Start: 2024-03-12 18:48:50 GMT [stable] Package: roary Version: 3.13.0+dfsg-1 Installed-Size: 670 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Description: high speed stand alone pan genome pipeline Homepage: http://sanger-pathogens.github.io/Roary/ Description-md5: 6d457fd706202fc2ef292eacf7b46029 Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing Section: science Priority: optional Filename: pool/main/r/roary/roary_3.13.0+dfsg-1_all.deb Size: 183740 MD5sum: 991a49663368c3a0a660af3107720dad SHA256: 1732e00b165a0cee53b42fb9b142ea5491cd7de00b91be2cc8709297d999de66 [sid] Package: roary Version: 3.13.0+dfsg-1 Installed-Size: 670 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Description: high speed stand alone pan genome pipeline Homepage: http://sanger-pathogens.github.io/Roary/ Description-md5: 6d457fd706202fc2ef292eacf7b46029 Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing Section: science Priority: optional Filename: pool/main/r/roary/roary_3.13.0+dfsg-1_all.deb Size: 183740 MD5sum: 991a49663368c3a0a660af3107720dad SHA256: 1732e00b165a0cee53b42fb9b142ea5491cd7de00b91be2cc8709297d999de66 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt roary=3.13.0+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.3.1~202401311821~1.3-2-g28295102 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt roary=3.13.0+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp3qb0b834 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp3qb0b834 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp3qb0b834/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', 'update'] 0m1.6s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-yf', 'dist-upgrade'] 0m2.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-yf', 'dist-upgrade'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.4s DUMP: 29fcf27583012b383113cec2bf757015 - 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.4s INFO: Running scripts post_setup 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_setup_dummy_users'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_setup_dummy_users'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_setup_forbid_home'] 0m3.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_setup_forbid_home'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.4s 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' 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat 0m3.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 0m4.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 0m4.0s INFO: Running scripts is_testable 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/is_testable_uninstallable'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/is_testable_uninstallable'] 0m4.0s INFO: Running scripts pre_test 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_test_exceptions'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_test_exceptions'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_test_root_password'] 0m4.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_test_root_password'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m4.3s DUMP: Package: roary Version: 3.13.0+dfsg-1 Installed-Size: 670 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Description-en: high speed stand alone pan genome pipeline Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes. Description-md5: 6d457fd706202fc2ef292eacf7b46029 Homepage: http://sanger-pathogens.github.io/Roary/ Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing Section: science Priority: optional Filename: pool/main/r/roary/roary_3.13.0+dfsg-1_all.deb Size: 183740 MD5sum: 991a49663368c3a0a660af3107720dad SHA256: 1732e00b165a0cee53b42fb9b142ea5491cd7de00b91be2cc8709297d999de66 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m4.3s INFO: apt-cache knows about the following packages: roary 0m4.3s INFO: Running scripts pre_install 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_database-server'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_database-server'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_exceptions'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_exceptions'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_extras'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_extras'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'policy'] 0m4.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'policy'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'policy', 'roary'] 0m4.4s DUMP: roary: Installed: (none) Candidate: 3.13.0+dfsg-1 Version table: 3.13.0+dfsg-1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'policy', 'roary'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-y', 'install', 'roary'] 0m37.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bedtools bioperl ca-certificates cd-hit fasttree fontconfig fontconfig-config fonts-dejavu-core libalgorithm-c3-perl libalgorithm-diff-perl libarray-utils-perl libb-hooks-op-check-perl libbio-perl-perl libblas3 libbrotli1 libbsd0 libcairo2 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libcurl4 libdata-optlist-perl libdata-stag-perl libdatrie1 libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdigest-md5-file-perl libdist-checkconflicts-perl libdynaloader-functions-perl libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-slurper-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libharfbuzz0b libheap-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu67 libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo liblapack3 libldap-2.4-2 liblmdb0 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmd0 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmpdec3 libmro-compat-perl libncurses6 libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparse-yapp-perl libperl5.32 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-object-perl libsm6 libspiffy-perl libsqlite3-0 libssh2-1 libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-uplevel-perl libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl liburi-perl libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxrender1 libxss1 libxt6 mafft mcl media-types ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.32 perl-openssl-defaults prank procps python3 python3-minimal python3.9 python3.9-minimal r-base-core r-cran-assertthat r-cran-brio r-cran-callr r-cran-cli 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-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lattice r-cran-lifecycle 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-pkgload r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer 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 readline-common sensible-utils sysstat ucf unzip x11-common xdg-utils xz-utils zip Suggested packages: groff-base libxml-sax-expatxs-perl gdbm-l10n libdata-dump-perl libdb-file-lock-perl libfile-mimeinfo-perl libfile-readbackwards-perl libfreezethaw-perl libmldbm-perl libdbd-csv-perl liblog-dispatch-filerotate-perl librrds-perl libxml-dom-perl libcrypt-ssleay-perl libscalar-number-perl lm-sensors tcl8.6 tk8.6 libauthen-ntlm-perl mcl-doc perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl 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-bit64 r-cran-rcpp 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 isag Recommended packages: bioperl-run perl-doc libcache-cache-perl libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl libxml-simple-perl libyaml-perl libace-perl liblist-moreutils-perl libxml-twig-perl libset-scalar-perl libalgorithm-diff-xs-perl bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraphviz-perl libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl libxml-dom-xpath-perl libxml-sax-perl libxml-sax-writer-perl libxml-libxml-perl libclass-c3-xs-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl libdevel-lexalias-perl libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl libldap-common libipc-shareable-perl liblog-dispatch-perl libdevel-partialdump-perl libgpm2 publicsuffix libsasl2-modules libtext-csv-xs-perl libdata-dump-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl blast2 lynx ruby psmisc 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-codetools 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 systemd | cron | cron-daemon libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: bedtools bioperl ca-certificates cd-hit fasttree fontconfig fontconfig-config fonts-dejavu-core libalgorithm-c3-perl libalgorithm-diff-perl libarray-utils-perl libb-hooks-op-check-perl libbio-perl-perl libblas3 libbrotli1 libbsd0 libcairo2 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libcurl4 libdata-optlist-perl libdata-stag-perl libdatrie1 libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdigest-md5-file-perl libdist-checkconflicts-perl libdynaloader-functions-perl libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-slurper-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libharfbuzz0b libheap-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu67 libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo liblapack3 libldap-2.4-2 liblmdb0 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmd0 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmpdec3 libmro-compat-perl libncurses6 libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparse-yapp-perl libperl5.32 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-object-perl libsm6 libspiffy-perl libsqlite3-0 libssh2-1 libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-uplevel-perl libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl liburi-perl libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxrender1 libxss1 libxt6 mafft mcl media-types ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.32 perl-openssl-defaults prank procps python3 python3-minimal python3.9 python3.9-minimal r-base-core r-cran-assertthat r-cran-brio r-cran-callr r-cran-cli 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-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lattice r-cran-lifecycle 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-pkgload r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer 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 readline-common roary sensible-utils sysstat ucf unzip x11-common xdg-utils xz-utils zip 0 upgraded, 246 newly installed, 0 to remove and 0 not upgraded. Need to get 126 MB of archives. After this operation, 370 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 perl-modules-5.32 all 5.32.1-4+deb11u3 [2823 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.19-2 [64.9 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.19-2 [44.7 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libperl5.32 amd64 5.32.1-4+deb11u3 [4121 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.32.1-4+deb11u3 [293 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2+deb11u2 [132 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 netbase all 6.3 [19.9 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u2 [102 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 xz-utils amd64 5.2.5-2.1~deb11u1 [220 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 bedtools amd64 2.30.0+dfsg-1 [663 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get:32 http://deb.debian.org/debian bullseye/main amd64 libbio-perl-perl all 1.7.7-2 [2607 kB] Get:33 http://deb.debian.org/debian bullseye/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:34 http://deb.debian.org/debian bullseye/main amd64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get:35 http://deb.debian.org/debian bullseye/main amd64 libexception-class-perl all 1.44-1 [32.3 kB] Get:36 http://deb.debian.org/debian bullseye/main amd64 libtest-deep-perl all 1.130-1 [49.3 kB] Get:37 http://deb.debian.org/debian bullseye/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:38 http://deb.debian.org/debian bullseye/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get:39 http://deb.debian.org/debian bullseye/main amd64 libtext-diff-perl all 1.45-1 [27.7 kB] Get:40 http://deb.debian.org/debian bullseye/main amd64 libtest-differences-perl all 0.67-1 [18.7 kB] Get:41 http://deb.debian.org/debian bullseye/main amd64 libsub-uplevel-perl all 0.2800-1.1 [16.5 kB] Get:42 http://deb.debian.org/debian bullseye/main amd64 libtest-exception-perl all 0.43-1 [18.7 kB] Get:43 http://deb.debian.org/debian bullseye/main amd64 libtest-warn-perl all 0.36-1 [16.2 kB] Get:44 http://deb.debian.org/debian bullseye/main amd64 libtest-most-perl all 0.37-1 [24.9 kB] Get:45 http://deb.debian.org/debian bullseye/main amd64 bioperl all 1.7.7-2 [246 kB] Get:46 http://deb.debian.org/debian bullseye/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB] Get:47 http://deb.debian.org/debian bullseye/main amd64 cd-hit amd64 4.8.1-3 [522 kB] Get:48 http://deb.debian.org/debian bullseye/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get:49 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:50 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:51 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get:52 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:53 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:54 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:55 http://deb.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get:56 http://deb.debian.org/debian bullseye/main amd64 libalgorithm-c3-perl all 0.11-1 [11.7 kB] Get:57 http://deb.debian.org/debian bullseye/main amd64 libarray-utils-perl all 0.5-1.1 [5796 B] Get:58 http://deb.debian.org/debian bullseye/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b3 [11.3 kB] Get:59 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get:60 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get:61 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get:62 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1.1~deb11u1 [543 kB] Get:63 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:64 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:65 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u2 [311 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u2 [772 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 libclass-c3-perl all 0.35-1 [22.9 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 libparams-util-perl amd64 1.102-1+b1 [25.6 kB] Get:75 http://deb.debian.org/debian bullseye/main amd64 libsub-install-perl all 0.928-1.1 [10.8 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 libdata-optlist-perl all 0.110-1.1 [10.8 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get:78 http://deb.debian.org/debian bullseye/main amd64 libdevel-callchecker-perl amd64 0.008-1+b2 [15.9 kB] Get:79 http://deb.debian.org/debian bullseye/main amd64 libparams-classify-perl amd64 0.015-1+b3 [25.7 kB] Get:80 http://deb.debian.org/debian bullseye/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:81 http://deb.debian.org/debian bullseye/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:82 http://deb.debian.org/debian bullseye/main amd64 libmodule-implementation-perl all 0.09-1.1 [12.4 kB] Get:83 http://deb.debian.org/debian bullseye/main amd64 libpackage-stash-perl all 0.39-1 [21.9 kB] Get:84 http://deb.debian.org/debian bullseye/main amd64 libclass-load-perl all 0.25-1 [16.1 kB] Get:85 http://deb.debian.org/debian bullseye/main amd64 libclass-load-xs-perl amd64 0.10-1+b5 [14.6 kB] Get:86 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get:87 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get:88 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get:89 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u1 [77.2 kB] Get:90 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:91 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:92 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get:93 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u11 [347 kB] Get:94 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get:95 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:96 http://deb.debian.org/debian bullseye/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:97 http://deb.debian.org/debian bullseye/main amd64 libdevel-globaldestruction-perl all 0.14-1.1 [8312 B] Get:98 http://deb.debian.org/debian bullseye/main amd64 libmro-compat-perl all 0.13-1 [12.2 kB] Get:99 http://deb.debian.org/debian bullseye/main amd64 libsub-identify-perl amd64 0.14-1+b3 [12.0 kB] Get:100 http://deb.debian.org/debian bullseye/main amd64 libdevel-overloadinfo-perl all 0.005-1 [7212 B] Get:101 http://deb.debian.org/debian bullseye/main amd64 libencode-locale-perl all 1.05-1.1 [13.2 kB] Get:102 http://deb.debian.org/debian bullseye/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:103 http://deb.debian.org/debian bullseye/main amd64 libhttp-date-perl all 6.05-1 [10.4 kB] Get:104 http://deb.debian.org/debian bullseye/main amd64 libfile-listing-perl all 6.14-1 [12.4 kB] Get:105 http://deb.debian.org/debian bullseye/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get:106 http://deb.debian.org/debian bullseye/main amd64 liburi-perl all 5.08-1 [90.6 kB] Get:107 http://deb.debian.org/debian bullseye/main amd64 libhtml-parser-perl amd64 3.75-1+b1 [105 kB] Get:108 http://deb.debian.org/debian bullseye/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get:109 http://deb.debian.org/debian bullseye/main amd64 libio-html-perl all 1.004-2 [16.1 kB] Get:110 http://deb.debian.org/debian bullseye/main amd64 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get:111 http://deb.debian.org/debian bullseye/main amd64 libhttp-message-perl all 6.28-1 [79.6 kB] Get:112 http://deb.debian.org/debian bullseye/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:113 http://deb.debian.org/debian bullseye/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get:114 http://deb.debian.org/debian bullseye/main amd64 perl-openssl-defaults amd64 5 [7360 B] Get:115 http://deb.debian.org/debian bullseye/main amd64 libnet-ssleay-perl amd64 1.88-3+b1 [321 kB] Get:116 http://deb.debian.org/debian bullseye/main amd64 libio-socket-ssl-perl all 2.069-1 [215 kB] Get:117 http://deb.debian.org/debian bullseye/main amd64 libnet-http-perl all 6.20-1 [25.1 kB] Get:118 http://deb.debian.org/debian bullseye/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get:119 http://deb.debian.org/debian bullseye/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:120 http://deb.debian.org/debian bullseye/main amd64 libwww-perl all 6.52-1 [192 kB] Get:121 http://deb.debian.org/debian bullseye/main amd64 libdigest-md5-file-perl all 0.08-1.1 [9608 B] Get:122 http://deb.debian.org/debian bullseye/main amd64 libdist-checkconflicts-perl all 0.11-1.1 [10.2 kB] Get:123 http://deb.debian.org/debian bullseye/main amd64 libenv-path-perl all 0.19-2 [19.5 kB] Get:124 http://deb.debian.org/debian bullseye/main amd64 libsub-exporter-perl all 0.987-1 [47.2 kB] Get:125 http://deb.debian.org/debian bullseye/main amd64 libeval-closure-perl all 0.14-1 [11.5 kB] Get:126 http://deb.debian.org/debian bullseye/main amd64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:127 http://deb.debian.org/debian bullseye/main amd64 libtext-glob-perl all 0.11-1 [8888 B] Get:128 http://deb.debian.org/debian bullseye/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:129 http://deb.debian.org/debian bullseye/main amd64 libfile-grep-perl all 0.02-1.1 [7904 B] Get:130 http://deb.debian.org/debian bullseye/main amd64 libfile-slurper-perl all 0.012-1 [8344 B] Get:131 http://deb.debian.org/debian bullseye/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:132 http://deb.debian.org/debian bullseye/main amd64 libfindbin-libs-perl all 2.190.02-1 [30.3 kB] Get:133 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2+deb11u1 [64.9 kB] Get:134 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB] Get:135 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:136 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1+deb11u1 [1374 kB] Get:137 http://deb.debian.org/debian bullseye/main amd64 libheap-perl all 0.80-3 [34.2 kB] Get:138 http://deb.debian.org/debian bullseye/main amd64 libset-object-perl amd64 1.41-1 [40.1 kB] Get:139 http://deb.debian.org/debian bullseye/main amd64 libgraph-perl all 1:0.9716-2 [109 kB] Get:140 http://deb.debian.org/debian bullseye/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get:141 http://deb.debian.org/debian bullseye/main amd64 libio-all-perl all 0.87-1 [66.7 kB] Get:142 http://deb.debian.org/debian bullseye/main amd64 libparse-yapp-perl all 1.21-2 [46.9 kB] Get:143 http://deb.debian.org/debian bullseye/main amd64 libxml-parser-perl amd64 2.46-2 [206 kB] Get:144 http://deb.debian.org/debian bullseye/main amd64 libxml-writer-perl all 0.900-1 [29.9 kB] Get:145 http://deb.debian.org/debian bullseye/main amd64 libgraph-readwrite-perl all 2.09-1.1 [44.9 kB] Get:146 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:147 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get:148 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get:149 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:150 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:151 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:152 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get:153 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get:154 http://deb.debian.org/debian bullseye/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get:155 http://deb.debian.org/debian bullseye/main amd64 liblog-log4perl-perl all 1.54-1 [378 kB] Get:156 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get:157 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get:158 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get:159 http://deb.debian.org/debian bullseye/main amd64 libmodule-runtime-conflicts-perl all 0.003-1.1 [7156 B] Get:160 http://deb.debian.org/debian bullseye/main amd64 libsub-name-perl amd64 0.26-1+b1 [13.8 kB] Get:161 http://deb.debian.org/debian bullseye/main amd64 libpackage-deprecationmanager-perl all 0.17-1.1 [16.6 kB] Get:162 http://deb.debian.org/debian bullseye/main amd64 libpackage-stash-xs-perl amd64 0.29-1+b2 [20.2 kB] Get:163 http://deb.debian.org/debian bullseye/main amd64 libmoose-perl amd64 2.2014-2 [802 kB] Get:164 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get:165 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get:166 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get:167 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get:168 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get:169 http://deb.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get:170 http://deb.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get:171 http://deb.debian.org/debian bullseye/main amd64 libperlio-utf8-strict-perl amd64 0.008-1+b1 [12.0 kB] Get:172 http://deb.debian.org/debian bullseye/main amd64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get:173 http://deb.debian.org/debian bullseye/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get:174 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:175 http://deb.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.11+dfsg-1 [1018 kB] Get:176 http://deb.debian.org/debian bullseye/main amd64 libtest-file-perl all 1.444-1 [24.2 kB] Get:177 http://deb.debian.org/debian bullseye/main amd64 libtest-files-perl all 0.15-1 [12.0 kB] Get:178 http://deb.debian.org/debian bullseye/main amd64 libtest-output-perl all 1.033-1 [16.8 kB] Get:179 http://deb.debian.org/debian bullseye/main amd64 libtext-csv-perl all 2.00-1 [105 kB] Get:180 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get:181 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u5 [290 kB] Get:182 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:183 http://deb.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:184 http://deb.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.11-2 [780 kB] Get:185 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get:186 http://deb.debian.org/debian bullseye/main amd64 mafft amd64 7.475-1 [1051 kB] Get:187 http://deb.debian.org/debian bullseye/main amd64 mcl amd64 1:14-137+ds-9+b1 [586 kB] Get:188 http://deb.debian.org/debian bullseye/main amd64 ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get:189 http://deb.debian.org/debian bullseye/main amd64 ncbi-blast+ amd64 2.11.0+ds-1 [11.3 MB] Get:190 http://deb.debian.org/debian bullseye/main amd64 sysstat amd64 12.5.2-2 [603 kB] Get:191 http://deb.debian.org/debian bullseye/main amd64 parallel all 20161222-1.1 [306 kB] Get:192 http://deb.debian.org/debian bullseye/main amd64 prank amd64 0.0.170427+dfsg-3 [395 kB] Get:193 http://deb.debian.org/debian bullseye/main amd64 zip amd64 3.0-12 [232 kB] Get:194 http://deb.debian.org/debian bullseye/main amd64 unzip amd64 6.0-26+deb11u1 [172 kB] Get:195 http://deb.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:196 http://deb.debian.org/debian bullseye/main amd64 r-base-core amd64 4.0.4-1 [25.1 MB] Get:197 http://deb.debian.org/debian bullseye/main amd64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get:198 http://deb.debian.org/debian bullseye/main amd64 r-cran-brio amd64 1.1.1-1 [31.7 kB] Get:199 http://deb.debian.org/debian bullseye/main amd64 r-cran-ps amd64 1.5.0-1 [277 kB] Get:200 http://deb.debian.org/debian bullseye/main amd64 r-cran-r6 all 2.5.0-1 [104 kB] Get:201 http://deb.debian.org/debian bullseye/main amd64 r-cran-processx amd64 3.4.5-1 [295 kB] Get:202 http://deb.debian.org/debian bullseye/main amd64 r-cran-callr all 3.5.1-1 [386 kB] Get:203 http://deb.debian.org/debian bullseye/main amd64 r-cran-glue amd64 1.4.2-1 [138 kB] Get:204 http://deb.debian.org/debian bullseye/main amd64 r-cran-cli all 2.3.0-1 [480 kB] Get:205 http://deb.debian.org/debian bullseye/main amd64 r-cran-colorspace amd64 2.0-0+dfsg-1 [1684 kB] Get:206 http://deb.debian.org/debian bullseye/main amd64 r-cran-crayon all 1.4.0-1 [143 kB] Get:207 http://deb.debian.org/debian bullseye/main amd64 r-cran-rprojroot all 2.0.2-1 [114 kB] Get:208 http://deb.debian.org/debian bullseye/main amd64 r-cran-desc all 1.2.0-3 [301 kB] Get:209 http://deb.debian.org/debian bullseye/main amd64 r-cran-diffobj amd64 0.3.2-1 [1069 kB] Get:210 http://deb.debian.org/debian bullseye/main amd64 r-cran-digest amd64 0.6.27-1 [192 kB] Get:211 http://deb.debian.org/debian bullseye/main amd64 r-cran-rlang amd64 0.4.10-1 [1176 kB] Get:212 http://deb.debian.org/debian bullseye/main amd64 r-cran-ellipsis amd64 0.3.1-1 [31.7 kB] Get:213 http://deb.debian.org/debian bullseye/main amd64 r-cran-evaluate all 0.14-2 [81.1 kB] Get:214 http://deb.debian.org/debian bullseye/main amd64 r-cran-fansi amd64 0.4.2-1 [345 kB] Get:215 http://deb.debian.org/debian bullseye/main amd64 r-cran-farver amd64 2.0.3-1+b1 [1393 kB] Get:216 http://deb.debian.org/debian bullseye/main amd64 r-cran-gtable all 0.3.0+dfsg-2 [163 kB] Get:217 http://deb.debian.org/debian bullseye/main amd64 r-cran-jsonlite amd64 1.7.2+dfsg-1 [447 kB] Get:218 http://deb.debian.org/debian bullseye/main amd64 r-cran-lifecycle all 0.2.0-2 [93.2 kB] Get:219 http://deb.debian.org/debian bullseye/main amd64 r-cran-magrittr amd64 2.0.1-1 [198 kB] Get:220 http://deb.debian.org/debian bullseye/main amd64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get:221 http://deb.debian.org/debian bullseye/main amd64 r-cran-withr all 2.4.1-1 [210 kB] Get:222 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgbuild all 1.2.0-1 [146 kB] Get:223 http://deb.debian.org/debian bullseye/main amd64 r-cran-rstudioapi all 0.13-1 [262 kB] Get:224 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgload amd64 1.1.0-1 [168 kB] Get:225 http://deb.debian.org/debian bullseye/main amd64 r-cran-praise all 1.0.0-4 [20.1 kB] Get:226 http://deb.debian.org/debian bullseye/main amd64 r-cran-utf8 amd64 1.1.4-2 [131 kB] Get:227 http://deb.debian.org/debian bullseye/main amd64 r-cran-vctrs amd64 0.3.6-1 [1107 kB] Get:228 http://deb.debian.org/debian bullseye/main amd64 r-cran-pillar all 1.4.7-1 [227 kB] Get:229 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:230 http://deb.debian.org/debian bullseye/main amd64 r-cran-tibble amd64 3.0.6+dfsg-1 [416 kB] Get:231 http://deb.debian.org/debian bullseye/main amd64 r-cran-rematch2 all 2.1.2-2 [46.3 kB] Get:232 http://deb.debian.org/debian bullseye/main amd64 r-cran-waldo all 0.2.3-2 [79.3 kB] Get:233 http://deb.debian.org/debian bullseye/main amd64 r-cran-testthat amd64 3.0.1-1 [1451 kB] Get:234 http://deb.debian.org/debian bullseye/main amd64 r-cran-isoband amd64 0.2.3-2 [2085 kB] Get:235 http://deb.debian.org/debian bullseye/main amd64 r-cran-mass amd64 7.3-53.1-1 [1115 kB] Get:236 http://deb.debian.org/debian bullseye/main amd64 r-cran-lattice amd64 0.20-41-1+b1 [1164 kB] Get:237 http://deb.debian.org/debian bullseye/main amd64 r-cran-nlme amd64 3.1.152-1 [2241 kB] Get:238 http://deb.debian.org/debian bullseye/main amd64 r-cran-matrix amd64 1.3-2-1 [3604 kB] Get:239 http://deb.debian.org/debian bullseye/main amd64 r-cran-mgcv amd64 1.8-34-1 [2998 kB] Get:240 http://deb.debian.org/debian bullseye/main amd64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get:241 http://deb.debian.org/debian bullseye/main amd64 r-cran-munsell all 0.5.0-2 [236 kB] Get:242 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcolorbrewer all 1.1-2-3 [54.4 kB] Get:243 http://deb.debian.org/debian bullseye/main amd64 r-cran-viridislite all 0.3.0-4 [59.2 kB] Get:244 http://deb.debian.org/debian bullseye/main amd64 r-cran-scales all 1.1.1-1 [557 kB] Get:245 http://deb.debian.org/debian bullseye/main amd64 r-cran-ggplot2 all 3.3.3+dfsg-1 [3158 kB] Get:246 http://deb.debian.org/debian bullseye/main amd64 roary all 3.13.0+dfsg-1 [184 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 126 MB in 2s (63.3 MB/s) Selecting previously unselected package perl-modules-5.32. 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Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libsqlite3-0:amd64 (3.34.1-3) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libsensors-config (1:3.6.0-7) ... Setting up libnghttp2-14:amd64 (1.43.0-1+deb11u1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up perl-openssl-defaults:amd64 (5) ... Setting up libgomp1:amd64 (10.2.1-6) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up zip (3.0-12) ... Setting up libblas3:amd64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up mcl (1:14-137+ds-9+b1) ... Setting up libx11-data (2:1.7.2-1+deb11u2) ... 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Setting up fasttree (2.1.11-2) ... Setting up netbase (6.3) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u5) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libbsd0:amd64 (0.11.3-1+deb11u1) ... Setting up readline-common (8.1-1) ... 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 libprocps8:amd64 (2:3.3.17-5) ... Setting up prank (0.0.170427+dfsg-3) ... Setting up libgdbm6:amd64 (1.19-2) ... 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 libxcb-render0:amd64 (1.14-3) ... Setting up libmbedx509-0:amd64 (2.16.9-0.1) ... 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Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libpaper1:amd64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up perl (5.32.1-4+deb11u3) ... Setting up libpackage-stash-xs-perl (0.29-1+b2) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libalgorithm-c3-perl (0.11-1) ... Setting up libset-object-perl (1.41-1) ... Setting up liblog-log4perl-perl (1.54-1) ... Setting up libperlio-utf8-strict-perl (0.008-1+b1) ... Setting up libxml-writer-perl (0.900-1) ... Setting up libenv-path-perl (0.19-2) ... Setting up libio-html-perl (1.004-2) ... Setting up libb-hooks-op-check-perl (0.22-1+b3) ... Setting up libfile-grep-perl (0.02-1.1) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up libparams-util-perl (1.102-1+b1) ... Setting up parallel (20161222-1.1) ... Setting up libspiffy-perl (0.46-1) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl (0.26-1+b1) ... Setting up libsub-uplevel-perl (0.2800-1.1) ... Setting up libdevel-globaldestruction-perl (0.14-1.1) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up liburi-perl (5.08-1) ... Setting up python3.9 (3.9.2-1) ... Setting up libtext-csv-perl (2.00-1) ... Setting up libnet-ssleay-perl (1.88-3+b1) ... Setting up cd-hit (4.8.1-3) ... Setting up libarray-utils-perl (0.5-1.1) ... Setting up libhttp-date-perl (6.05-1) ... Setting up libfile-slurper-perl (0.012-1) ... Setting up libfile-which-perl (1.23-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up libfile-listing-perl (6.14-1) ... Setting up libparse-yapp-perl (1.21-2) ... Setting up libdynaloader-functions-perl (0.003-1.1) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libtest-deep-perl (1.130-1) ... Setting up mafft (7.475-1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libsub-identify-perl (0.14-1+b3) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libhtml-tagset-perl (3.20-4) ... Setting up libtest-file-perl (1.444-1) ... Setting up libtk8.6:amd64 (8.6.11-2) ... Setting up libheap-perl (0.80-3) ... Setting up libpango-1.0-0:amd64 (1.46.2-3) ... Setting up liblwp-mediatypes-perl (6.04-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up libnet-http-perl (6.20-1) ... Setting up libencode-locale-perl (1.05-1.1) ... Setting up python3 (3.9.2-3) ... Setting up libexception-class-perl (1.44-1) ... Setting up libfindbin-libs-perl (2.190.02-1) ... Setting up libio-all-perl (0.87-1) ... Setting up libclass-c3-perl (0.35-1) ... Setting up libgraph-perl (1:0.9716-2) ... Setting up libdevel-callchecker-perl (0.008-1+b2) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up libsub-install-perl (0.928-1.1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up ncbi-blast+ (2.11.0+ds-1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up libtest-exception-perl (0.43-1) ... Setting up libtext-diff-perl (1.45-1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up libdata-optlist-perl (0.110-1.1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdata-stag-perl (0.14-2) ... Setting up libhtml-parser-perl (3.75-1+b1) ... Setting up libbio-perl-perl (1.7.7-2) ... Setting up libmro-compat-perl (0.13-1) ... Setting up libpangoft2-1.0-0:amd64 (1.46.2-3) ... Setting up libio-socket-ssl-perl (2.069-1) ... Setting up libsub-exporter-perl (0.987-1) ... Setting up libpangocairo-1.0-0:amd64 (1.46.2-3) ... Setting up libhttp-message-perl (6.28-1) ... Setting up libeval-closure-perl (0.14-1) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl (0.015-1+b3) ... Setting up libtest-differences-perl (0.67-1) ... Setting up libtest-files-perl (0.15-1) ... Setting up libmodule-runtime-perl (0.016-1) ... 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 libdist-checkconflicts-perl (0.11-1.1) ... Setting up libtest-output-perl (1.033-1) ... 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 r-cran-viridislite (0.3.0-4) ... Setting up r-cran-r6 (2.5.0-1) ... Setting up r-cran-magrittr (2.0.1-1) ... 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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 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 libpackage-deprecationmanager-perl (0.17-1.1) ... Setting up libdevel-overloadinfo-perl (0.005-1) ... Setting up libclass-load-xs-perl (0.10-1+b5) ... Setting up bioperl (1.7.7-2) ... Setting up r-cran-ellipsis (0.3.1-1) ... Setting up r-cran-callr (3.5.1-1) ... Setting up libmoose-perl (2.2014-2) ... 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 liblwp-protocol-https-perl (6.10-1) ... Setting up libwww-perl (6.52-1) ... Setting up libdigest-md5-file-perl (0.08-1.1) ... Setting up libxml-parser-perl:amd64 (2.46-2) ... Setting up libgraph-readwrite-perl (2.09-1.1) ... Setting up roary (3.13.0+dfsg-1) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m37.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-y', 'install', 'roary'] 0m37.7s INFO: Running scripts post_install 0m37.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_install_exceptions'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_install_exceptions'] 0m37.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 0m38.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 0m38.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp3qb0b834 to sid 0m38.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m38.9s INFO: Running scripts pre_distupgrade 0m38.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m38.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m38.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_distupgrade_exceptions'] 0m38.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_distupgrade_exceptions'] 0m38.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m38.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m38.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m38.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m38.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m38.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m38.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', 'update'] 0m43.8s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9971 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7227 kB] Fetched 17.4 MB in 4s (4715 kB/s) Reading package lists... 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', 'update'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-yf', 'dist-upgrade'] 1m29.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libicu67 libldap-2.4-2 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libncurses6 libperl5.32 libprocps8 libpython3.9-minimal libpython3.9-stdlib libquadmath0 libsub-identify-perl libtiff5 libwebp6 perl-modules-5.32 python3.9 python3.9-minimal r-cran-assertthat r-cran-ellipsis r-cran-prettyunits Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libcom-err2 libcurl4 libdb5.3 libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libhogweed6 libnettle8 libpng16-16 libpsl5 libreadline8 libsemanage1 libss2 libssh2-1 libxt6 The following NEW packages will be installed: fonts-dejavu-mono gcc-14-base libapt-pkg6.0t64 libcap2 libclone-perl libcom-err2t64 libconst-fast-perl libcurl4t64 libdata-compare-perl libdb5.3t64 libext2fs2t64 libffi8 libgdbm-compat4t64 libgdbm6t64 libglib2.0-0t64 libgnutls30t64 libhogweed6t64 libicu72 libldap-2.5-0 liblerc4 libmbedcrypto7 libmbedtls14 libmbedx509-1 libnettle8t64 libpadwalker-perl libpath-tiny-perl libperl5.38t64 libpng16-16t64 libproc2-0 libpsl5t64 libpython3.11-minimal libpython3.11-stdlib libreadline8t64 libsemanage2 libsepol2 libsharpyuv0 libss2t64 libssh2-1t64 libssl3t64 libtiff6 libtingea0 libunistring5 libuv1 libwebp7 libxt6t64 perl-modules-5.38 python3.11 python3.11-minimal r-cran-fs usrmerge The following packages will be upgraded: adduser apt base-files base-passwd bash bedtools bioperl bsdutils ca-certificates cd-hit coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils fontconfig fontconfig-config fonts-dejavu-core gcc-10-base gcc-9-base gpgv grep gzip hostname init-system-helpers libacl1 libalgorithm-c3-perl libarray-utils-perl libattr1 libaudit-common libaudit1 libb-hooks-op-check-perl libbio-perl-perl libblas3 libblkid1 libbrotli1 libbsd0 libbz2-1.0 libc-bin libc6 libcairo2 libcap-ng0 libcapture-tiny-perl libclass-c3-perl libclass-load-perl libclass-load-xs-perl libcrypt1 libdata-optlist-perl libdata-stag-perl libdatrie1 libdebconfclient0 libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdist-checkconflicts-perl libdynaloader-functions-perl libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-slurper-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgcc-s1 libgcrypt20 libgfortran5 libgmp10 libgomp1 libgpg-error0 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libheap-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libidn2-0 libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblmdb0 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz4-1 liblzma5 libmd0 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmount1 libmpdec3 libmro-compat-perl libncurses6 libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnsl2 libnumber-compare-perl libp11-kit0 libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpam-modules libpam-modules-bin libpam-runtime libpam0g libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparse-yapp-perl libpcre2-8-0 libpcre3 libperlio-utf8-strict-perl libpixman-1-0 libpython3-stdlib libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsensors-config libsensors5 libset-object-perl libsmartcols1 libsqlite3-0 libstdc++6 libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-uplevel-perl libsystemd0 libtasn1-6 libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libthai-data libthai0 libtinfo6 libtirpc-common libtirpc3 libtk8.6 libtry-tiny-perl libudev1 liburi-perl libuuid1 libwww-perl libx11-6 libx11-data libxcb-render0 libxcb-shm0 libxcb1 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxrender1 libxxhash0 libzstd1 login logsave lsb-base mafft mawk mcl media-types mount ncbi-blast+ ncbi-data ncurses-base ncurses-bin netbase openssl parallel passwd perl perl-base perl-openssl-defaults procps python3 python3-minimal r-base-core r-cran-brio r-cran-callr r-cran-cli 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-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgload r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer 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 readline-common sed sensible-utils sysstat sysvinit-utils tar tzdata ucf unzip util-linux x11-common xz-utils zip zlib1g 286 upgraded, 50 newly installed, 18 to remove and 0 not upgraded. Need to get 173 MB of archives. After this operation, 145 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15.1 [2752 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15.1 [602 kB] Get:4 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240303-1 [42.8 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240303-1 [72.2 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-10 [159 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2 [74.8 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-10 [191 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-10 [117 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-10 [30.1 kB] Get:12 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-4 [616 kB] Get:13 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-10 [1231 kB] Get:14 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.6.0-0.2 [250 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:16 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:17 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.6 [1510 kB] Get:18 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-7 [32.2 kB] Get:19 http://deb.debian.org/debian sid/main amd64 lsb-base all 11.6 [4584 B] Get:20 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23 [252 kB] Get:21 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.17 [89.0 kB] Get:22 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:23 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-10 [97.3 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.1.5-1.1 [2058 kB] Get:26 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3+b2 [2952 kB] Get:27 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:28 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:29 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:30 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:31 http://deb.debian.org/debian sid/main amd64 gzip amd64 1.12-1 [140 kB] Get:32 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.4+20240113-1 [104 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:36 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b1 [10.6 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libxml-parser-perl amd64 2.47-1+b2 [199 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libsub-name-perl amd64 0.27-1+b2 [12.5 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libsub-identify-perl amd64 0.14-3+b2 [11.2 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libset-object-perl amd64 1.42-1+b4 [37.5 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b2 [11.4 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libparams-util-perl amd64 1.102-3 [24.0 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libparams-classify-perl amd64 0.015-2+b3 [22.4 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libpackage-stash-xs-perl amd64 0.30-1+b3 [20.2 kB] Get:46 http://deb.debian.org/debian sid/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get:47 http://deb.debian.org/debian sid/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libmoose-perl amd64 2.2207-1+b1 [766 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libhtml-parser-perl amd64 3.81-1+b2 [99.0 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libdevel-callchecker-perl amd64 0.008-2+b2 [15.1 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libclass-load-xs-perl amd64 0.10-2+b3 [14.1 kB] Get:52 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3.2 [2899 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-5 [697 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.23-5.1 [72.7 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.23-5.1 [48.5 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libperl5.38t64 amd64 5.38.2-3.2 [4266 kB] Get:57 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3.2 [236 kB] Get:58 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3.2 [1643 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b2 [19.6 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2.1 [11.4 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-2 [16.9 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2.1 [48.5 kB] Get:63 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.86 [119 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.3-6 [67.7 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:68 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.4-1+b1 [364 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.3-6 [54.2 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.3-6 [260 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5+b2 [38.2 kB] Get:74 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3.1 [87.6 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.1-2 [102 kB] Get:76 http://deb.debian.org/debian sid/main amd64 liburi-perl all 5.27-1 [98.4 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:81 http://deb.debian.org/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:84 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.1.5-1.1 [1241 kB] Get:85 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:90 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:93 http://deb.debian.org/debian sid/main amd64 liblwp-protocol-https-perl all 6.13-1 [10.7 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libwww-perl all 6.76-1 [183 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libclass-load-perl all 0.25-2 [15.3 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:104 http://deb.debian.org/debian sid/main amd64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get:105 http://deb.debian.org/debian sid/main amd64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libclass-c3-perl all 0.35-2 [21.0 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libmro-compat-perl all 0.15-2 [11.8 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get:109 http://deb.debian.org/debian sid/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libeval-closure-perl all 0.14-3 [11.2 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get:114 http://deb.debian.org/debian sid/main amd64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get:115 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271+b2 [10.2 kB] Get:117 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240303-1 [713 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.7.13+b1 [984 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.4-1+b1 [126 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libhogweed6t64 amd64 3.9.1-2.2 [328 kB] Get:123 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b3 [58.5 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libnettle8t64 amd64 3.9.1-2.2 [296 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.1-2 [421 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.3-1.1 [1425 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:132 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b2 [90.3 kB] Get:134 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-4 [973 kB] Get:135 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:136 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-1.1+b1 [649 kB] Get:137 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:139 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.13+b1 [1368 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:141 http://deb.debian.org/debian sid/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:142 http://deb.debian.org/debian sid/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:143 http://deb.debian.org/debian sid/main amd64 usrmerge all 39 [13.1 kB] Get:144 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:145 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libss2t64 amd64 1.47.0-2.3+b1 [25.2 kB] Get:147 http://deb.debian.org/debian sid/main amd64 libcom-err2t64 amd64 1.47.0-2.3+b1 [20.5 kB] Get:148 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-5.1 [135 kB] Get:150 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-5.1 [333 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5.1 [79.6 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5.1 [33.0 kB] Get:153 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:154 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b2 [57.1 kB] Get:155 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.16+dfsg-1 [185 kB] Get:156 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.59.0-1+b1 [74.1 kB] Get:157 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.6.0-3.2 [430 kB] Get:158 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:159 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b1 [215 kB] Get:160 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2.3+b1 [20.2 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.0-2.3+b1 [206 kB] Get:162 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2.3+b1 [572 kB] Get:163 http://deb.debian.org/debian sid/main amd64 r-cran-ps amd64 1.7.6-1 [310 kB] Get:164 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.3-1 [1669 kB] Get:165 http://deb.debian.org/debian sid/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:166 http://deb.debian.org/debian sid/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:167 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.3.3-2 [26.8 MB] Get:168 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.52.1+ds-1 [35.1 kB] Get:169 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.52.1+ds-1 [216 kB] Get:170 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.52.1+ds-1 [48.3 kB] Get:171 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get:172 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.78.4-4 [1453 kB] Get:173 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b2 [438 kB] Get:174 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-2 [530 kB] Get:175 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.43-3 [278 kB] Get:176 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3.1 [69.2 kB] Get:177 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-3.1 [167 kB] Get:178 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:179 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:181 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:182 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-10 [143 kB] Get:183 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.8-3 [817 kB] Get:184 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.8-3 [1879 kB] Get:185 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get:186 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get:187 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:188 http://deb.debian.org/debian sid/main amd64 tzdata all 2024a-1 [255 kB] Get:189 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.1-1 [894 kB] Get:190 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.8-3 [1791 kB] Get:191 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.8-3 [597 kB] Get:192 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get:193 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.3-6 [140 kB] Get:194 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:195 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:196 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:197 http://deb.debian.org/debian sid/main amd64 libpcre3 amd64 2:8.39-15+b1 [342 kB] Get:198 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:199 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get:200 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get:201 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:202 http://deb.debian.org/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:203 http://deb.debian.org/debian sid/main amd64 xz-utils amd64 5.6.0-0.2 [489 kB] Get:204 http://deb.debian.org/debian sid/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get:205 http://deb.debian.org/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:206 http://deb.debian.org/debian sid/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:207 http://deb.debian.org/debian sid/main amd64 bioperl all 1.7.8-1 [246 kB] Get:208 http://deb.debian.org/debian sid/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:209 http://deb.debian.org/debian sid/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:210 http://deb.debian.org/debian sid/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get:211 http://deb.debian.org/debian sid/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:212 http://deb.debian.org/debian sid/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get:213 http://deb.debian.org/debian sid/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get:214 http://deb.debian.org/debian sid/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get:215 http://deb.debian.org/debian sid/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get:216 http://deb.debian.org/debian sid/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get:217 http://deb.debian.org/debian sid/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get:218 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240303-1 [136 kB] Get:219 http://deb.debian.org/debian sid/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get:220 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:221 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:222 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:223 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:224 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get:225 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240303-1 [147 kB] Get:226 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240303-1 [836 kB] Get:227 http://deb.debian.org/debian sid/main amd64 gcc-10-base amd64 10.5.0-3 [36.6 kB] Get:228 http://deb.debian.org/debian sid/main amd64 gcc-9-base amd64 9.5.0-5 [28.8 kB] Get:229 http://deb.debian.org/debian sid/main amd64 libarray-utils-perl all 0.5-3 [6184 B] Get:230 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:231 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.12.1-1 [129 kB] Get:232 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:233 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:234 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:235 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:236 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:237 http://deb.debian.org/debian sid/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:238 http://deb.debian.org/debian sid/main amd64 libdata-compare-perl all 1.29-1 [19.6 kB] Get:239 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:240 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.19-1 [41.4 kB] Get:241 http://deb.debian.org/debian sid/main amd64 libenv-path-perl all 0.19-4 [19.1 kB] Get:242 http://deb.debian.org/debian sid/main amd64 libfile-grep-perl all 0.02-3 [8352 B] Get:243 http://deb.debian.org/debian sid/main amd64 libfile-slurper-perl all 0.014-1 [8560 B] Get:244 http://deb.debian.org/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:245 http://deb.debian.org/debian sid/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get:246 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:247 http://deb.debian.org/debian sid/main amd64 libheap-perl all 0.80-5 [34.3 kB] Get:248 http://deb.debian.org/debian sid/main amd64 libgraph-perl all 1:0.9727-1 [111 kB] Get:249 http://deb.debian.org/debian sid/main amd64 libio-all-perl all 0.87-2 [67.3 kB] Get:250 http://deb.debian.org/debian sid/main amd64 libparse-yapp-perl all 1.21-3 [42.5 kB] Get:251 http://deb.debian.org/debian sid/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB] Get:252 http://deb.debian.org/debian sid/main amd64 libgraph-readwrite-perl all 2.10-1 [45.2 kB] Get:253 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:254 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:255 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:256 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:257 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:258 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:259 http://deb.debian.org/debian sid/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get:260 http://deb.debian.org/debian sid/main amd64 liblog-log4perl-perl all 1.57-1 [367 kB] Get:261 http://deb.debian.org/debian sid/main amd64 libmbedcrypto7 amd64 2.28.7-1 [280 kB] Get:262 http://deb.debian.org/debian sid/main amd64 libmbedx509-1 amd64 2.28.7-1 [130 kB] Get:263 http://deb.debian.org/debian sid/main amd64 libmbedtls14 amd64 2.28.7-1 [165 kB] Get:264 http://deb.debian.org/debian sid/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:265 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.1 [10.8 kB] Get:266 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] Get:267 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:268 http://deb.debian.org/debian sid/main amd64 libpadwalker-perl amd64 2.5-1+b5 [18.6 kB] Get:269 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:270 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:271 http://deb.debian.org/debian sid/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:272 http://deb.debian.org/debian sid/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:273 http://deb.debian.org/debian sid/main amd64 libpath-tiny-perl all 0.144-1 [56.4 kB] Get:274 http://deb.debian.org/debian sid/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get:275 http://deb.debian.org/debian sid/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get:276 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get:277 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:278 http://deb.debian.org/debian sid/main amd64 libtest-file-perl all 1.993-1 [24.5 kB] Get:279 http://deb.debian.org/debian sid/main amd64 libtest-files-perl all 0.24-1 [19.3 kB] Get:280 http://deb.debian.org/debian sid/main amd64 libtest-output-perl all 1.034-1 [16.0 kB] Get:281 http://deb.debian.org/debian sid/main amd64 libtext-csv-perl all 2.04-1 [112 kB] Get:282 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get:283 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:284 http://deb.debian.org/debian sid/main amd64 libtingea0 amd64 21-361-2+b1 [51.3 kB] Get:285 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:286 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:287 http://deb.debian.org/debian sid/main amd64 libuv1 amd64 1.48.0-1 [147 kB] Get:288 http://deb.debian.org/debian sid/main amd64 mafft amd64 7.505-1 [1078 kB] Get:289 http://deb.debian.org/debian sid/main amd64 mcl amd64 1:22-282+ds-2 [474 kB] Get:290 http://deb.debian.org/debian sid/main amd64 ncbi-data all 6.1.20170106+dfsg2-1 [3541 kB] Get:291 http://deb.debian.org/debian sid/main amd64 ncbi-blast+ amd64 2.12.0+ds-4 [12.5 MB] Get:292 http://deb.debian.org/debian sid/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get:293 http://deb.debian.org/debian sid/main amd64 parallel all 20231122+ds-1 [1946 kB] Get:294 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.2-1 [1325 kB] Get:295 http://deb.debian.org/debian sid/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:296 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:297 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:298 http://deb.debian.org/debian sid/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:299 http://deb.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:300 http://deb.debian.org/debian sid/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:301 http://deb.debian.org/debian sid/main amd64 zip amd64 3.0-13 [230 kB] Get:302 http://deb.debian.org/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:303 http://deb.debian.org/debian sid/main amd64 r-cran-brio amd64 1.1.4-1 [37.4 kB] Get:304 http://deb.debian.org/debian sid/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:305 http://deb.debian.org/debian sid/main amd64 r-cran-processx amd64 3.8.3-1 [345 kB] Get:306 http://deb.debian.org/debian sid/main amd64 r-cran-callr all 3.7.5-1 [430 kB] Get:307 http://deb.debian.org/debian sid/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB] Get:308 http://deb.debian.org/debian sid/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:309 http://deb.debian.org/debian sid/main amd64 r-cran-desc all 1.4.3-1 [351 kB] Get:310 http://deb.debian.org/debian sid/main amd64 r-cran-diffobj amd64 0.3.5-1+b1 [1122 kB] Get:311 http://deb.debian.org/debian sid/main amd64 r-cran-digest amd64 0.6.35-1 [203 kB] Get:312 http://deb.debian.org/debian sid/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get:313 http://deb.debian.org/debian sid/main amd64 r-cran-evaluate all 0.23-1 [90.6 kB] Get:314 http://deb.debian.org/debian sid/main amd64 r-cran-farver amd64 2.1.1-1 [1404 kB] Get:315 http://deb.debian.org/debian sid/main amd64 r-cran-fs amd64 1.6.3+dfsg-1 [227 kB] Get:316 http://deb.debian.org/debian sid/main amd64 r-cran-gtable all 0.3.4+dfsg-1 [221 kB] Get:317 http://deb.debian.org/debian sid/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:318 http://deb.debian.org/debian sid/main amd64 r-cran-mass amd64 7.3-60.0.1-1 [1118 kB] Get:319 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-5-1 [1394 kB] Get:320 http://deb.debian.org/debian sid/main amd64 r-cran-nlme amd64 3.1.164-1 [2280 kB] Get:321 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.6-5-1 [3789 kB] Get:322 http://deb.debian.org/debian sid/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get:323 http://deb.debian.org/debian sid/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:324 http://deb.debian.org/debian sid/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:325 http://deb.debian.org/debian sid/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:326 http://deb.debian.org/debian sid/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:327 http://deb.debian.org/debian sid/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get:328 http://deb.debian.org/debian sid/main amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3405 kB] Get:329 http://deb.debian.org/debian sid/main amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [443 kB] Get:330 http://deb.debian.org/debian sid/main amd64 r-cran-pkgbuild all 1.4.3-1 [210 kB] Get:331 http://deb.debian.org/debian sid/main amd64 r-cran-rprojroot all 2.0.4-1 [124 kB] Get:332 http://deb.debian.org/debian sid/main amd64 r-cran-pkgload all 1.3.4-1 [208 kB] Get:333 http://deb.debian.org/debian sid/main amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] Get:334 http://deb.debian.org/debian sid/main amd64 r-cran-rstudioapi all 0.15.0-1 [282 kB] Get:335 http://deb.debian.org/debian sid/main amd64 r-cran-waldo all 0.5.2-1 [120 kB] Get:336 http://deb.debian.org/debian sid/main amd64 r-cran-testthat amd64 3.2.1-1 [1644 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 173 MB in 2s (78.5 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21262 files and directories currently installed.) Preparing to unpack .../coreutils_9.4-3+b2_amd64.deb ... Unpacking coreutils (9.4-3+b2) over (8.32-4+b1) ... Setting up coreutils (9.4-3+b2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21267 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-6_amd64.deb ... Unpacking dash (0.5.12-6) over (0.5.11+git20200708+dd9ef66-5) ... Setting up dash (0.5.12-6) ... Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' (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 ... 21266 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.10-1_amd64.deb ... Unpacking diffutils (1:3.10-1) over (1:3.7-5) ... Setting up diffutils (1:3.10-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21268 files and directories currently installed.) Preparing to unpack .../findutils_4.9.0-5_amd64.deb ... Unpacking findutils (4.9.0-5) over (4.8.0-1) ... Setting up findutils (4.9.0-5) ... (Reading database ... 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Unpacking libtinfo6:amd64 (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Setting up libtinfo6:amd64 (6.4+20240113-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21268 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4+20240113-1_amd64.deb ... Unpacking ncurses-bin (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-bin (6.4+20240113-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21268 files and directories currently installed.) Preparing to unpack .../00-libb-hooks-op-check-perl_0.22-3+b1_amd64.deb ... Unpacking libb-hooks-op-check-perl:amd64 (0.22-3+b1) over (0.22-1+b3) ... Preparing to unpack .../01-libxml-parser-perl_2.47-1+b2_amd64.deb ... Unpacking libxml-parser-perl (2.47-1+b2) over (2.46-2) ... Preparing to unpack .../02-libsub-name-perl_0.27-1+b2_amd64.deb ... 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Unpacking perl-modules-5.38 (5.38.2-3.2) ... dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libsasl2-modules-db:amd64 depends on libdb5.3. libpython3.9-stdlib:amd64 depends on libdb5.3. libperl5.32:amd64 depends on libdb5.3. libpam-modules:amd64 depends on libdb5.3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22687 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg1-0.8) ... Selecting previously unselected package libdb5.3t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22681 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-5) ... dpkg: libgdbm6:amd64: dependency problems, but removing anyway as you requested: libperl5.32:amd64 depends on libgdbm6 (>= 1.18-3). libgdbm-compat4:amd64 depends on libgdbm6 (>= 1.16). (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22688 files and directories currently installed.) Removing libgdbm-compat4:amd64 (1.19-2) ... Selecting previously unselected package libgdbm-compat4t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22682 files and directories currently installed.) Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.23-5.1) ... Selecting previously unselected package libperl5.38t64:amd64. Preparing to unpack .../libperl5.38t64_5.38.2-3.2_amd64.deb ... Unpacking libperl5.38t64:amd64 (5.38.2-3.2) ... Preparing to unpack .../perl-base_5.38.2-3.2_amd64.deb ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23212 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.66-5_amd64.deb ... Unpacking libcap2:amd64 (1:2.66-5) ... Setting up libcap2:amd64 (1:2.66-5) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23220 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.3-2_amd64.deb ... Unpacking libgcrypt20:amd64 (1.10.3-2) over (1.8.7-6) ... Setting up libgcrypt20:amd64 (1.10.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23222 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.9.4-1+b2_amd64.deb ... Unpacking liblz4-1:amd64 (1.9.4-1+b2) over (1.9.3-2) ... Setting up liblz4-1:amd64 (1.9.4-1+b2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23223 files and directories currently installed.) Preparing to unpack .../libsystemd0_255.4-1+b1_amd64.deb ... Unpacking libsystemd0:amd64 (255.4-1+b1) over (247.3-7+deb11u4) ... Setting up libsystemd0:amd64 (255.4-1+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23225 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.36-4_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-4) over (1:4.4.18-4) ... Setting up libcrypt1:amd64 (1:4.4.36-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23225 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-6_amd64.deb ... Unpacking libpam-modules-bin (1.5.3-6) over (1.4.0-9+deb11u1) ... Replacing files in old package libpam-modules:amd64 (1.4.0-9+deb11u1) ... Setting up libpam-modules-bin (1.5.3-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23229 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-6_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.3-6) over (1.4.0-9+deb11u1) ... dpkg: warning: unable to delete old directory '/lib/x86_64-linux-gnu/security': Directory not empty Setting up libpam-modules:amd64 (1.5.3-6) ... Installing new version of config file /etc/security/limits.conf ... Installing new version of config file /etc/security/namespace.init ... Installing new version of config file /etc/security/sepermit.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23227 files and directories currently installed.) Preparing to unpack .../libbz2-1.0_1.0.8-5+b2_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.8-5+b2) over (1.0.8-4) ... Setting up libbz2-1.0:amd64 (1.0.8-5+b2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23410 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.3-1.1_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.3-1.1) ... Setting up libnettle8t64:amd64 (3.9.1-2.2) ... Setting up libhogweed6t64:amd64 (3.9.1-2.2) ... Setting up libgnutls30t64:amd64 (3.8.3-1.1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23442 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.5-1_all.deb ... Unpacking libsemanage-common (3.5-1) over (3.1-1) ... Setting up libsemanage-common (3.5-1) ... Installing new version of config file /etc/selinux/semanage.conf ... Selecting previously unselected package libsepol2:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23442 files and directories currently installed.) Preparing to unpack .../libsepol2_3.5-2_amd64.deb ... Unpacking libsepol2:amd64 (3.5-2) ... Setting up libsepol2:amd64 (3.5-2) ... Selecting previously unselected package libsemanage2:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23446 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.5-1+b2_amd64.deb ... Unpacking libsemanage2:amd64 (3.5-1+b2) ... Setting up libsemanage2:amd64 (3.5-1+b2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23451 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.13+dfsg1-4_amd64.deb ... Unpacking passwd (1:4.13+dfsg1-4) over (1:4.8.1-1) ... Setting up passwd (1:4.13+dfsg1-4) ... Installing new version of config file /etc/default/useradd ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23480 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.137_all.deb ... moving unchanged adduser.conf to adduser.conf.update-old. New dpkg-conffile will come from the package. Unpacking adduser (3.137) over (3.118+deb11u1) ... Setting up adduser (3.137) ... Installing new version of config file /etc/deluser.conf ... (Reading database ... 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Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-automatic.gpg ... (Reading database ... (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 ... 23443 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-1_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-1) over (2.5.1-1+deb11u1) ... Setting up libseccomp2:amd64 (2.5.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23443 files and directories currently installed.) Preparing to unpack .../apt_2.7.13+b1_amd64.deb ... Unpacking apt (2.7.13+b1) over (2.2.4) ... Setting up apt (2.7.13+b1) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt-compat ... Removing obsolete conffile /etc/kernel/postinst.d/apt-auto-removal ... (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 ... 23437 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-3_all.deb ... Unpacking libnumber-compare-perl (0.03-3) over (0.03-1.1) ... Setting up libnumber-compare-perl (0.03-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23437 files and directories currently installed.) Preparing to unpack .../libtext-glob-perl_0.11-3_all.deb ... Unpacking libtext-glob-perl (0.11-3) over (0.11-1) ... Setting up libtext-glob-perl (0.11-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23437 files and directories currently installed.) Preparing to unpack .../libfile-find-rule-perl_0.34-3_all.deb ... Unpacking libfile-find-rule-perl (0.34-3) over (0.34-1) ... Setting up perl-modules-5.38 (5.38.2-3.2) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-5) ... Setting up libgdbm6t64:amd64 (1.23-5.1) ... Setting up libgdbm-compat4t64:amd64 (1.23-5.1) ... Setting up libperl5.38t64:amd64 (5.38.2-3.2) ... Setting up perl (5.38.2-3.2) ... Setting up libfile-find-rule-perl (0.34-3) ... Selecting previously unselected package usrmerge. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23437 files and directories currently installed.) Preparing to unpack .../archives/usrmerge_39_all.deb ... Unpacking usrmerge (39) ... Setting up usrmerge (39) ... (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 ... 23444 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.66_all.deb ... Unpacking init-system-helpers (1.66) over (1.60) ... Setting up init-system-helpers (1.66) ... (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 ... 23444 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4+20240113-1_all.deb ... Unpacking ncurses-base (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-base (6.4+20240113-1) ... dpkg: libss2:amd64: dependency problems, but removing anyway as you requested: e2fsprogs depends on libss2 (>= 1.38). (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23439 files and directories currently installed.) Preparing to unpack .../libss2t64_1.47.0-2.3+b1_amd64.deb ... Unpacking libss2t64:amd64 (1.47.0-2.3+b1) ... dpkg: libcom-err2:amd64: dependency problems, but removing anyway as you requested: libkrb5-3:amd64 depends on libcom-err2 (>= 1.43.9). libgssapi-krb5-2:amd64 depends on libcom-err2 (>= 1.43.9). e2fsprogs depends on libcom-err2 (>= 1.43.9). (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 ... 23446 files and directories currently installed.) Removing libcom-err2:amd64 (1.46.2-2) ... Selecting previously unselected package libcom-err2t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23441 files and directories currently installed.) Preparing to unpack .../0-libcom-err2t64_1.47.0-2.3+b1_amd64.deb ... Unpacking libcom-err2t64:amd64 (1.47.0-2.3+b1) ... Preparing to unpack .../1-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) over (1.0.9-2+b2) ... Preparing to unpack .../2-libgssapi-krb5-2_1.20.1-5.1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-5.1) over (1.18.3-6+deb11u4) ... Preparing to unpack .../3-libkrb5-3_1.20.1-5.1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-5.1) over (1.18.3-6+deb11u4) ... Preparing to unpack .../4-libk5crypto3_1.20.1-5.1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-5.1) over (1.18.3-6+deb11u4) ... Preparing to unpack .../5-libkrb5support0_1.20.1-5.1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-5.1) over (1.18.3-6+deb11u4) ... Preparing to unpack .../6-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) over (1.6.1-2) ... Preparing to unpack .../7-libsasl2-2_2.1.28+dfsg1-4+b2_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-4+b2) over (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../8-libldap-2.5-0_2.5.16+dfsg-1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.16+dfsg-1) ... Preparing to unpack .../9-libnghttp2-14_1.59.0-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.59.0-1+b1) over (1.43.0-1+deb11u1) ... dpkg: libcurl4:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libcurl4 (>= 7.28.0). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23459 files and directories currently installed.) Removing libcurl4:amd64 (7.74.0-1.3+deb11u11) ... Selecting previously unselected package libcurl4t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23452 files and directories currently installed.) Preparing to unpack .../libcurl4t64_8.6.0-3.2_amd64.deb ... Unpacking libcurl4t64:amd64 (8.6.0-3.2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23459 files and directories currently installed.) Removing libpsl5:amd64 (0.21.0-1.2) ... Selecting previously unselected package libpsl5t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23453 files and directories currently installed.) Preparing to unpack .../libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23460 files and directories currently installed.) Removing libssh2-1:amd64 (1.9.0-2) ... Selecting previously unselected package libssh2-1t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23452 files and directories currently installed.) Preparing to unpack .../libssh2-1t64_1.11.0-4.1+b1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-4.1+b1) ... Preparing to unpack .../logsave_1.47.0-2.3+b1_amd64.deb ... Unpacking logsave (1.47.0-2.3+b1) over (1.46.2-2) ... dpkg: libext2fs2:amd64: dependency problems, but removing anyway as you requested: e2fsprogs depends on libext2fs2 (= 1.46.2-2). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23463 files and directories currently installed.) Removing libext2fs2:amd64 (1.46.2-2) ... Selecting previously unselected package libext2fs2t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23456 files and directories currently installed.) Preparing to unpack .../libext2fs2t64_1.47.0-2.3+b1_amd64.deb ... Unpacking libext2fs2t64:amd64 (1.47.0-2.3+b1) ... Setting up libcom-err2t64:amd64 (1.47.0-2.3+b1) ... Setting up libext2fs2t64:amd64 (1.47.0-2.3+b1) ... Setting up libss2t64:amd64 (1.47.0-2.3+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23465 files and directories currently installed.) Preparing to unpack .../0-e2fsprogs_1.47.0-2.3+b1_amd64.deb ... Unpacking e2fsprogs (1.47.0-2.3+b1) over (1.46.2-2) ... dpkg: warning: unable to delete old directory '/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/udev': Directory not empty Preparing to unpack .../1-r-cran-ps_1.7.6-1_amd64.deb ... Unpacking r-cran-ps (1.7.6-1) over (1.5.0-1) ... Preparing to unpack .../2-r-cran-rlang_1.1.3-1_amd64.deb ... Unpacking r-cran-rlang (1.1.3-1) over (0.4.10-1) ... Preparing to unpack .../3-r-cran-pillar_1.9.0+dfsg-1_all.deb ... Unpacking r-cran-pillar (1.9.0+dfsg-1) over (1.4.7-1) ... Preparing to unpack .../4-r-cran-tibble_3.2.1+dfsg-2_amd64.deb ... Unpacking r-cran-tibble (3.2.1+dfsg-2) over (3.0.6+dfsg-1) ... Preparing to unpack .../5-r-base-core_4.3.3-2_amd64.deb ... Unpacking r-base-core (4.3.3-2) over (4.0.4-1) ... Preparing to unpack .../6-libpangocairo-1.0-0_1.52.1+ds-1_amd64.deb ... Unpacking libpangocairo-1.0-0:amd64 (1.52.1+ds-1) over (1.46.2-3) ... Preparing to unpack .../7-libpango-1.0-0_1.52.1+ds-1_amd64.deb ... Unpacking libpango-1.0-0:amd64 (1.52.1+ds-1) over (1.46.2-3) ... Preparing to unpack .../8-libpangoft2-1.0-0_1.52.1+ds-1_amd64.deb ... Unpacking libpangoft2-1.0-0:amd64 (1.52.1+ds-1) over (1.46.2-3) ... Preparing to unpack .../9-libharfbuzz0b_8.3.0-2+b1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (8.3.0-2+b1) over (2.7.4-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23255 files and directories currently installed.) Removing libglib2.0-0:amd64 (2.66.8-1+deb11u1) ... Selecting previously unselected package libglib2.0-0t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23229 files and directories currently installed.) Preparing to unpack .../libglib2.0-0t64_2.78.4-4_amd64.deb ... libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:amd64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... removed '/var/lib/dpkg/info/libglib2.0-0:amd64.postrm' Unpacking libglib2.0-0t64:amd64 (2.78.4-4) ... Preparing to unpack .../libfreetype6_2.13.2+dfsg-1+b2_amd64.deb ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-3.1) ... Preparing to unpack .../libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) over (2:1.7.2-1+deb11u2) ... Preparing to unpack .../libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) over (1.14-3) ... Preparing to unpack .../libx11-6_2%3a1.8.7-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.7-1) over (2:1.7.2-1+deb11u2) ... (Reading database ... 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Setting up libsensors5:amd64 (1:3.6.0-9) ... Setting up libncursesw6:amd64 (6.4+20240113-1) ... Setting up libk5crypto3:amd64 (1.20.1-5.1) ... Setting up libparams-util-perl (1.102-3) ... Setting up logsave (1.47.0-2.3+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-4+b2) ... Setting up libgfortran5:amd64 (14-20240303-1) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libwebp7:amd64 (1.3.2-0.4+b1) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libsub-name-perl:amd64 (0.27-1+b2) ... Setting up libdata-stag-perl (0.14-3) ... Setting up mount (2.39.3-10) ... Setting up sensible-utils (0.0.22) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libpath-tiny-perl (0.144-1) ... Setting up procps (2:4.0.4-4) ... Installing new version of config file /etc/init.d/procps ... Installing new version of config file /etc/sysctl.conf ... Installing new version of config file /etc/sysctl.d/README.sysctl ... Setting up libtingea0:amd64 (21-361-2+b1) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up libthai-data (0.1.29-2) ... Setting up libdevel-globaldestruction-perl (0.14-4) ... Setting up netbase (6.4) ... Installing new version of config file /etc/ethertypes ... Installing new version of config file /etc/protocols ... Installing new version of config file /etc/rpc ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:amd64 (1.20.1-5.1) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b1) ... Setting up openssl (3.1.5-1.1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libbsd0:amd64 (0.12.1-1) ... Setting up readline-common (8.2-3.1) ... Setting up bedtools (2.31.1+dfsg-2) ... Setting up liburi-perl (5.27-1) ... Setting up gcc-9-base:amd64 (9.5.0-5) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libtext-csv-perl (2.04-1) ... Setting up libnet-ssleay-perl:amd64 (1.94-1+b1) ... Setting up cd-hit (4.8.1-4) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up liblapack3:amd64 (3.12.0-3) ... Setting up libmbedx509-1:amd64 (2.28.7-1) ... Setting up libmbedtls14:amd64 (2.28.7-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Installing new version of config file /etc/fonts/conf.d/README ... Installing new version of config file /etc/fonts/fonts.conf ... Setting up libtest-warn-perl (0.37-2) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libnet-http-perl (6.23-1) ... Setting up e2fsprogs (1.47.0-2.3+b1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up libexception-class-perl (1.45-1) ... Setting up libclass-c3-perl (0.35-2) ... Setting up libgraph-perl (1:0.9727-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2+b2) ... Setting up libldap-2.5-0:amd64 (2.5.16+dfsg-1) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 37 added, 20 removed; done. Setting up libtest-exception-perl (0.43-3) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b2) ... Setting up mcl (1:22-282+ds-2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5.1) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libtest-output-perl (1.034-1) ... Setting up ucf (3.0043+nmu1) ... Setting up libreadline8t64:amd64 (8.2-3.1) ... Setting up libhtml-parser-perl:amd64 (3.81-1+b2) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libmro-compat-perl (0.15-2) ... Setting up sysstat (12.7.5-2) ... Installing new version of config file /etc/cron.d/sysstat ... Installing new version of config file /etc/cron.daily/sysstat ... Installing new version of config file /etc/init.d/sysstat ... Installing new version of config file /etc/sysstat/sysstat ... Installing new version of config file /etc/sysstat/sysstat.ioconf ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libeval-closure-perl (0.14-3) ... Setting up libtirpc3:amd64 (1.3.4+ds-1) ... Setting up libpaper1:amd64 (1.1.29) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libcurl4t64:amd64 (8.6.0-3.2) ... Setting up libtest-most-perl (0.38-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.8-3) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b3) ... Setting up libpango-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libpaper-utils (1.1.29) ... Setting up libcairo2:amd64 (1.18.0-2) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libdist-checkconflicts-perl (0.11-2) ... Setting up parallel (20231122+ds-1) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up libpangoft2-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up bioperl (1.7.8-1) ... Setting up python3.11 (3.11.8-3) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up python3 (3.11.8-1) ... Setting up libmodule-runtime-conflicts-perl (0.003-2) ... Setting up libtest-files-perl (0.24-1) ... Setting up libclass-load-perl (0.25-2) ... Setting up ncbi-blast+ (2.12.0+ds-4) ... Setting up r-base-core (4.3.3-2) ... Installing new version of config file /etc/R/Makeconf ... Installing new version of config file /etc/R/Renviron.site ... Installing new version of config file /etc/R/repositories ... Replacing config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.5.2-1) ... Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-5-1) ... Setting up r-cran-ps (1.7.6-1) ... Setting up r-cran-nlme (3.1.164-1) ... Setting up r-cran-farver (2.1.1-1) ... Setting up libpackage-deprecationmanager-perl (0.18-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libdevel-overloadinfo-perl (0.007-1) ... Setting up libclass-load-xs-perl (0.10-2+b3) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up r-cran-fs (1.6.3+dfsg-1) ... Setting up r-cran-brio (1.1.4-1) ... Setting up r-cran-diffobj (0.3.5-1+b1) ... Setting up r-cran-rlang (1.1.3-1) ... Setting up r-cran-withr (3.0.0+dfsg-1) ... Setting up r-cran-processx (3.8.3-1) ... Setting up libmoose-perl:amd64 (2.2207-1+b1) ... Setting up r-cran-digest (0.6.35-1) ... Setting up r-cran-evaluate (0.23-1) ... Setting up r-cran-prettyunits (1.2.0-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-mass (7.3-60.0.1-1) ... Setting up r-cran-glue (1.7.0-1) ... Setting up r-cran-cli (3.6.2-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-cran-rprojroot (2.0.4-1) ... Setting up r-cran-jsonlite (1.8.8+dfsg-1) ... Setting up r-cran-rstudioapi (0.15.0-1) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-colorspace (2.1-0+dfsg-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-scales (1.3.0-1) ... Setting up r-cran-gtable (0.3.4+dfsg-1) ... Setting up r-cran-matrix (1.6-5-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up r-cran-ellipsis (0.3.2-2) ... Setting up r-cran-callr (3.7.5-1) ... Setting up r-cran-desc (1.4.3-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-cran-waldo (0.5.2-1) ... Setting up r-cran-pkgbuild (1.4.3-1) ... Setting up r-cran-pkgload (1.3.4-1) ... Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... Setting up r-cran-testthat (3.2.1-1) ... Setting up liblwp-protocol-https-perl (6.13-1) ... Setting up libwww-perl (6.76-1) ... Setting up libxml-parser-perl (2.47-1+b2) ... Setting up libgraph-readwrite-perl (2.10-1) ... Processing triggers for libc-bin (2.37-15.1) ... Processing triggers for debianutils (5.17) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 1m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-yf', 'dist-upgrade'] 1m29.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m30.5s DUMP: 54551ebd6e22a313d13c7242b238c002 - 1m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'show', '--no-all-versions', 'roary'] 1m30.7s DUMP: Package: roary Version: 3.13.0+dfsg-1 Installed-Size: 670 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Description-en: high speed stand alone pan genome pipeline Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes. Description-md5: 6d457fd706202fc2ef292eacf7b46029 Homepage: http://sanger-pathogens.github.io/Roary/ Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing Section: science Priority: optional Filename: pool/main/r/roary/roary_3.13.0+dfsg-1_all.deb Size: 183740 MD5sum: 991a49663368c3a0a660af3107720dad SHA256: 1732e00b165a0cee53b42fb9b142ea5491cd7de00b91be2cc8709297d999de66 1m30.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'show', '--no-all-versions', 'roary'] 1m30.7s INFO: apt-cache knows about the following packages: roary 1m30.7s INFO: Running scripts pre_install 1m30.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_database-server'] 1m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_database-server'] 1m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_exceptions'] 1m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_exceptions'] 1m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_extras'] 1m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_extras'] 1m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_foreign_architecture'] 1m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_foreign_architecture'] 1m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'policy'] 1m30.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'policy'] 1m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'policy', 'roary'] 1m30.9s DUMP: roary: Installed: 3.13.0+dfsg-1 Candidate: 3.13.0+dfsg-1 Version table: *** 3.13.0+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'policy', 'roary'] 1m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-y', 'install', 'roary'] 1m31.4s DUMP: Reading package lists... Building dependency tree... Reading state information... roary is already the newest version (3.13.0+dfsg-1). The following packages were automatically installed and are no longer required: libicu67 libldap-2.4-2 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libncurses6 libperl5.32 libprocps8 libpython3.9-minimal libpython3.9-stdlib libquadmath0 libsub-identify-perl libtiff5 libwebp6 perl-modules-5.32 python3.9 python3.9-minimal r-cran-assertthat r-cran-ellipsis r-cran-prettyunits Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-y', 'install', 'roary'] 1m31.4s INFO: Running scripts post_install 1m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_install_exceptions'] 1m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_install_exceptions'] 1m31.4s INFO: Running scripts post_distupgrade 1m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_distupgrade_exceptions'] 1m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_distupgrade_exceptions'] 1m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_distupgrade_zz_backports'] 1m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_distupgrade_zz_backports'] 1m31.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 1m32.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 1m32.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 1m34.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 1m34.0s INFO: Running scripts pre_install 1m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_database-server'] 1m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_database-server'] 1m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_exceptions'] 1m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_exceptions'] 1m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_extras'] 1m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_extras'] 1m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_foreign_architecture'] 1m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_foreign_architecture'] 1m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'policy'] 1m34.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'policy'] 1m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'policy', 'roary'] 1m34.2s DUMP: roary: Installed: 3.13.0+dfsg-1 Candidate: 3.13.0+dfsg-1 Version table: *** 3.13.0+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-cache', 'policy', 'roary'] 1m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-y', 'install', 'roary=3.13.0+dfsg-1'] 1m34.9s DUMP: Reading package lists... Building dependency tree... Reading state information... roary is already the newest version (3.13.0+dfsg-1). The following packages were automatically installed and are no longer required: libicu67 libldap-2.4-2 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libncurses6 libperl5.32 libprocps8 libpython3.9-minimal libpython3.9-stdlib libquadmath0 libsub-identify-perl libtiff5 libwebp6 perl-modules-5.32 python3.9 python3.9-minimal r-cran-assertthat r-cran-ellipsis r-cran-prettyunits Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m34.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-y', 'install', 'roary=3.13.0+dfsg-1'] 1m34.9s INFO: Running scripts post_install 1m34.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_install_exceptions'] 1m34.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_install_exceptions'] 1m35.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 1m36.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 1m36.4s INFO: /bin converted to /usr/bin by /usr merge 1m36.5s INFO: /lib converted to /usr/lib by /usr merge 1m36.5s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 1m36.5s INFO: /lib64 converted to /usr/lib64 by /usr merge 1m36.5s INFO: /sbin converted to /usr/sbin by /usr merge 1m38.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', '-ac', '--ignore-obsolete'] 1m41.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', '-ac', '--ignore-obsolete'] 1m41.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m41.8s DUMP: 0.15.6 1m41.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m41.8s INFO: Running adequate version 0.15.6 now. 1m41.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'roary'] 1m42.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'roary'] 1m42.0s INFO: Running scripts pre_remove 1m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m47.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m47.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_remove_exceptions'] 1m47.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/pre_remove_exceptions'] 1m47.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m47.7s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.13+b1 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bedtools bedtools 2.31.1+dfsg-2 install ok installed bioperl bioperl 1.7.8-1 install ok installed bsdutils bsdutils 1:2.39.3-10 install ok installed ca-certificates ca-certificates 20240203 install ok installed cd-hit cd-hit 4.8.1-4 install ok installed coreutils coreutils 9.4-3+b2 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.3+b1 install ok installed fasttree fasttree 2.1.11-2 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig fontconfig 2.15.0-1.1 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed gcc-10-base:amd64 gcc-10-base 10.5.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240303-1 install ok installed gcc-9-base:amd64 gcc-9-base 9.5.0-5 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libalgorithm-c3-perl libalgorithm-c3-perl 0.11-2 install ok installed libalgorithm-diff-perl libalgorithm-diff-perl 1.201-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.13+b1 install ok installed libarray-utils-perl libarray-utils-perl 0.5-3 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libb-hooks-op-check-perl:amd64 libb-hooks-op-check-perl 0.22-3+b1 install ok installed libbio-perl-perl libbio-perl-perl 1.7.8-1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.39.3-10 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.12.1-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-15.1 install ok installed libc6:amd64 libc6 2.37-15.1 install ok installed libcairo2:amd64 libcairo2 1.18.0-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcapture-tiny-perl libcapture-tiny-perl 0.48-2 install ok installed libclass-c3-perl libclass-c3-perl 0.35-2 install ok installed libclass-data-inheritable-perl libclass-data-inheritable-perl 0.08-3 install ok installed libclass-load-perl libclass-load-perl 0.25-2 install ok installed libclass-load-xs-perl libclass-load-xs-perl 0.10-2+b3 install ok installed libclone-perl:amd64 libclone-perl 0.46-1+b2 install ok installed libcom-err2t64:amd64 libcom-err2t64 1.47.0-2.3+b1 install ok installed libconst-fast-perl libconst-fast-perl 0.014-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcurl4t64:amd64 libcurl4t64 8.6.0-3.2 install ok installed libdata-compare-perl libdata-compare-perl 1.29-1 install ok installed libdata-optlist-perl libdata-optlist-perl 0.114-1 install ok installed libdata-stag-perl libdata-stag-perl 0.14-3 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b2 install ok installed libdeflate0:amd64 libdeflate0 1.19-1 install ok installed libdevel-callchecker-perl:amd64 libdevel-callchecker-perl 0.008-2+b2 install ok installed libdevel-globaldestruction-perl libdevel-globaldestruction-perl 0.14-4 install ok installed libdevel-overloadinfo-perl libdevel-overloadinfo-perl 0.007-1 install ok installed libdevel-stacktrace-perl libdevel-stacktrace-perl 2.0500-1 install ok installed libdigest-md5-file-perl libdigest-md5-file-perl 0.08-1.1 install ok installed libdist-checkconflicts-perl libdist-checkconflicts-perl 0.11-2 install ok installed libdynaloader-functions-perl libdynaloader-functions-perl 0.003-3 install ok installed libencode-locale-perl libencode-locale-perl 1.05-3 install ok installed libenv-path-perl libenv-path-perl 0.19-4 install ok installed libeval-closure-perl libeval-closure-perl 0.14-3 install ok installed libexception-class-perl libexception-class-perl 1.45-1 install ok installed libexpat1:amd64 libexpat1 2.6.1-2 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.3+b1 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libfile-grep-perl libfile-grep-perl 0.02-3 install ok installed libfile-listing-perl libfile-listing-perl 6.16-1 install ok installed libfile-slurper-perl libfile-slurper-perl 0.014-1 install ok installed libfile-which-perl libfile-which-perl 1.27-2 install ok installed libfindbin-libs-perl libfindbin-libs-perl 3.0.2-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b2 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240303-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.23-5.1 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.23-5.1 install ok installed libgfortran5:amd64 libgfortran5 14-20240303-1 deinstall ok config-files libglib2.0-0:amd64 libglib2.0-0 2.66.8-1+deb11u1 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.78.4-4 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.3-1.1 install ok installed libgomp1:amd64 libgomp1 14-20240303-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgraph-perl libgraph-perl 1:0.9727-1 install ok installed libgraph-readwrite-perl libgraph-readwrite-perl 2.10-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5.1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2+b1 install ok installed libheap-perl libheap-perl 0.80-5 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libhtml-parser-perl:amd64 libhtml-parser-perl 3.81-1+b2 install ok installed libhtml-tagset-perl libhtml-tagset-perl 3.20-6 install ok installed libhtml-tree-perl libhtml-tree-perl 5.07-3 install ok installed libhttp-cookies-perl libhttp-cookies-perl 6.11-1 install ok installed libhttp-date-perl libhttp-date-perl 6.06-1 install ok installed libhttp-message-perl libhttp-message-perl 6.45-1 install ok installed libhttp-negotiate-perl libhttp-negotiate-perl 6.01-2 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libicu72:amd64 libicu72 72.1-4+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libio-all-perl libio-all-perl 0.87-2 install ok installed libio-html-perl libio-html-perl 1.004-3 install ok installed libio-socket-ssl-perl libio-socket-ssl-perl 2.085-1 install ok installed libio-string-perl libio-string-perl 1.08-4 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5.1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-5.1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-5.1 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.16+dfsg-1 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b1 install ok installed liblog-log4perl-perl liblog-log4perl-perl 1.57-1 install ok installed liblwp-mediatypes-perl liblwp-mediatypes-perl 6.04-2 install ok installed liblwp-protocol-https-perl liblwp-protocol-https-perl 6.13-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.6.0-0.2 install ok installed libmbedcrypto3:amd64 libmbedcrypto3 2.16.9-0.1 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.7-1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.9-0.1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.7-1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.9-0.1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.7-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmodule-implementation-perl libmodule-implementation-perl 0.09-2 install ok installed libmodule-runtime-conflicts-perl libmodule-runtime-conflicts-perl 0.003-2 install ok installed libmodule-runtime-perl libmodule-runtime-perl 0.016-2 install ok installed libmoose-perl:amd64 libmoose-perl 2.2207-1+b1 install ok installed libmount1:amd64 libmount1 2.39.3-10 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-2 install ok installed libmro-compat-perl libmro-compat-perl 0.15-2 install ok installed libncurses6:amd64 libncurses6 6.4+20240113-1 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnet-http-perl libnet-http-perl 6.23-1 install ok installed libnet-ssleay-perl:amd64 libnet-ssleay-perl 1.94-1+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.59.0-1+b1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpackage-deprecationmanager-perl libpackage-deprecationmanager-perl 0.18-1 install ok installed libpackage-stash-perl libpackage-stash-perl 0.40-1 install ok installed libpackage-stash-xs-perl:amd64 libpackage-stash-xs-perl 0.30-1+b3 install ok installed libpadwalker-perl libpadwalker-perl 2.5-1+b5 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-6 install ok installed libpam-runtime libpam-runtime 1.5.3-6 install ok installed libpam0g:amd64 libpam0g 1.5.3-6 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.52.1+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.52.1+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.52.1+ds-1 install ok installed libpaper-utils libpaper-utils 1.1.29 install ok installed libpaper1:amd64 libpaper1 1.1.29 install ok installed libparams-classify-perl:amd64 libparams-classify-perl 0.015-2+b3 install ok installed libparams-util-perl libparams-util-perl 1.102-3 install ok installed libparse-yapp-perl libparse-yapp-perl 1.21-3 install ok installed libpath-tiny-perl libpath-tiny-perl 0.144-1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpcre3:amd64 libpcre3 2:8.39-15+b1 install ok installed libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u3 install ok installed libperl5.38t64:amd64 libperl5.38t64 5.38.2-3.2 install ok installed libperlio-utf8-strict-perl libperlio-utf8-strict-perl 0.010-1+b2 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.43-3 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-4 install ok installed libprocps8:amd64 libprocps8 2:3.3.17-5 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.8-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.8-3 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.8-3 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 14-20240303-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-3.1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b3 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-4+b2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-4+b2 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsensors-config libsensors-config 1:3.6.0-9 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-9 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libset-object-perl libset-object-perl 1.42-1+b4 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.4+b1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-10 install ok installed libspiffy-perl libspiffy-perl 0.46-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.1-1 install ok installed libss2t64:amd64 libss2t64 1.47.0-2.3+b1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-4.1+b1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libssl3t64:amd64 libssl3t64 3.1.5-1.1 install ok installed libstdc++6:amd64 libstdc++6 14-20240303-1 install ok installed libsub-exporter-perl libsub-exporter-perl 0.990-1 install ok installed libsub-exporter-progressive-perl libsub-exporter-progressive-perl 0.001013-3 install ok installed libsub-identify-perl libsub-identify-perl 0.14-3+b2 install ok installed libsub-install-perl libsub-install-perl 0.929-1 install ok installed libsub-name-perl:amd64 libsub-name-perl 0.27-1+b2 install ok installed libsub-uplevel-perl libsub-uplevel-perl 0.2800-3 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.14+dfsg-1 install ok installed libtest-deep-perl libtest-deep-perl 1.204-1 install ok installed libtest-differences-perl libtest-differences-perl 0.71-1 install ok installed libtest-exception-perl libtest-exception-perl 0.43-3 install ok installed libtest-file-perl libtest-file-perl 1.993-1 install ok installed libtest-files-perl libtest-files-perl 0.24-1 install ok installed libtest-most-perl libtest-most-perl 0.38-1 install ok installed libtest-output-perl libtest-output-perl 1.034-1 install ok installed libtest-warn-perl libtest-warn-perl 0.37-2 install ok installed libtext-csv-perl libtext-csv-perl 2.04-1 install ok installed libtext-diff-perl libtext-diff-perl 1.45-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff5:amd64 libtiff5 4.2.0-1+deb11u5 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtimedate-perl libtimedate-perl 2.3300-2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtingea0:amd64 libtingea0 21-361-2+b1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.1 install ok installed libtirpc3:amd64 libtirpc3 1.3.4+ds-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.14-1 install ok installed libtry-tiny-perl libtry-tiny-perl 0.31-2 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed liburi-perl liburi-perl 5.27-1 install ok installed libuuid1:amd64 libuuid1 2.39.3-10 install ok installed libuv1:amd64 libuv1 1.48.0-1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2.1+deb11u2 install ok installed libwebp7:amd64 libwebp7 1.3.2-0.4+b1 install ok installed libwww-perl libwww-perl 6.76-1 install ok installed libwww-robotrules-perl libwww-robotrules-perl 6.02-1 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxft2:amd64 libxft2 2.3.6-1+b1 install ok installed libxml-parser-perl libxml-parser-perl 2.47-1+b2 install ok installed libxml-writer-perl libxml-writer-perl 0.900-2 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.3+b1 install ok installed lsb-base lsb-base 11.6 install ok installed mafft mafft 7.505-1 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mcl mcl 1:22-282+ds-2 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.39.3-10 install ok installed ncbi-blast+ ncbi-blast+ 2.12.0+ds-4 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-1 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.1.5-1.1 install ok installed parallel parallel 20231122+ds-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl perl 5.38.2-3.2 install ok installed perl-base perl-base 5.38.2-3.2 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.1-4+deb11u3 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3.2 install ok installed perl-openssl-defaults:amd64 perl-openssl-defaults 7+b2 install ok installed prank prank 0.0.170427+dfsg-3 install ok installed procps procps 2:4.0.4-4 install ok installed python3 python3 3.11.8-1 install ok installed python3-minimal python3-minimal 3.11.8-1 install ok installed python3.11 python3.11 3.11.8-3 install ok installed python3.11-minimal python3.11-minimal 3.11.8-3 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed r-base-core r-base-core 4.3.3-2 install ok installed r-cran-assertthat r-cran-assertthat 0.2.1-2 install ok installed r-cran-brio r-cran-brio 1.1.4-1 install ok installed r-cran-callr r-cran-callr 3.7.5-1 install ok installed r-cran-cli r-cran-cli 3.6.2-1 install ok installed r-cran-colorspace r-cran-colorspace 2.1-0+dfsg-1 install ok installed r-cran-crayon r-cran-crayon 1.5.2-1 install ok installed r-cran-desc r-cran-desc 1.4.3-1 install ok installed r-cran-diffobj r-cran-diffobj 0.3.5-1+b1 install ok installed r-cran-digest r-cran-digest 0.6.35-1 install ok installed r-cran-ellipsis r-cran-ellipsis 0.3.2-2 install ok installed r-cran-evaluate r-cran-evaluate 0.23-1 install ok installed r-cran-fansi r-cran-fansi 1.0.5-1 install ok installed r-cran-farver r-cran-farver 2.1.1-1 install ok installed r-cran-fs r-cran-fs 1.6.3+dfsg-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.4.4+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.7.0-1 install ok installed r-cran-gtable r-cran-gtable 0.3.4+dfsg-1 install ok installed r-cran-isoband r-cran-isoband 0.2.7-1 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.8+dfsg-1 install ok installed r-cran-labeling r-cran-labeling 0.4.3-1 install ok installed r-cran-lattice r-cran-lattice 0.22-5-1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-mass r-cran-mass 7.3-60.0.1-1 install ok installed r-cran-matrix r-cran-matrix 1.6-5-1 install ok installed r-cran-mgcv r-cran-mgcv 1.9-1-1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-2 install ok installed r-cran-nlme r-cran-nlme 3.1.164-1 install ok installed r-cran-pillar r-cran-pillar 1.9.0+dfsg-1 install ok installed r-cran-pkgbuild r-cran-pkgbuild 1.4.3-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgload r-cran-pkgload 1.3.4-1 install ok installed r-cran-praise r-cran-praise 1.0.0-4 install ok installed r-cran-prettyunits r-cran-prettyunits 1.2.0-1 install ok installed r-cran-processx r-cran-processx 3.8.3-1 install ok installed r-cran-ps r-cran-ps 1.7.6-1 install ok installed r-cran-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-3-1 install ok installed r-cran-rematch2 r-cran-rematch2 2.1.2-2 install ok installed r-cran-rlang r-cran-rlang 1.1.3-1 install ok installed r-cran-rprojroot r-cran-rprojroot 2.0.4-1 install ok installed r-cran-rstudioapi r-cran-rstudioapi 0.15.0-1 install ok installed r-cran-scales r-cran-scales 1.3.0-1 install ok installed r-cran-testthat r-cran-testthat 3.2.1-1 install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-2 install ok installed r-cran-utf8 r-cran-utf8 1.2.4-1 install ok installed r-cran-vctrs r-cran-vctrs 0.6.5-1 install ok installed r-cran-viridislite r-cran-viridislite 0.4.2-2 install ok installed r-cran-waldo r-cran-waldo 0.5.2-1 install ok installed r-cran-withr r-cran-withr 3.0.0+dfsg-1 install ok installed readline-common readline-common 8.2-3.1 install ok installed roary roary 3.13.0+dfsg-1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.22 install ok installed sysstat sysstat 12.7.5-2 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-1 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usrmerge usrmerge 39 install ok installed util-linux util-linux 2.39.3-10 install ok installed x11-common x11-common 1:7.7+23 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed xz-utils xz-utils 5.6.0-0.2 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 1m47.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m47.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libhogweed6:amd64=3.9.1-2+b1', 'libnettle8:amd64=3.9.1-2+b1', 'bedtools-', 'bioperl-', 'ca-certificates-', 'cd-hit-', 'fasttree-', 'fontconfig-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'libalgorithm-c3-perl-', 'libalgorithm-diff-perl-', 'libarray-utils-perl-', 'libb-hooks-op-check-perl:amd64-', 'libbio-perl-perl-', 'libblas3:amd64-', 'libbrotli1:amd64-', 'libbsd0:amd64-', 'libcairo2:amd64-', 'libcapture-tiny-perl-', 'libclass-c3-perl-', 'libclass-data-inheritable-perl-', 'libclass-load-perl-', 'libclass-load-xs-perl-', 'libclone-perl:amd64-', 'libconst-fast-perl-', 'libcurl4t64:amd64-', 'libdata-compare-perl-', 'libdata-optlist-perl-', 'libdata-stag-perl-', 'libdatrie1:amd64-', 'libdeflate0:amd64-', 'libdevel-callchecker-perl:amd64-', 'libdevel-globaldestruction-perl-', 'libdevel-overloadinfo-perl-', 'libdevel-stacktrace-perl-', 'libdigest-md5-file-perl-', 'libdist-checkconflicts-perl-', 'libdynaloader-functions-perl-', 'libencode-locale-perl-', 'libenv-path-perl-', 'libeval-closure-perl-', 'libexception-class-perl-', 'libexpat1:amd64-', 'libfile-grep-perl-', 'libfile-listing-perl-', 'libfile-slurper-perl-', 'libfile-which-perl-', 'libfindbin-libs-perl-', 'libfontconfig1:amd64-', 'libfreetype6:amd64-', 'libfribidi0:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libgomp1:amd64-', 'libgraph-perl-', 'libgraph-readwrite-perl-', 'libgraphite2-3:amd64-', 'libharfbuzz0b:amd64-', 'libheap-perl-', 'libhogweed6t64:amd64-', 'libhtml-parser-perl:amd64-', 'libhtml-tagset-perl-', 'libhtml-tree-perl-', 'libhttp-cookies-perl-', 'libhttp-date-perl-', 'libhttp-message-perl-', 'libhttp-negotiate-perl-', 'libice6:amd64-', 'libicu67:amd64-', 'libicu72:amd64-', 'libio-all-perl-', 'libio-html-perl-', 'libio-socket-ssl-perl-', 'libio-string-perl-', 'libjbig0:amd64-', 'libjpeg62-turbo:amd64-', 'liblapack3:amd64-', 'libldap-2.4-2:amd64-', 'libldap-2.5-0:amd64-', 'liblerc4:amd64-', 'liblmdb0:amd64-', 'liblog-log4perl-perl-', 'liblwp-mediatypes-perl-', 'liblwp-protocol-https-perl-', 'libmbedcrypto3:amd64-', 'libmbedcrypto7:amd64-', 'libmbedtls12:amd64-', 'libmbedtls14:amd64-', 'libmbedx509-0:amd64-', 'libmbedx509-1:amd64-', 'libmodule-implementation-perl-', 'libmodule-runtime-conflicts-perl-', 'libmodule-runtime-perl-', 'libmoose-perl:amd64-', 'libmpdec3:amd64-', 'libmro-compat-perl-', 'libncurses6:amd64-', 'libncursesw6:amd64-', 'libnet-http-perl-', 'libnet-ssleay-perl:amd64-', 'libnettle8t64:amd64-', 'libnghttp2-14:amd64-', 'libpackage-deprecationmanager-perl-', 'libpackage-stash-perl-', 'libpackage-stash-xs-perl:amd64-', 'libpadwalker-perl-', 'libpango-1.0-0:amd64-', 'libpangocairo-1.0-0:amd64-', 'libpangoft2-1.0-0:amd64-', 'libpaper-utils-', 'libpaper1:amd64-', 'libparams-classify-perl:amd64-', 'libparams-util-perl-', 'libparse-yapp-perl-', 'libpath-tiny-perl-', 'libperl5.32:amd64-', 'libperlio-utf8-strict-perl-', 'libpixman-1-0:amd64-', 'libpng16-16t64:amd64-', 'libproc2-0:amd64-', 'libprocps8:amd64-', 'libpsl5t64:amd64-', 'libpython3-stdlib:amd64-', 'libpython3.11-minimal:amd64-', 'libpython3.11-stdlib:amd64-', 'libpython3.9-minimal:amd64-', 'libpython3.9-stdlib:amd64-', 'libquadmath0:amd64-', 'libreadline8t64:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libsensors-config-', 'libsensors5:amd64-', 'libset-object-perl-', 'libsharpyuv0:amd64-', 'libsm6:amd64-', 'libspiffy-perl-', 'libsqlite3-0:amd64-', 'libssh2-1t64:amd64-', 'libsub-exporter-perl-', 'libsub-exporter-progressive-perl-', 'libsub-identify-perl-', 'libsub-install-perl-', 'libsub-name-perl:amd64-', 'libsub-uplevel-perl-', 'libtcl8.6:amd64-', 'libtest-deep-perl-', 'libtest-differences-perl-', 'libtest-exception-perl-', 'libtest-file-perl-', 'libtest-files-perl-', 'libtest-most-perl-', 'libtest-output-perl-', 'libtest-warn-perl-', 'libtext-csv-perl-', 'libtext-diff-perl-', 'libthai-data-', 'libthai0:amd64-', 'libtiff5:amd64-', 'libtiff6:amd64-', 'libtimedate-perl-', 'libtingea0:amd64-', 'libtk8.6:amd64-', 'libtry-tiny-perl-', 'liburi-perl-', 'libuv1:amd64-', 'libwebp6:amd64-', 'libwebp7:amd64-', 'libwww-perl-', 'libwww-robotrules-perl-', 'libx11-6:amd64-', 'libx11-data-', 'libxau6:amd64-', 'libxcb-render0:amd64-', 'libxcb-shm0:amd64-', 'libxcb1:amd64-', 'libxdmcp6:amd64-', 'libxext6:amd64-', 'libxft2:amd64-', 'libxml-parser-perl-', 'libxml-writer-perl-', 'libxrender1:amd64-', 'libxss1:amd64-', 'libxt6t64:amd64-', 'mafft-', 'mcl-', 'media-types-', 'ncbi-blast+-', 'ncbi-data-', 'netbase-', 'openssl-', 'parallel-', 'perl-modules-5.32-', 'perl-openssl-defaults:amd64-', 'prank-', 'procps-', 'python3-', 'python3-minimal-', 'python3.11-', 'python3.11-minimal-', 'python3.9-', 'python3.9-minimal-', 'r-base-core-', 'r-cran-assertthat-', 'r-cran-brio-', 'r-cran-callr-', 'r-cran-cli-', 'r-cran-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-fs-', 'r-cran-ggplot2-', 'r-cran-glue-', 'r-cran-gtable-', 'r-cran-isoband-', 'r-cran-jsonlite-', 'r-cran-labeling-', 'r-cran-lattice-', 'r-cran-lifecycle-', '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-pkgload-', 'r-cran-praise-', 'r-cran-prettyunits-', 'r-cran-processx-', 'r-cran-ps-', 'r-cran-r6-', 'r-cran-rcolorbrewer-', '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-', 'readline-common-', 'sensible-utils-', 'sysstat-', 'ucf-', 'unzip-', 'x11-common-', 'xdg-utils-', 'xz-utils-', 'zip-', 'roary-'] 1m52.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Package 'libglib2.0-0' is not installed, so not removed The following packages will be REMOVED: bedtools bioperl ca-certificates cd-hit fasttree fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libalgorithm-c3-perl libalgorithm-diff-perl libarray-utils-perl libb-hooks-op-check-perl libbio-perl-perl libblas3 libbrotli1 libbsd0 libcairo2 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libclone-perl libconst-fast-perl libcurl4t64 libdata-compare-perl libdata-optlist-perl libdata-stag-perl libdatrie1 libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdigest-md5-file-perl libdist-checkconflicts-perl libdynaloader-functions-perl libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libfile-grep-perl libfile-listing-perl libfile-slurper-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libharfbuzz0b libheap-perl libhogweed6t64 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu67 libicu72 libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo liblapack3 libldap-2.4-2 libldap-2.5-0 liblerc4 liblmdb0 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto3 libmbedcrypto7 libmbedtls12 libmbedtls14 libmbedx509-0 libmbedx509-1 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmpdec3 libmro-compat-perl libncurses6 libncursesw6 libnet-http-perl libnet-ssleay-perl libnettle8t64 libnghttp2-14 libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparse-yapp-perl libpath-tiny-perl libperl5.32 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16t64 libproc2-0 libprocps8 libpsl5t64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-object-perl libsharpyuv0 libsm6 libspiffy-perl libsqlite3-0 libssh2-1t64 libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-uplevel-perl libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libthai-data libthai0 libtiff5 libtiff6 libtimedate-perl libtingea0 libtk8.6 libtry-tiny-perl liburi-perl libuv1 libwebp6 libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxrender1 libxss1 libxt6t64 mafft mcl media-types ncbi-blast+ ncbi-data netbase openssl parallel perl-modules-5.32 perl-openssl-defaults prank procps python3 python3-minimal python3.11 python3.11-minimal python3.9 python3.9-minimal r-base-core r-cran-assertthat r-cran-brio r-cran-callr r-cran-cli r-cran-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-fs r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lattice r-cran-lifecycle 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-pkgload r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer 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 readline-common roary sensible-utils sysstat ucf unzip x11-common xdg-utils xz-utils zip The following NEW packages will be installed: libhogweed6 libnettle8 0 upgraded, 2 newly installed, 264 to remove and 0 not upgraded. Need to get 623 kB of archives. After this operation, 454 MB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libhogweed6 amd64 3.9.1-2+b1 [328 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libnettle8 amd64 3.9.1-2+b1 [296 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 623 kB in 0s (11.6 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 ... 23754 files and directories currently installed.) Removing roary (3.13.0+dfsg-1) ... Removing bedtools (2.31.1+dfsg-2) ... Removing bioperl (1.7.8-1) ... Removing r-cran-ggplot2 (3.4.4+dfsg-1) ... Removing r-cran-scales (1.3.0-1) ... Removing r-cran-rcolorbrewer (1.1-3-1) ... Removing r-cran-mgcv (1.9-1-1) ... Removing r-cran-matrix (1.6-5-1) ... Removing r-cran-viridislite (0.4.2-2) ... Removing r-cran-testthat (3.2.1-1) ... Removing libgraph-readwrite-perl (2.10-1) ... Removing libxml-parser-perl (2.47-1+b2) ... Removing cd-hit (4.8.1-4) ... Removing fasttree (2.1.11-2) ... Removing libmoose-perl:amd64 (2.2207-1+b1) ... Removing libdevel-overloadinfo-perl (0.007-1) ... Removing libmro-compat-perl (0.15-2) ... Removing libclass-c3-perl (0.35-2) ... Removing libalgorithm-c3-perl (0.11-2) ... Removing libtest-files-perl (0.24-1) ... Removing libtest-most-perl (0.38-1) ... Removing libtest-differences-perl (0.71-1) ... Removing libtext-diff-perl (1.45-2) ... Removing libalgorithm-diff-perl (1.201-1) ... Removing libarray-utils-perl (0.5-3) ... Removing libmodule-runtime-conflicts-perl (0.003-2) ... Removing libpackage-deprecationmanager-perl (0.18-1) ... Removing libbio-perl-perl (1.7.8-1) ... Removing libtest-output-perl (1.034-1) ... Removing libcapture-tiny-perl (0.48-2) ... Removing libexception-class-perl (1.45-1) ... Removing libclass-data-inheritable-perl (0.08-3) ... Removing libclass-load-xs-perl (0.10-2+b3) ... Removing libclass-load-perl (0.25-2) ... Removing libdata-compare-perl (1.29-1) ... Removing libconst-fast-perl (0.014-2) ... Removing libeval-closure-perl (0.14-3) ... Removing libsub-exporter-perl (0.990-1) ... Removing libdata-optlist-perl (0.114-1) ... Removing libdata-stag-perl (0.14-3) ... Removing libtiff5:amd64 (4.2.0-1+deb11u5) ... Removing libdevel-globaldestruction-perl (0.14-4) ... Removing libdevel-stacktrace-perl (2.0500-1) ... Removing libdigest-md5-file-perl (0.08-1.1) ... Removing libdist-checkconflicts-perl (0.11-2) ... Removing libenv-path-perl (0.19-4) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing ncbi-blast+ (2.12.0+ds-4) ... Removing python3 (3.11.8-1) ... Removing python3.11 (3.11.8-3) ... Removing libfile-grep-perl (0.02-3) ... Removing libfile-slurper-perl (0.014-1) ... Removing libfile-which-perl (1.27-2) ... Removing libfindbin-libs-perl (3.0.2-1) ... Removing libgraph-perl (1:0.9727-1) ... Removing libheap-perl (0.80-5) ... Removing libpackage-stash-perl (0.40-1) ... Removing libmodule-implementation-perl (0.09-2) ... Removing libmodule-runtime-perl (0.016-2) ... Removing libparams-classify-perl:amd64 (0.015-2+b3) ... Removing libdevel-callchecker-perl:amd64 (0.008-2+b2) ... Removing libb-hooks-op-check-perl:amd64 (0.22-3+b1) ... Removing libdynaloader-functions-perl (0.003-3) ... Removing libwww-perl (6.76-1) ... Removing libhttp-negotiate-perl (6.01-2) ... Removing libfile-listing-perl (6.16-1) ... dpkg: libgomp1:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libgomp1 (>= 4.9). Removing libgomp1:amd64 (14-20240303-1) ... dpkg: libgraphite2-3:amd64: dependency problems, but removing anyway as you requested: libharfbuzz0b:amd64 depends on libgraphite2-3 (>= 1.2.2). Removing libgraphite2-3:amd64 (1.3.14-2) ... dpkg: librtmp1:amd64: dependency problems, but removing anyway as you requested: libcurl4t64:amd64 depends on librtmp1 (>= 2.3). Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b3) ... dpkg: r-cran-withr: dependency problems, but removing anyway as you requested: r-cran-pkgload depends on r-cran-withr (>= 2.4.3). Removing r-cran-withr (3.0.0+dfsg-1) ... dpkg: r-base-core: dependency problems, but removing anyway as you requested: r-cran-tibble depends on r-base-core (>= 4.3.1-2). r-cran-tibble depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rematch2 depends on r-base-core (>= 4.0.0-3). r-cran-rematch2 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-r6 depends on r-base-core (>= 4.1.1-2). r-cran-r6 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-praise depends on r-base-core (>= 4.0.0-3). r-cran-praise depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgconfig depends on r-base-core (>= 4.0.0-3). r-cran-pkgconfig depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pillar depends on r-base-core (>= 4.3.0-1). r-cran-pillar depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-munsell depends on r-base-core (>= 4.0.0-3). r-cran-munsell depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-magrittr depends on r-base-core (>= 4.2.0-1). r-cran-magrittr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-isoband depends on r-base-core (>= 4.2.2.20221110-1). r-cran-isoband depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-farver depends on r-base-core (>= 4.2.1-1). r-cran-farver depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-ellipsis depends on r-base-core (>= 4.1.1-2). r-cran-ellipsis depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-diffobj depends on r-base-core (>= 4.2.1-2). r-cran-diffobj depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-crayon depends on r-base-core (>= 4.2.1-2). r-cran-crayon depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-colorspace depends on r-base-core (>= 4.2.2.20221110-2). r-cran-colorspace depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-assertthat depends on r-base-core (>= 4.0.0-3). r-cran-assertthat depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-waldo depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-vctrs depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-utf8 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-tibble depends on r-base-core (>= 4.3.1-2). r-cran-tibble depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rstudioapi depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rprojroot depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rlang depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rematch2 depends on r-base-core (>= 4.0.0-3). r-cran-rematch2 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-r6 depends on r-base-core (>= 4.1.1-2). r-cran-r6 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-ps depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-processx depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-prettyunits depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-praise depends on r-base-core (>= 4.0.0-3). r-cran-praise depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgload depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgconfig depends on r-base-core (>= 4.0.0-3). r-cran-pkgconfig depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgbuild depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pillar depends on r-base-core (>= 4.3.0-1). r-cran-pillar depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-nlme depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-munsell depends on r-base-core (>= 4.0.0-3). r-cran-munsell depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-mass depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-magrittr depends on r-base-core (>= 4.2.0-1). r-cran-magrittr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-lifecycle depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-lattice depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-labeling depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-jsonlite depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-isoband depends on r-base-core (>= 4.2.2.20221110-1). r-cran-isoband depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-gtable depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-glue depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-fs depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-farver depends on r-base-core (>= 4.2.1-1). r-cran-farver depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-fansi depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-evaluate depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-ellipsis depends on r-base-core (>= 4.1.1-2). r-cran-ellipsis depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-digest depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-diffobj depends on r-base-core (>= 4.2.1-2). r-cran-diffobj depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-desc depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-crayon depends on r-base-core (>= 4.2.1-2). r-cran-crayon depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-colorspace depends on r-base-core (>= 4.2.2.20221110-2). r-cran-colorspace depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-cli depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-callr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-brio depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-assertthat depends on r-base-core (>= 4.0.0-3). r-cran-assertthat depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. Removing r-base-core (4.3.3-2) ... dpkg: ca-certificates: dependency problems, but removing anyway as you requested: liblwp-protocol-https-perl depends on ca-certificates. Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.52.1+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.52.1+ds-1) ... Removing libpango-1.0-0:amd64 (1.52.1+ds-1) ... Removing fontconfig (2.15.0-1.1) ... Removing libtk8.6:amd64 (8.6.14-1) ... Removing libxft2:amd64 (2.3.6-1+b1) ... Removing libcairo2:amd64 (1.18.0-2) ... Removing libfontconfig1:amd64 (2.15.0-1.1) ... Removing fontconfig-config (2.15.0-1.1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing libharfbuzz0b:amd64 (8.3.0-2+b1) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b2) ... Removing libcurl4t64:amd64 (8.6.0-3.2) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libxt6t64:amd64 (1:1.2.1-1.2) ... Removing libxss1:amd64 (1:1.2.3-1) ... dpkg: libx11-6:amd64: dependency problems, but removing anyway as you requested: libxrender1:amd64 depends on libx11-6 (>= 2:1.6.0). libxext6:amd64 depends on libx11-6 (>= 2:1.6.0). Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... dpkg: libxcb1:amd64: dependency problems, but removing anyway as you requested: libxcb-render0:amd64 depends on libxcb1 (>= 1.8). Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libbsd0:amd64 (0.12.1-1) ... dpkg: libhttp-message-perl: dependency problems, but removing anyway as you requested: libhttp-cookies-perl depends on libhttp-message-perl. Removing libhttp-message-perl (6.45-1) ... Removing libclone-perl:amd64 (0.46-1+b2) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.19-1) ... Removing libencode-locale-perl (1.05-3) ... dpkg: python3.11-minimal: dependency problems, but removing anyway as you requested: python3-minimal depends on python3.11-minimal (>= 3.11.8-1~). Removing python3.11-minimal (3.11.8-3) ... Removing libexpat1:amd64 (2.6.1-2) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing libgfortran5:amd64 (14-20240303-1) ... Removing libglib2.0-0t64:amd64 (2.78.4-4) ... Selecting previously unselected package libhogweed6:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17466 files and directories currently installed.) Preparing to unpack .../libhogweed6_3.9.1-2+b1_amd64.deb ... Unpacking libhogweed6:amd64 (3.9.1-2+b1) ... Replaced by files in installed package libhogweed6t64:amd64 (3.9.1-2.2) ... dpkg: libhogweed6t64:amd64: dependency problems, but removing anyway as you requested: libgnutls30t64:amd64 depends on libhogweed6 (>= 3.6); however: Package libhogweed6:amd64 is not configured yet. Package libhogweed6t64:amd64 which provides libhogweed6 is to be removed. (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 ... 17471 files and directories currently installed.) Removing libhogweed6t64:amd64 (3.9.1-2.2) ... Setting up libhogweed6:amd64 (3.9.1-2+b1) ... Selecting previously unselected package libnettle8:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17464 files and directories currently installed.) Preparing to unpack .../libnettle8_3.9.1-2+b1_amd64.deb ... Unpacking libnettle8:amd64 (3.9.1-2+b1) ... Replaced by files in installed package libnettle8t64:amd64 (3.9.1-2.2) ... dpkg: libnettle8t64:amd64: dependency problems, but removing anyway as you requested: libhogweed6:amd64 depends on libnettle8; however: Package libnettle8:amd64 is not configured yet. Package libnettle8t64:amd64 which provides libnettle8 is to be removed. libgnutls30t64:amd64 depends on libnettle8 (>= 3.9~); however: Package libnettle8:amd64 is not configured yet. Package libnettle8t64:amd64 which provides libnettle8 is to be removed. (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 ... 17471 files and directories currently installed.) Removing libnettle8t64:amd64 (3.9.1-2.2) ... Setting up libnettle8:amd64 (3.9.1-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17462 files and directories currently installed.) Removing libhtml-tree-perl (5.07-3) ... Removing libhtml-parser-perl:amd64 (3.81-1+b2) ... Removing libhtml-tagset-perl (3.20-6) ... Removing libhttp-cookies-perl (6.11-1) ... Removing libhttp-date-perl (6.06-1) ... Removing libicu67:amd64 (67.1-7) ... Removing libicu72:amd64 (72.1-4+b1) ... Removing libio-all-perl (0.87-2) ... Removing libio-html-perl (1.004-3) ... Removing liblwp-protocol-https-perl (6.13-1) ... Removing libio-socket-ssl-perl (2.085-1) ... Removing libio-string-perl (1.08-4) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing libldap-2.5-0:amd64 (2.5.16+dfsg-1) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing liblmdb0:amd64 (0.9.31-1+b1) ... Removing liblog-log4perl-perl (1.57-1) ... Removing liblwp-mediatypes-perl (6.04-2) ... Removing libmbedtls12:amd64 (2.16.9-0.1) ... Removing libmbedx509-0:amd64 (2.16.9-0.1) ... Removing libmbedcrypto3:amd64 (2.16.9-0.1) ... Removing libmbedtls14:amd64 (2.28.7-1) ... Removing libmbedx509-1:amd64 (2.28.7-1) ... Removing libmbedcrypto7:amd64 (2.28.7-1) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec3:amd64 (2.5.1-2) ... Removing libncurses6:amd64 (6.4+20240113-1) ... Removing libpython3-stdlib:amd64 (3.11.8-1) ... Removing libpython3.11-stdlib:amd64 (3.11.8-3) ... find: '/usr/lib/python3': No such file or directory Removing parallel (20231122+ds-1) ... Removing 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Removing 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Removing procps (2:4.0.4-4) ... Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing libnet-http-perl (6.23-1) ... Removing libnet-ssleay-perl:amd64 (1.94-1+b1) ... Removing libnghttp2-14:amd64 (1.59.0-1+b1) ... Removing libpackage-stash-xs-perl:amd64 (0.30-1+b3) ... Removing libpadwalker-perl (2.5-1+b5) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libparams-util-perl (1.102-3) ... Removing libparse-yapp-perl (1.21-3) ... Removing libpath-tiny-perl (0.144-1) ... Removing libperl5.32:amd64 (5.32.1-4+deb11u3) ... Removing libperlio-utf8-strict-perl (0.010-1+b2) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libpng16-16t64:amd64 (1.6.43-3) ... Removing libproc2-0:amd64 (2:4.0.4-4) ... Removing libprocps8:amd64 (2:3.3.17-5) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing python3-minimal (3.11.8-1) ... Removing libpython3.11-minimal:amd64 (3.11.8-3) ... find: '/usr/lib/python3': No such file or directory Removing libpython3.9-minimal:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libquadmath0:amd64 (14-20240303-1) ... Removing libreadline8t64:amd64 (8.2-3.1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsasl2-2:amd64 (2.1.28+dfsg1-4+b2) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b2) ... Removing sysstat (12.7.5-2) ... Removing libsensors5:amd64 (1:3.6.0-9) ... Removing libsensors-config (1:3.6.0-9) ... Removing libset-object-perl (1.42-1+b4) ... Removing libwebp7:amd64 (1.3.2-0.4+b1) ... Removing libsharpyuv0:amd64 (1.3.2-0.4+b1) ... Removing libspiffy-perl (0.46-1) ... Removing libsqlite3-0:amd64 (3.45.1-1) ... Removing libssh2-1t64:amd64 (1.11.0-4.1+b1) ... Removing libsub-exporter-progressive-perl (0.001013-3) ... Removing libsub-identify-perl (0.14-3+b2) ... Removing libsub-install-perl (0.929-1) ... Removing libsub-name-perl:amd64 (0.27-1+b2) ... Removing libtest-warn-perl (0.37-2) ... Removing libtest-exception-perl (0.43-3) ... Removing libsub-uplevel-perl (0.2800-3) ... Removing libtcl8.6:amd64 (8.6.14+dfsg-1) ... Removing libtest-deep-perl (1.204-1) ... Removing libtest-file-perl (1.993-1) ... Removing libtext-csv-perl (2.04-1) ... Removing libthai-data (0.1.29-2) ... Removing libtimedate-perl (2.3300-2) ... Removing mcl (1:22-282+ds-2) ... Removing libtingea0:amd64 (21-361-2+b1) ... Removing libtry-tiny-perl (0.31-2) ... Removing libwww-robotrules-perl (6.02-1) ... Removing liburi-perl (5.27-1) ... Removing r-cran-pkgload (1.3.4-1) ... Removing r-cran-fs (1.6.3+dfsg-1) ... Removing libuv1:amd64 (1.48.0-1) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libxml-writer-perl (0.900-2) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing mafft (7.505-1) ... Removing media-types (10.1.0) ... Removing ncbi-data (6.1.20170106+dfsg2-1) ... Removing netbase (6.4) ... Removing openssl (3.1.5-1.1) ... Removing perl-modules-5.32 (5.32.1-4+deb11u3) ... Removing perl-openssl-defaults:amd64 (7+b2) ... Removing prank (0.0.170427+dfsg-3) ... Removing r-cran-assertthat (0.2.1-2) ... Removing r-cran-brio (1.1.4-1) ... Removing r-cran-pkgbuild (1.4.3-1) ... Removing r-cran-callr (3.7.5-1) ... Removing r-cran-waldo (0.5.2-1) ... Removing r-cran-rematch2 (2.1.2-2) ... Removing r-cran-tibble (3.2.1+dfsg-2) ... Removing r-cran-munsell (0.5.0-2) ... Removing r-cran-colorspace (2.1-0+dfsg-1) ... Removing r-cran-diffobj (0.3.5-1+b1) ... Removing r-cran-crayon (1.5.2-1) ... Removing r-cran-desc (1.4.3-1) ... Removing r-cran-digest (0.6.35-1) ... Removing r-cran-ellipsis (0.3.2-2) ... Removing r-cran-evaluate (0.23-1) ... Removing r-cran-pillar (1.9.0+dfsg-1) ... Removing r-cran-fansi (1.0.5-1) ... Removing r-cran-farver (2.1.1-1) ... Removing r-cran-gtable (0.3.4+dfsg-1) ... Removing r-cran-isoband (0.2.7-1) ... Removing r-cran-jsonlite (1.8.8+dfsg-1) ... Removing r-cran-labeling (0.4.3-1) ... Removing r-cran-nlme (3.1.164-1) ... Removing r-cran-lattice (0.22-5-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-60.0.1-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-praise (1.0.0-4) ... Removing r-cran-prettyunits (1.2.0-1) ... Removing r-cran-processx (3.8.3-1) ... Removing r-cran-ps (1.7.6-1) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rprojroot (2.0.4-1) ... Removing r-cran-rstudioapi (0.15.0-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing readline-common (8.2-3.1) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.22) ... Removing unzip (6.0-28) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing xz-utils (5.6.0-0.2) ... Removing zip (3.0-13) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-glue (1.7.0-1) ... Removing r-cran-rlang (1.1.3-1) ... Removing r-cran-cli (3.6.2-1) ... Processing triggers for libc-bin (2.37-15.1) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. 1m52.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libhogweed6:amd64=3.9.1-2+b1', 'libnettle8:amd64=3.9.1-2+b1', 'bedtools-', 'bioperl-', 'ca-certificates-', 'cd-hit-', 'fasttree-', 'fontconfig-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'libalgorithm-c3-perl-', 'libalgorithm-diff-perl-', 'libarray-utils-perl-', 'libb-hooks-op-check-perl:amd64-', 'libbio-perl-perl-', 'libblas3:amd64-', 'libbrotli1:amd64-', 'libbsd0:amd64-', 'libcairo2:amd64-', 'libcapture-tiny-perl-', 'libclass-c3-perl-', 'libclass-data-inheritable-perl-', 'libclass-load-perl-', 'libclass-load-xs-perl-', 'libclone-perl:amd64-', 'libconst-fast-perl-', 'libcurl4t64:amd64-', 'libdata-compare-perl-', 'libdata-optlist-perl-', 'libdata-stag-perl-', 'libdatrie1:amd64-', 'libdeflate0:amd64-', 'libdevel-callchecker-perl:amd64-', 'libdevel-globaldestruction-perl-', 'libdevel-overloadinfo-perl-', 'libdevel-stacktrace-perl-', 'libdigest-md5-file-perl-', 'libdist-checkconflicts-perl-', 'libdynaloader-functions-perl-', 'libencode-locale-perl-', 'libenv-path-perl-', 'libeval-closure-perl-', 'libexception-class-perl-', 'libexpat1:amd64-', 'libfile-grep-perl-', 'libfile-listing-perl-', 'libfile-slurper-perl-', 'libfile-which-perl-', 'libfindbin-libs-perl-', 'libfontconfig1:amd64-', 'libfreetype6:amd64-', 'libfribidi0:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libgomp1:amd64-', 'libgraph-perl-', 'libgraph-readwrite-perl-', 'libgraphite2-3:amd64-', 'libharfbuzz0b:amd64-', 'libheap-perl-', 'libhogweed6t64:amd64-', 'libhtml-parser-perl:amd64-', 'libhtml-tagset-perl-', 'libhtml-tree-perl-', 'libhttp-cookies-perl-', 'libhttp-date-perl-', 'libhttp-message-perl-', 'libhttp-negotiate-perl-', 'libice6:amd64-', 'libicu67:amd64-', 'libicu72:amd64-', 'libio-all-perl-', 'libio-html-perl-', 'libio-socket-ssl-perl-', 'libio-string-perl-', 'libjbig0:amd64-', 'libjpeg62-turbo:amd64-', 'liblapack3:amd64-', 'libldap-2.4-2:amd64-', 'libldap-2.5-0:amd64-', 'liblerc4:amd64-', 'liblmdb0:amd64-', 'liblog-log4perl-perl-', 'liblwp-mediatypes-perl-', 'liblwp-protocol-https-perl-', 'libmbedcrypto3:amd64-', 'libmbedcrypto7:amd64-', 'libmbedtls12:amd64-', 'libmbedtls14:amd64-', 'libmbedx509-0:amd64-', 'libmbedx509-1:amd64-', 'libmodule-implementation-perl-', 'libmodule-runtime-conflicts-perl-', 'libmodule-runtime-perl-', 'libmoose-perl:amd64-', 'libmpdec3:amd64-', 'libmro-compat-perl-', 'libncurses6:amd64-', 'libncursesw6:amd64-', 'libnet-http-perl-', 'libnet-ssleay-perl:amd64-', 'libnettle8t64:amd64-', 'libnghttp2-14:amd64-', 'libpackage-deprecationmanager-perl-', 'libpackage-stash-perl-', 'libpackage-stash-xs-perl:amd64-', 'libpadwalker-perl-', 'libpango-1.0-0:amd64-', 'libpangocairo-1.0-0:amd64-', 'libpangoft2-1.0-0:amd64-', 'libpaper-utils-', 'libpaper1:amd64-', 'libparams-classify-perl:amd64-', 'libparams-util-perl-', 'libparse-yapp-perl-', 'libpath-tiny-perl-', 'libperl5.32:amd64-', 'libperlio-utf8-strict-perl-', 'libpixman-1-0:amd64-', 'libpng16-16t64:amd64-', 'libproc2-0:amd64-', 'libprocps8:amd64-', 'libpsl5t64:amd64-', 'libpython3-stdlib:amd64-', 'libpython3.11-minimal:amd64-', 'libpython3.11-stdlib:amd64-', 'libpython3.9-minimal:amd64-', 'libpython3.9-stdlib:amd64-', 'libquadmath0:amd64-', 'libreadline8t64:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libsensors-config-', 'libsensors5:amd64-', 'libset-object-perl-', 'libsharpyuv0:amd64-', 'libsm6:amd64-', 'libspiffy-perl-', 'libsqlite3-0:amd64-', 'libssh2-1t64:amd64-', 'libsub-exporter-perl-', 'libsub-exporter-progressive-perl-', 'libsub-identify-perl-', 'libsub-install-perl-', 'libsub-name-perl:amd64-', 'libsub-uplevel-perl-', 'libtcl8.6:amd64-', 'libtest-deep-perl-', 'libtest-differences-perl-', 'libtest-exception-perl-', 'libtest-file-perl-', 'libtest-files-perl-', 'libtest-most-perl-', 'libtest-output-perl-', 'libtest-warn-perl-', 'libtext-csv-perl-', 'libtext-diff-perl-', 'libthai-data-', 'libthai0:amd64-', 'libtiff5:amd64-', 'libtiff6:amd64-', 'libtimedate-perl-', 'libtingea0:amd64-', 'libtk8.6:amd64-', 'libtry-tiny-perl-', 'liburi-perl-', 'libuv1:amd64-', 'libwebp6:amd64-', 'libwebp7:amd64-', 'libwww-perl-', 'libwww-robotrules-perl-', 'libx11-6:amd64-', 'libx11-data-', 'libxau6:amd64-', 'libxcb-render0:amd64-', 'libxcb-shm0:amd64-', 'libxcb1:amd64-', 'libxdmcp6:amd64-', 'libxext6:amd64-', 'libxft2:amd64-', 'libxml-parser-perl-', 'libxml-writer-perl-', 'libxrender1:amd64-', 'libxss1:amd64-', 'libxt6t64:amd64-', 'mafft-', 'mcl-', 'media-types-', 'ncbi-blast+-', 'ncbi-data-', 'netbase-', 'openssl-', 'parallel-', 'perl-modules-5.32-', 'perl-openssl-defaults:amd64-', 'prank-', 'procps-', 'python3-', 'python3-minimal-', 'python3.11-', 'python3.11-minimal-', 'python3.9-', 'python3.9-minimal-', 'r-base-core-', 'r-cran-assertthat-', 'r-cran-brio-', 'r-cran-callr-', 'r-cran-cli-', 'r-cran-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-fs-', 'r-cran-ggplot2-', 'r-cran-glue-', 'r-cran-gtable-', 'r-cran-isoband-', 'r-cran-jsonlite-', 'r-cran-labeling-', 'r-cran-lattice-', 'r-cran-lifecycle-', '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-pkgload-', 'r-cran-praise-', 'r-cran-prettyunits-', 'r-cran-processx-', 'r-cran-ps-', 'r-cran-r6-', 'r-cran-rcolorbrewer-', '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-', 'readline-common-', 'sensible-utils-', 'sysstat-', 'ucf-', 'unzip-', 'x11-common-', 'xdg-utils-', 'xz-utils-', 'zip-', 'roary-'] 1m52.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libhogweed6:amd64=3.9.1-2+b1', 'libnettle8:amd64=3.9.1-2+b1'] 1m53.4s DUMP: Reading package lists... Building dependency tree... Reading state information... debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 0 newly installed, 2 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/623 kB of archives. After this operation, 0 B of additional disk space will be used. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 7531 files and directories currently installed.) Preparing to unpack .../libhogweed6_3.9.1-2+b1_amd64.deb ... Unpacking libhogweed6:amd64 (3.9.1-2+b1) over (3.9.1-2+b1) ... Preparing to unpack .../libnettle8_3.9.1-2+b1_amd64.deb ... Unpacking libnettle8:amd64 (3.9.1-2+b1) over (3.9.1-2+b1) ... Setting up libnettle8:amd64 (3.9.1-2+b1) ... Setting up libhogweed6:amd64 (3.9.1-2+b1) ... Processing triggers for libc-bin (2.37-15.1) ... 1m53.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libhogweed6:amd64=3.9.1-2+b1', 'libnettle8:amd64=3.9.1-2+b1'] 1m53.4s INFO: Running scripts post_remove 1m53.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_remove_exceptions'] 1m53.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_remove_exceptions'] 1m53.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg', '--purge', 'bedtools', 'bioperl', 'ca-certificates', 'cd-hit', 'fasttree', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libarray-utils-perl', 'libb-hooks-op-check-perl:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclone-perl:amd64', 'libconst-fast-perl', 'libcurl4t64:amd64', 'libdata-compare-perl', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhogweed6t64:amd64', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedcrypto7:amd64', 'libmbedtls12:amd64', 'libmbedtls14:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmpdec3:amd64', 'libmro-compat-perl', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnettle8t64:amd64', 'libnghttp2-14:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libparse-yapp-perl', 'libpath-tiny-perl', 'libperl5.32:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libprocps8:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-object-perl', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl:amd64', 'libsub-uplevel-perl', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-warn-perl', 'libtext-csv-perl', 'libtext-diff-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtingea0:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libuv1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl-modules-5.32', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-cran-assertthat', 'r-cran-brio', 'r-cran-callr', 'r-cran-cli', 'r-cran-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-fs', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-isoband', 'r-cran-jsonlite', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', '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-pkgload', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-ps', 'r-cran-r6', 'r-cran-rcolorbrewer', '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', 'readline-common', 'sensible-utils', 'sysstat', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip'] 1m54.4s DUMP: dpkg: warning: ignoring request to remove bedtools which isn't installed dpkg: warning: ignoring request to remove bioperl which isn't installed (Reading database ... 7535 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove cd-hit which isn't installed dpkg: warning: ignoring request to remove fasttree which isn't installed Purging configuration files for fontconfig (2.15.0-1.1) ... Purging configuration files for fontconfig-config (2.15.0-1.1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/usr/share/fonts/truetype/dejavu' not empty so not removed dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed dpkg: warning: ignoring request to remove libalgorithm-c3-perl which isn't installed dpkg: warning: ignoring request to remove libalgorithm-diff-perl which isn't installed dpkg: warning: ignoring request to remove libarray-utils-perl which isn't installed dpkg: warning: ignoring request to remove libb-hooks-op-check-perl which isn't installed dpkg: warning: ignoring request to remove libbio-perl-perl 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 libcapture-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libclass-c3-perl which isn't installed dpkg: warning: ignoring request to remove libclass-data-inheritable-perl which isn't installed dpkg: warning: ignoring request to remove libclass-load-perl which isn't installed dpkg: warning: ignoring request to remove libclass-load-xs-perl which isn't installed dpkg: warning: ignoring request to remove libclone-perl which isn't installed dpkg: warning: ignoring request to remove libconst-fast-perl which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libdata-compare-perl which isn't installed dpkg: warning: ignoring request to remove libdata-optlist-perl which isn't installed dpkg: warning: ignoring request to remove libdata-stag-perl which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdevel-callchecker-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-globaldestruction-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-overloadinfo-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-stacktrace-perl which isn't installed dpkg: warning: ignoring request to remove libdigest-md5-file-perl which isn't installed dpkg: warning: ignoring request to remove libdist-checkconflicts-perl which isn't installed dpkg: warning: ignoring request to remove libdynaloader-functions-perl which isn't installed dpkg: warning: ignoring request to remove libencode-locale-perl which isn't installed dpkg: warning: ignoring request to remove libenv-path-perl which isn't installed dpkg: warning: ignoring request to remove libeval-closure-perl which isn't installed dpkg: warning: ignoring request to remove libexception-class-perl which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfile-grep-perl which isn't installed dpkg: warning: ignoring request to remove libfile-listing-perl which isn't installed dpkg: warning: ignoring request to remove libfile-slurper-perl which isn't installed dpkg: warning: ignoring request to remove libfile-which-perl which isn't installed dpkg: warning: ignoring request to remove libfindbin-libs-perl which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 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 libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.78.4-4) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraph-perl which isn't installed dpkg: warning: ignoring request to remove libgraph-readwrite-perl which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libheap-perl which isn't installed dpkg: warning: ignoring request to remove libhogweed6t64 which isn't installed dpkg: warning: ignoring request to remove libhtml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tagset-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tree-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-cookies-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-date-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-message-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-negotiate-perl which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu67 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libio-all-perl which isn't installed dpkg: warning: ignoring request to remove libio-html-perl which isn't installed dpkg: warning: ignoring request to remove libio-socket-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libio-string-perl which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove liblog-log4perl-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-mediatypes-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-protocol-https-perl which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7 which isn't installed dpkg: warning: ignoring request to remove libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1 which isn't installed dpkg: warning: ignoring request to remove libmodule-implementation-perl which isn't installed dpkg: warning: ignoring request to remove libmodule-runtime-conflicts-perl which isn't installed dpkg: warning: ignoring request to remove libmodule-runtime-perl which isn't installed dpkg: warning: ignoring request to remove libmoose-perl which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libmro-compat-perl 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 libnet-http-perl which isn't installed dpkg: warning: ignoring request to remove libnet-ssleay-perl which isn't installed dpkg: warning: ignoring request to remove libnettle8t64 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libpackage-deprecationmanager-perl which isn't installed dpkg: warning: ignoring request to remove libpackage-stash-perl which isn't installed dpkg: warning: ignoring request to remove libpackage-stash-xs-perl which isn't installed dpkg: warning: ignoring request to remove libpadwalker-perl which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.29) ... dpkg: warning: ignoring request to remove libparams-classify-perl which isn't installed dpkg: warning: ignoring request to remove libparams-util-perl which isn't installed dpkg: warning: ignoring request to remove libparse-yapp-perl which isn't installed dpkg: warning: ignoring request to remove libpath-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libperl5.32 which isn't installed dpkg: warning: ignoring request to remove libperlio-utf8-strict-perl which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libprocps8 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.8-3) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-3.1) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed Purging configuration files for libsensors-config (1:3.6.0-9) ... dpkg: warning: ignoring request to remove libsensors5 which isn't installed dpkg: warning: ignoring request to remove libset-object-perl which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libspiffy-perl which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libsub-exporter-perl which isn't installed dpkg: warning: ignoring request to remove libsub-exporter-progressive-perl which isn't installed dpkg: warning: ignoring request to remove libsub-identify-perl which isn't installed dpkg: warning: ignoring request to remove libsub-install-perl which isn't installed dpkg: warning: ignoring request to remove libsub-name-perl which isn't installed dpkg: warning: ignoring request to remove libsub-uplevel-perl which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtest-deep-perl which isn't installed dpkg: warning: ignoring request to remove libtest-differences-perl which isn't installed dpkg: warning: ignoring request to remove libtest-exception-perl which isn't installed dpkg: warning: ignoring request to remove libtest-file-perl which isn't installed dpkg: warning: ignoring request to remove libtest-files-perl which isn't installed dpkg: warning: ignoring request to remove libtest-most-perl which isn't installed dpkg: warning: ignoring request to remove libtest-output-perl which isn't installed dpkg: warning: ignoring request to remove libtest-warn-perl which isn't installed dpkg: warning: ignoring request to remove libtext-csv-perl which isn't installed dpkg: warning: ignoring request to remove libtext-diff-perl which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtimedate-perl which isn't installed dpkg: warning: ignoring request to remove libtingea0 which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove liburi-perl which isn't installed dpkg: warning: ignoring request to remove libuv1 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwww-perl which isn't installed dpkg: warning: ignoring request to remove libwww-robotrules-perl 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 libxau6 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 libxcb1 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 libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libxml-writer-perl which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6t64 which isn't installed dpkg: warning: ignoring request to remove mafft which isn't installed dpkg: warning: ignoring request to remove mcl which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-1) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.1.5-1.1) ... Purging configuration files for parallel (20231122+ds-1) ... dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed dpkg: warning: ignoring request to remove perl-openssl-defaults which isn't installed dpkg: warning: ignoring request to remove prank which isn't installed Purging configuration files for procps (2:4.0.4-4) ... Purging configuration files for python3 (3.11.8-1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.8-3) ... dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for r-base-core (4.3.3-2) ... 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-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-fs 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-isoband 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-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-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-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 readline-common (8.2-3.1) ... dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for sysstat (12.7.5-2) ... Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: while removing x11-common, directory '/etc/init.d' not empty so not removed dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove xz-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 1m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg', '--purge', 'bedtools', 'bioperl', 'ca-certificates', 'cd-hit', 'fasttree', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libarray-utils-perl', 'libb-hooks-op-check-perl:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclone-perl:amd64', 'libconst-fast-perl', 'libcurl4t64:amd64', 'libdata-compare-perl', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhogweed6t64:amd64', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedcrypto7:amd64', 'libmbedtls12:amd64', 'libmbedtls14:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmpdec3:amd64', 'libmro-compat-perl', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnettle8t64:amd64', 'libnghttp2-14:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libparse-yapp-perl', 'libpath-tiny-perl', 'libperl5.32:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libprocps8:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-object-perl', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl:amd64', 'libsub-uplevel-perl', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-warn-perl', 'libtext-csv-perl', 'libtext-diff-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtingea0:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libuv1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl-modules-5.32', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-cran-assertthat', 'r-cran-brio', 'r-cran-callr', 'r-cran-cli', 'r-cran-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-fs', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-isoband', 'r-cran-jsonlite', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', '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-pkgload', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-ps', 'r-cran-r6', 'r-cran-rcolorbrewer', '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', 'readline-common', 'sensible-utils', 'sysstat', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip'] 1m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg', '--purge', 'roary'] 1m54.5s DUMP: dpkg: warning: ignoring request to remove roary which isn't installed 1m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg', '--purge', 'roary'] 1m54.5s INFO: Running scripts post_purge 1m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_purge_exceptions'] 1m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_purge_exceptions'] 1m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg', '--purge', '--pending'] 1m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg', '--purge', '--pending'] 1m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg', '--remove', '--pending'] 1m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg', '--remove', '--pending'] 1m54.5s INFO: Running scripts post_test 1m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_test_exceptions'] 1m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'tmp/scripts/post_test_exceptions'] 1m54.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 1m55.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 1m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg-divert', '--list'] 1m55.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 1m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'dpkg-divert', '--list'] 1m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', 'clean'] 1m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3qb0b834', 'apt-get', 'clean'] 1m55.3s DEBUG: Recording chroot state 1m56.1s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-dejavu-mono, fonts-dejavu-core /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-dejavu-mono, fonts-dejavu-core /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned /usr/local/share/fonts/ not owned /usr/local/share/fonts/.uuid not owned /usr/share/fonts/ owned by: fonts-dejavu-mono, fonts-dejavu-core /usr/share/fonts/.uuid not owned /usr/share/fonts/truetype/ owned by: fonts-dejavu-mono, fonts-dejavu-core /usr/share/fonts/truetype/.uuid not owned /usr/share/fonts/truetype/dejavu/ owned by: fonts-dejavu-mono, fonts-dejavu-core /usr/share/fonts/truetype/dejavu/.uuid not owned 1m56.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/shm'] 1m56.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/shm'] 1m56.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/console'] 1m56.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/console'] 1m56.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/ptmx'] 1m56.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/ptmx'] 1m56.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/pts'] 1m56.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/dev/pts'] 1m56.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/proc'] 1m56.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3qb0b834/proc'] 1m56.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 1m56.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp3qb0b834'] 1m56.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp3qb0b834 1m56.9s INFO: PASS: Upgrading between Debian distributions. 1m56.9s INFO: PASS: All tests. 1m56.9s INFO: piuparts run ends. ret=0 End: 2024-03-12 18:50:47 GMT