound2-data', 'libatinject-jsr330-api-java', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbarclay-java', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcbor0: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', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4: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', 'libelf1:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libexpat1:amd64', 'libfabric1', 'libfastinfoset-java', 'libfido2-1:amd64', 'libfontconfig1:amd64', 'libfreemarker-java', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgatk-native-bindings-java', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', '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', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgraphite2-3:amd64', 'libgsl-dev', 'libgsl25:amd64', 'libgslcblas0:amd64', 'libguava-java', 'libguice-java', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libice6:amd64', 'libicu67: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', 'liblightcouch-java', 'libllvm11:amd64', 'liblog4j2-java', 'libmaven-file-management-java', 'libmaven-parent-java', 'libmaven-resolver-java', 'libmaven-shared-io-java', 'libmaven-shared-utils-java', 'libmaven3-core-java', 'libmd0:amd64', 'libmongodb-java', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java: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', 'libopenmpi3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32: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', 'libpmix2:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1:amd64', 'libreadline8:amd64', 'librelaxng-datatype-java', 'librngom-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsisu-inject-java', 'libsisu-plexus-java', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstax-ex-java', 'libstreambuffer-java', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtk8.6:amd64', 'libtxw2-java', 'libucx0:amd64', 'libvulkan1:amd64', 'libwagon-http-java', 'libwagon-provider-api-java', 'libwebp6: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-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxsom-java', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libxz-java', 'libz3-4:amd64', 'littler', 'mafft', 'mapdamage', 'media-types', 'ocl-icd-libopencl1:amd64', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', '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:amd64', 'python3-setproctitle:amd64', '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'] 2m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg', '--purge', 'paleomix'] 2m5.6s DUMP: dpkg: warning: ignoring request to remove paleomix which isn't installed 2m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg', '--purge', 'paleomix'] 2m5.6s INFO: Running scripts post_purge 2m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_purge_exceptions'] 2m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_purge_exceptions'] 2m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg', '--purge', '--pending'] 2m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg', '--purge', '--pending'] 2m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg', '--remove', '--pending'] 2m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg', '--remove', '--pending'] 2m5.6s INFO: Running scripts post_test 2m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_test_exceptions'] 2m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'tmp/scripts/post_test_exceptions'] 2m5.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 2m6.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 2m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg-divert', '--list'] 2m6.0s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 2m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'dpkg-divert', '--list'] 2m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', 'clean'] 2m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv68ck88f', 'apt-get', 'clean'] 2m6.1s DEBUG: Recording chroot state 2m6.7s INFO: Warning: Package purging left files on system: /usr/local/share/fonts/ not owned /usr/local/share/fonts/.uuid not owned /usr/share/fonts/ owned by: fonts-dejavu-core /usr/share/fonts/.uuid not owned /usr/share/fonts/truetype/ owned by: fonts-dejavu-core /usr/share/fonts/truetype/.uuid not owned /usr/share/fonts/truetype/dejavu/ owned by: fonts-dejavu-core /usr/share/fonts/truetype/dejavu/.uuid not owned 2m7.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/shm'] 2m7.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/shm'] 2m7.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/console'] 2m7.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/console'] 2m7.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/ptmx'] 2m7.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/ptmx'] 2m7.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/pts'] 2m7.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/dev/pts'] 2m7.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/proc'] 2m7.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv68ck88f/proc'] 2m7.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 2m7.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpv68ck88f'] 2m7.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpv68ck88f 2m7.3s INFO: PASS: Upgrading between Debian distributions. 2m7.3s INFO: PASS: All tests. 2m7.3s INFO: piuparts run ends. ret=0 End: 2024-01-22 18:28:28 GMT