Start: 2024-10-08 05:07:23 GMT [bullseye] 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 [bullseye-next] 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 --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt 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 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt roary=3.13.0+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpgd_bfy2r 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpgd_bfy2r 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpgd_bfy2r/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', 'update'] 0m0.6s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', 'update'] 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', '-yf', 'dist-upgrade'] 0m0.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', '-yf', 'dist-upgrade'] 0m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.0s DUMP: f58ca9ba0b3223edf5b7797c101a5448 - 0m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.0s INFO: Running scripts post_setup 0m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_setup_dummy_users'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_setup_dummy_users'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_setup_forbid_home'] 0m1.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_setup_forbid_home'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_setup_force-unsafe-io'] 0m1.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_setup_force-unsafe-io'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_setup_minimize'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_setup_minimize'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_setup_squeeze-backports'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_setup_squeeze-backports'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_setup_zz_backports'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_setup_zz_backports'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m1.5s 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+deb11u11 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+deb11u2 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+deb11u2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u11 install ok installed libc6:amd64 libc6 2.31-13+deb11u11 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+deb11u5 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+deb11u5 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+deb11u5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u5 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u5 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+deb11u2 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+deb11u2 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+deb11u5 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+deb11u5 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u2 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+deb11u2 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+deb11u2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m1.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat 0m1.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m1.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m1.8s INFO: Running scripts is_testable 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/is_testable_uninstallable'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/is_testable_uninstallable'] 0m1.8s INFO: Running scripts pre_test 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_test_exceptions'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_test_exceptions'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_test_root_password'] 0m1.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_test_root_password'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m1.9s 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 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m1.9s INFO: apt-cache knows about the following packages: roary 0m1.9s INFO: Running scripts pre_install 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_database-server'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_database-server'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_exceptions'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_exceptions'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_extras'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_extras'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_foreign_architecture'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_foreign_architecture'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'policy'] 0m2.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.11,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'policy'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'policy', 'roary'] 0m2.0s 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 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'policy', 'roary'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', '-y', 'install', 'roary'] 0m29.4s 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+deb11u1 [156 kB] Get:93 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u13 [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+deb11u4 [1377 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 12s (10.1 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 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) ... 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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+deb11u11) ... 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. 0m29.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', '-y', 'install', 'roary'] 0m29.4s INFO: Running scripts post_install 0m29.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_install_exceptions'] 0m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_install_exceptions'] 0m29.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m30.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m30.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpgd_bfy2r to bullseye-next 0m30.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main deb http://security.debian.org bullseye-security main deb http://deb.debian.org/debian/ bullseye-updates main deb http://deb.debian.org/debian/ bullseye-proposed-updates main 0m30.1s INFO: Running scripts pre_distupgrade 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_distupgrade_exceptions'] 0m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_distupgrade_exceptions'] 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', 'update'] 0m31.0s DUMP: Get:1 http://security.debian.org bullseye-security InRelease [27.2 kB] Get:2 http://security.debian.org bullseye-security/main amd64 Packages [301 kB] Get:3 http://security.debian.org bullseye-security/main Translation-en [194 kB] Hit:4 http://deb.debian.org/debian bullseye InRelease Get:5 http://deb.debian.org/debian bullseye-updates InRelease [44.1 kB] Get:6 http://deb.debian.org/debian bullseye-proposed-updates InRelease [54.0 kB] Get:7 http://deb.debian.org/debian bullseye-updates/main amd64 Packages [18.8 kB] Get:8 http://deb.debian.org/debian bullseye-updates/main Translation-en [10.9 kB] Fetched 650 kB in 1s (1214 kB/s) Reading package lists... 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', 'update'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', '-yf', 'dist-upgrade'] 0m32.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: e2fsprogs libcom-err2 libexpat1 libext2fs2 libgnutls30 libnghttp2-14 libsqlite3-0 libss2 libsystemd0 libudev1 logsave 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3957 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://security.debian.org bullseye-security/main amd64 libsystemd0 amd64 247.3-7+deb11u6 [377 kB] Get:2 http://security.debian.org bullseye-security/main amd64 logsave amd64 1.46.2-2+deb11u1 [75.0 kB] Get:3 http://security.debian.org bullseye-security/main amd64 libext2fs2 amd64 1.46.2-2+deb11u1 [257 kB] Get:4 http://security.debian.org bullseye-security/main amd64 e2fsprogs amd64 1.46.2-2+deb11u1 [614 kB] Get:5 http://security.debian.org bullseye-security/main amd64 libcom-err2 amd64 1.46.2-2+deb11u1 [74.3 kB] Get:6 http://security.debian.org bullseye-security/main amd64 libgnutls30 amd64 3.7.1-5+deb11u6 [1340 kB] Get:7 http://security.debian.org bullseye-security/main amd64 libudev1 amd64 247.3-7+deb11u6 [169 kB] Get:8 http://security.debian.org bullseye-security/main amd64 libexpat1 amd64 2.2.10-2+deb11u6 [99.0 kB] Get:9 http://security.debian.org bullseye-security/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u2 [77.0 kB] Get:10 http://security.debian.org bullseye-security/main amd64 libsqlite3-0 amd64 3.34.1-3+deb11u1 [797 kB] Get:11 http://security.debian.org bullseye-security/main amd64 libss2 amd64 1.46.2-2+deb11u1 [78.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3957 kB in 0s (98.6 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 ... 21256 files and directories currently installed.) Preparing to unpack .../libsystemd0_247.3-7+deb11u6_amd64.deb ... Unpacking libsystemd0:amd64 (247.3-7+deb11u6) over (247.3-7+deb11u5) ... Setting up libsystemd0:amd64 (247.3-7+deb11u6) ... (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 ... 21256 files and directories currently installed.) Preparing to unpack .../logsave_1.46.2-2+deb11u1_amd64.deb ... Unpacking logsave (1.46.2-2+deb11u1) over (1.46.2-2) ... Preparing to unpack .../libext2fs2_1.46.2-2+deb11u1_amd64.deb ... Unpacking libext2fs2:amd64 (1.46.2-2+deb11u1) over (1.46.2-2) ... Setting up libext2fs2:amd64 (1.46.2-2+deb11u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21256 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.46.2-2+deb11u1_amd64.deb ... Unpacking e2fsprogs (1.46.2-2+deb11u1) over (1.46.2-2) ... Preparing to unpack .../libcom-err2_1.46.2-2+deb11u1_amd64.deb ... Unpacking libcom-err2:amd64 (1.46.2-2+deb11u1) over (1.46.2-2) ... Setting up libcom-err2:amd64 (1.46.2-2+deb11u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21256 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.1-5+deb11u6_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.1-5+deb11u6) over (3.7.1-5+deb11u5) ... Setting up libgnutls30:amd64 (3.7.1-5+deb11u6) ... (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 ... 21256 files and directories currently installed.) Preparing to unpack .../libudev1_247.3-7+deb11u6_amd64.deb ... Unpacking libudev1:amd64 (247.3-7+deb11u6) over (247.3-7+deb11u5) ... Setting up libudev1:amd64 (247.3-7+deb11u6) ... (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 ... 21256 files and directories currently installed.) Preparing to unpack .../libexpat1_2.2.10-2+deb11u6_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2+deb11u6) over (2.2.10-2+deb11u5) ... Preparing to unpack .../libnghttp2-14_1.43.0-1+deb11u2_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.43.0-1+deb11u2) over (1.43.0-1+deb11u1) ... Preparing to unpack .../libsqlite3-0_3.34.1-3+deb11u1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.34.1-3+deb11u1) over (3.34.1-3) ... Preparing to unpack .../libss2_1.46.2-2+deb11u1_amd64.deb ... Unpacking libss2:amd64 (1.46.2-2+deb11u1) over (1.46.2-2) ... Setting up libexpat1:amd64 (2.2.10-2+deb11u6) ... Setting up libsqlite3-0:amd64 (3.34.1-3+deb11u1) ... Setting up libnghttp2-14:amd64 (1.43.0-1+deb11u2) ... Setting up libss2:amd64 (1.46.2-2+deb11u1) ... Setting up logsave (1.46.2-2+deb11u1) ... Setting up e2fsprogs (1.46.2-2+deb11u1) ... Processing triggers for libc-bin (2.31-13+deb11u11) ... 0m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', '-yf', 'dist-upgrade'] 0m32.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m32.2s DUMP: 6e00c1375a7bee6828c5a4679505c708 - 0m32.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m32.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m32.3s 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 0m32.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m32.3s INFO: apt-cache knows about the following packages: roary 0m32.3s INFO: Running scripts pre_install 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_database-server'] 0m32.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_database-server'] 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_exceptions'] 0m32.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_exceptions'] 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_extras'] 0m32.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_extras'] 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_foreign_architecture'] 0m32.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_foreign_architecture'] 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m32.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'policy'] 0m32.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.11,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m32.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'policy'] 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'policy', 'roary'] 0m32.4s 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 bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m32.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'policy', 'roary'] 0m32.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', '-y', 'install', 'roary'] 0m32.6s DUMP: Reading package lists... Building dependency tree... Reading state information... roary is already the newest version (3.13.0+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', '-y', 'install', 'roary'] 0m32.6s INFO: Running scripts post_install 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_install_exceptions'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_install_exceptions'] 0m32.6s INFO: Running scripts post_distupgrade 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_distupgrade_exceptions'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_distupgrade_exceptions'] 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_distupgrade_zz_backports'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_distupgrade_zz_backports'] 0m32.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m33.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m33.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m34.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m34.0s INFO: Running scripts pre_install 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_database-server'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_database-server'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_exceptions'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_exceptions'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_extras'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_extras'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_foreign_architecture'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_foreign_architecture'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'policy'] 0m34.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.11,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'policy'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'policy', 'roary'] 0m34.1s 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 bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-cache', 'policy', 'roary'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', '-y', 'install', 'roary=3.13.0+dfsg-1'] 0m34.3s DUMP: Reading package lists... Building dependency tree... Reading state information... roary is already the newest version (3.13.0+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m34.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', '-y', 'install', 'roary=3.13.0+dfsg-1'] 0m34.3s INFO: Running scripts post_install 0m34.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_install_exceptions'] 0m34.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_install_exceptions'] 0m34.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m35.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m35.2s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m35.2s INFO: /bin converted to /usr/bin by /usr merge 0m35.2s INFO: /lib converted to /usr/lib by /usr merge 0m35.2s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m35.2s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m35.2s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m35.2s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m35.2s INFO: /lib/systemd/system-sleep converted to /usr/lib/systemd/system-sleep by /usr merge 0m35.2s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m35.2s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m35.2s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m35.2s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m35.2s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m35.2s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m35.2s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m35.2s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m35.2s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m35.2s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m35.2s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m35.2s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m35.2s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m35.2s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m35.2s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m35.2s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m35.2s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m35.2s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m35.2s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m35.2s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m35.2s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m35.2s INFO: /sbin converted to /usr/sbin by /usr merge 0m35.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', '-ac', '--ignore-obsolete'] 0m37.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', '-ac', '--ignore-obsolete'] 0m37.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m37.2s DUMP: 0.15.6 0m37.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m37.2s INFO: Running adequate version 0.15.6 now. 0m37.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'roary'] 0m37.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'roary'] 0m37.3s INFO: Running scripts pre_remove 0m37.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m37.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m37.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m37.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m37.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_remove_exceptions'] 0m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/pre_remove_exceptions'] 0m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m39.9s 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+deb11u11 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bedtools bedtools 2.30.0+dfsg-1 install ok installed bioperl bioperl 1.7.7-2 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u2 install ok installed ca-certificates ca-certificates 20210119 install ok installed cd-hit cd-hit 4.8.1-3 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+deb11u1 install ok installed fasttree fasttree 2.1.11-2 install ok installed findutils findutils 4.8.0-1 install ok installed fontconfig fontconfig 2.13.1-4.2 install ok installed fontconfig-config fontconfig-config 2.13.1-4.2 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-2 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libalgorithm-c3-perl libalgorithm-c3-perl 0.11-1 install ok installed libalgorithm-diff-perl libalgorithm-diff-perl 1.201-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libarray-utils-perl libarray-utils-perl 0.5-1.1 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 libb-hooks-op-check-perl libb-hooks-op-check-perl 0.22-1+b3 install ok installed libbio-perl-perl libbio-perl-perl 1.7.7-2 install ok installed libblas3:amd64 libblas3 3.9.0-3+deb11u1 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u2 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b2 install ok installed libbsd0:amd64 libbsd0 0.11.3-1+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u11 install ok installed libc6:amd64 libc6 2.31-13+deb11u11 install ok installed libcairo2:amd64 libcairo2 1.16.0-5 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcapture-tiny-perl libcapture-tiny-perl 0.48-1 install ok installed libclass-c3-perl libclass-c3-perl 0.35-1 install ok installed libclass-data-inheritable-perl libclass-data-inheritable-perl 0.08-3 install ok installed libclass-load-perl libclass-load-perl 0.25-1 install ok installed libclass-load-xs-perl libclass-load-xs-perl 0.10-1+b5 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2+deb11u1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libcurl4:amd64 libcurl4 7.74.0-1.3+deb11u13 install ok installed libdata-optlist-perl libdata-optlist-perl 0.110-1.1 install ok installed libdata-stag-perl libdata-stag-perl 0.14-2 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libdeflate0:amd64 libdeflate0 1.7-1 install ok installed libdevel-callchecker-perl libdevel-callchecker-perl 0.008-1+b2 install ok installed libdevel-globaldestruction-perl libdevel-globaldestruction-perl 0.14-1.1 install ok installed libdevel-overloadinfo-perl libdevel-overloadinfo-perl 0.005-1 install ok installed libdevel-stacktrace-perl libdevel-stacktrace-perl 2.0400-1 install ok installed libdigest-md5-file-perl libdigest-md5-file-perl 0.08-1.1 install ok installed libdist-checkconflicts-perl libdist-checkconflicts-perl 0.11-1.1 install ok installed libdynaloader-functions-perl libdynaloader-functions-perl 0.003-1.1 install ok installed libencode-locale-perl libencode-locale-perl 1.05-1.1 install ok installed libenv-path-perl libenv-path-perl 0.19-2 install ok installed libeval-closure-perl libeval-closure-perl 0.14-1 install ok installed libexception-class-perl libexception-class-perl 1.44-1 install ok installed libexpat1:amd64 libexpat1 2.2.10-2+deb11u6 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2+deb11u1 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-1 install ok installed libfile-grep-perl libfile-grep-perl 0.02-1.1 install ok installed libfile-listing-perl libfile-listing-perl 6.14-1 install ok installed libfile-slurper-perl libfile-slurper-perl 0.012-1 install ok installed libfile-which-perl libfile-which-perl 1.23-1 install ok installed libfindbin-libs-perl libfindbin-libs-perl 2.190.02-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.13.1-4.2 install ok installed libfreetype6:amd64 libfreetype6 2.10.4+dfsg-1+deb11u1 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2+deb11u1 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.19-2 install ok installed libgdbm6:amd64 libgdbm6 1.19-2 install ok installed libgfortran5:amd64 libgfortran5 10.2.1-6 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.66.8-1+deb11u4 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u6 install ok installed libgomp1:amd64 libgomp1 10.2.1-6 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgraph-perl libgraph-perl 1:0.9716-2 install ok installed libgraph-readwrite-perl libgraph-readwrite-perl 2.09-1.1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u5 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 2.7.4-1 install ok installed libheap-perl libheap-perl 0.80-3 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libhtml-parser-perl libhtml-parser-perl 3.75-1+b1 install ok installed libhtml-tagset-perl libhtml-tagset-perl 3.20-4 install ok installed libhtml-tree-perl libhtml-tree-perl 5.07-2 install ok installed libhttp-cookies-perl libhttp-cookies-perl 6.10-1 install ok installed libhttp-date-perl libhttp-date-perl 6.05-1 install ok installed libhttp-message-perl libhttp-message-perl 6.28-1 install ok installed libhttp-negotiate-perl libhttp-negotiate-perl 6.01-1 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libio-all-perl libio-all-perl 0.87-1 install ok installed libio-html-perl libio-html-perl 1.004-2 install ok installed libio-socket-ssl-perl libio-socket-ssl-perl 2.069-1 install ok installed libio-string-perl libio-string-perl 1.08-3.1 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.0.6-4 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u5 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u5 install ok installed liblapack3:amd64 liblapack3 3.9.0-3+deb11u1 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 install ok installed liblmdb0:amd64 liblmdb0 0.9.24-1 install ok installed liblog-log4perl-perl liblog-log4perl-perl 1.54-1 install ok installed liblwp-mediatypes-perl liblwp-mediatypes-perl 6.04-1 install ok installed liblwp-protocol-https-perl liblwp-protocol-https-perl 6.10-1 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 libmbedcrypto3:amd64 libmbedcrypto3 2.16.9-0.1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.9-0.1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.9-0.1 install ok installed libmd0:amd64 libmd0 1.0.3-3 install ok installed libmodule-implementation-perl libmodule-implementation-perl 0.09-1.1 install ok installed libmodule-runtime-conflicts-perl libmodule-runtime-conflicts-perl 0.003-1.1 install ok installed libmodule-runtime-perl libmodule-runtime-perl 0.016-1 install ok installed libmoose-perl libmoose-perl 2.2014-2 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u2 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-1 install ok installed libmro-compat-perl libmro-compat-perl 0.13-1 install ok installed libncurses6:amd64 libncurses6 6.2+20201114-2+deb11u2 install ok installed libncursesw6:amd64 libncursesw6 6.2+20201114-2+deb11u2 install ok installed libnet-http-perl libnet-http-perl 6.20-1 install ok installed libnet-ssleay-perl libnet-ssleay-perl 1.88-3+b1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.43.0-1+deb11u2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-1.1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpackage-deprecationmanager-perl libpackage-deprecationmanager-perl 0.17-1.1 install ok installed libpackage-stash-perl libpackage-stash-perl 0.39-1 install ok installed libpackage-stash-xs-perl libpackage-stash-xs-perl 0.29-1+b2 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.46.2-3 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.46.2-3 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.46.2-3 install ok installed libpaper-utils libpaper-utils 1.1.28+b1 install ok installed libpaper1:amd64 libpaper1 1.1.28+b1 install ok installed libparams-classify-perl libparams-classify-perl 0.015-1+b3 install ok installed libparams-util-perl libparams-util-perl 1.102-1+b1 install ok installed libparse-yapp-perl libparse-yapp-perl 1.21-2 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 libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u3 install ok installed libperlio-utf8-strict-perl libperlio-utf8-strict-perl 0.008-1+b1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.40.0-1.1~deb11u1 install ok installed libpng16-16:amd64 libpng16-16 1.6.37-3 install ok installed libprocps8:amd64 libprocps8 2:3.3.17-5 install ok installed libpsl5:amd64 libpsl5 0.21.0-1.2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.9.2-3 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed libquadmath0:amd64 libquadmath0 10.2.1-6 install ok installed libreadline8:amd64 libreadline8 8.1-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-2.1+deb11u1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-2.1+deb11u1 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsensors-config libsensors-config 1:3.6.0-7 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-7 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libset-object-perl libset-object-perl 1.41-1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u2 install ok installed libspiffy-perl libspiffy-perl 0.46-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.34.1-3+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2+deb11u1 install ok installed libssh2-1:amd64 libssh2-1 1.9.0-2+deb11u1 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 libsub-exporter-perl libsub-exporter-perl 0.987-1 install ok installed libsub-exporter-progressive-perl libsub-exporter-progressive-perl 0.001013-1 install ok installed libsub-identify-perl libsub-identify-perl 0.14-1+b3 install ok installed libsub-install-perl libsub-install-perl 0.928-1.1 install ok installed libsub-name-perl libsub-name-perl 0.26-1+b1 install ok installed libsub-uplevel-perl libsub-uplevel-perl 0.2800-1.1 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u6 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.11+dfsg-1 install ok installed libtest-deep-perl libtest-deep-perl 1.130-1 install ok installed libtest-differences-perl libtest-differences-perl 0.67-1 install ok installed libtest-exception-perl libtest-exception-perl 0.43-1 install ok installed libtest-file-perl libtest-file-perl 1.444-1 install ok installed libtest-files-perl libtest-files-perl 0.15-1 install ok installed libtest-most-perl libtest-most-perl 0.37-1 install ok installed libtest-output-perl libtest-output-perl 1.033-1 install ok installed libtest-warn-perl libtest-warn-perl 0.36-1 install ok installed libtext-csv-perl libtext-csv-perl 2.00-1 install ok installed libtext-diff-perl libtext-diff-perl 1.45-1 install ok installed libtext-glob-perl libtext-glob-perl 0.11-1 install ok installed libthai-data libthai-data 0.1.28-3 install ok installed libthai0:amd64 libthai0 0.1.28-3 install ok installed libtiff5:amd64 libtiff5 4.2.0-1+deb11u5 install ok installed libtimedate-perl libtimedate-perl 2.3300-2 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libtk8.6:amd64 libtk8.6 8.6.11-2 install ok installed libtry-tiny-perl libtry-tiny-perl 0.30-1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u6 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed liburi-perl liburi-perl 5.08-1 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u2 install ok installed libwebp6:amd64 libwebp6 0.6.1-2.1+deb11u2 install ok installed libwww-perl libwww-perl 6.52-1 install ok installed libwww-robotrules-perl libwww-robotrules-perl 6.02-1 install ok installed libx11-6:amd64 libx11-6 2:1.7.2-1+deb11u2 install ok installed libx11-data libx11-data 2:1.7.2-1+deb11u2 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.14-3 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.14-3 install ok installed libxcb1:amd64 libxcb1 1.14-3 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.3-1.1 install ok installed libxft2:amd64 libxft2 2.3.2-2 install ok installed libxml-parser-perl:amd64 libxml-parser-perl 2.46-2 install ok installed libxml-writer-perl libxml-writer-perl 0.900-1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6:amd64 libxt6 1:1.2.0-1 install ok installed 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+deb11u1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mafft mafft 7.475-1 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mcl mcl 1:14-137+ds-9+b1 install ok installed media-types media-types 4.0.0 install ok installed mount mount 2.36.1-8+deb11u2 install ok installed ncbi-blast+ ncbi-blast+ 2.11.0+ds-1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-9 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 netbase netbase 6.3 install ok installed openssl openssl 1.1.1w-0+deb11u1 install ok installed parallel parallel 20161222-1.1 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl perl 5.32.1-4+deb11u3 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.1-4+deb11u3 install ok installed perl-openssl-defaults:amd64 perl-openssl-defaults 5 install ok installed prank prank 0.0.170427+dfsg-3 install ok installed procps procps 2:3.3.17-5 install ok installed python3 python3 3.9.2-3 install ok installed python3-minimal python3-minimal 3.9.2-3 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 4.0.4-1 install ok installed r-cran-assertthat r-cran-assertthat 0.2.1-2 install ok installed r-cran-brio r-cran-brio 1.1.1-1 install ok installed r-cran-callr r-cran-callr 3.5.1-1 install ok installed r-cran-cli r-cran-cli 2.3.0-1 install ok installed r-cran-colorspace r-cran-colorspace 2.0-0+dfsg-1 install ok installed r-cran-crayon r-cran-crayon 1.4.0-1 install ok installed r-cran-desc r-cran-desc 1.2.0-3 install ok installed r-cran-diffobj r-cran-diffobj 0.3.2-1 install ok installed r-cran-digest r-cran-digest 0.6.27-1 install ok installed r-cran-ellipsis r-cran-ellipsis 0.3.1-1 install ok installed r-cran-evaluate r-cran-evaluate 0.14-2 install ok installed r-cran-fansi r-cran-fansi 0.4.2-1 install ok installed r-cran-farver r-cran-farver 2.0.3-1+b1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.3.3+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.4.2-1 install ok installed r-cran-gtable r-cran-gtable 0.3.0+dfsg-2 install ok installed r-cran-isoband r-cran-isoband 0.2.3-2 install ok installed r-cran-jsonlite r-cran-jsonlite 1.7.2+dfsg-1 install ok installed r-cran-labeling r-cran-labeling 0.4.2-1 install ok installed r-cran-lattice r-cran-lattice 0.20-41-1+b1 install ok installed r-cran-lifecycle r-cran-lifecycle 0.2.0-2 install ok installed r-cran-magrittr r-cran-magrittr 2.0.1-1 install ok installed r-cran-mass r-cran-mass 7.3-53.1-1 install ok installed r-cran-matrix r-cran-matrix 1.3-2-1 install ok installed r-cran-mgcv r-cran-mgcv 1.8-34-1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-2 install ok installed r-cran-nlme r-cran-nlme 3.1.152-1 install ok installed r-cran-pillar r-cran-pillar 1.4.7-1 install ok installed r-cran-pkgbuild r-cran-pkgbuild 1.2.0-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgload r-cran-pkgload 1.1.0-1 install ok installed r-cran-praise r-cran-praise 1.0.0-4 install ok installed r-cran-prettyunits r-cran-prettyunits 1.1.1-2 install ok installed r-cran-processx r-cran-processx 3.4.5-1 install ok installed r-cran-ps r-cran-ps 1.5.0-1 install ok installed r-cran-r6 r-cran-r6 2.5.0-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-2-3 install ok installed r-cran-rematch2 r-cran-rematch2 2.1.2-2 install ok installed r-cran-rlang r-cran-rlang 0.4.10-1 install ok installed r-cran-rprojroot r-cran-rprojroot 2.0.2-1 install ok installed r-cran-rstudioapi r-cran-rstudioapi 0.13-1 install ok installed r-cran-scales r-cran-scales 1.1.1-1 install ok installed r-cran-testthat r-cran-testthat 3.0.1-1 install ok installed r-cran-tibble r-cran-tibble 3.0.6+dfsg-1 install ok installed r-cran-utf8 r-cran-utf8 1.1.4-2 install ok installed r-cran-vctrs r-cran-vctrs 0.3.6-1 install ok installed r-cran-viridislite r-cran-viridislite 0.3.0-4 install ok installed r-cran-waldo r-cran-waldo 0.2.3-2 install ok installed r-cran-withr r-cran-withr 2.4.1-1 install ok installed readline-common readline-common 8.1-1 install ok installed roary roary 3.13.0+dfsg-1 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.14 install ok installed sysstat sysstat 12.5.2-2 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed ucf ucf 3.0043 install ok installed unzip unzip 6.0-26+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u2 install ok installed x11-common x11-common 1:7.7+22 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed xz-utils xz-utils 5.2.5-2.1~deb11u1 install ok installed zip zip 3.0-12 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', 'remove', '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:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libcurl4:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', '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:amd64', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu67: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', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmd0:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl', 'libmpdec3:amd64', 'libmro-compat-perl', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnghttp2-14:amd64', 'libnumber-compare-perl', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparams-util-perl', 'libparse-yapp-perl', 'libperl5.32:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-object-perl', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl', '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', 'libtext-glob-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtimedate-perl', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libwebp6: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:amd64', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.32', 'perl-openssl-defaults:amd64', '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', 'roary'] 0m41.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: 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, 0 newly installed, 246 to remove and 0 not upgraded. After this operation, 370 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21256 files and directories currently installed.) Removing roary (3.13.0+dfsg-1) ... Removing bedtools (2.30.0+dfsg-1) ... Removing bioperl (1.7.7-2) ... Removing r-cran-ggplot2 (3.3.3+dfsg-1) ... Removing r-cran-mgcv (1.8-34-1) ... Removing r-cran-matrix (1.3-2-1) ... Removing r-cran-scales (1.1.1-1) ... Removing r-cran-rcolorbrewer (1.1-2-3) ... Removing r-cran-isoband (0.2.3-2) ... Removing r-cran-testthat (3.0.1-1) ... Removing r-cran-pkgload (1.1.0-1) ... Removing r-cran-pkgbuild (1.2.0-1) ... Removing r-cran-withr (2.4.1-1) ... Removing r-cran-waldo (0.2.3-2) ... Removing libgraph-readwrite-perl (2.09-1.1) ... Removing libxml-parser-perl:amd64 (2.46-2) ... Removing cd-hit (4.8.1-3) ... Removing fasttree (2.1.11-2) ... Removing libmoose-perl (2.2014-2) ... Removing libdevel-overloadinfo-perl (0.005-1) ... Removing libmro-compat-perl (0.13-1) ... Removing libclass-c3-perl (0.35-1) ... Removing libalgorithm-c3-perl (0.11-1) ... Removing libtest-files-perl (0.15-1) ... Removing libtest-most-perl (0.37-1) ... Removing libtest-differences-perl (0.67-1) ... Removing libtext-diff-perl (1.45-1) ... Removing libalgorithm-diff-perl (1.201-1) ... Removing libarray-utils-perl (0.5-1.1) ... Removing libmodule-runtime-conflicts-perl (0.003-1.1) ... Removing libpackage-deprecationmanager-perl (0.17-1.1) ... Removing libbio-perl-perl (1.7.7-2) ... Removing libtest-output-perl (1.033-1) ... Removing libcapture-tiny-perl (0.48-1) ... Removing libexception-class-perl (1.44-1) ... Removing libclass-data-inheritable-perl (0.08-3) ... Removing libclass-load-xs-perl (0.10-1+b5) ... Removing libclass-load-perl (0.25-1) ... Removing libeval-closure-perl (0.14-1) ... Removing libsub-exporter-perl (0.987-1) ... Removing libdata-optlist-perl (0.110-1.1) ... Removing libdata-stag-perl (0.14-2) ... Removing libdevel-globaldestruction-perl (0.14-1.1) ... Removing libdevel-stacktrace-perl (2.0400-1) ... Removing libdigest-md5-file-perl (0.08-1.1) ... Removing libdist-checkconflicts-perl (0.11-1.1) ... Removing libenv-path-perl (0.19-2) ... Removing ncbi-blast+ (2.11.0+ds-1) ... Removing python3 (3.9.2-3) ... Removing python3-minimal (3.9.2-3) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing libfile-find-rule-perl (0.34-1) ... Removing libfile-grep-perl (0.02-1.1) ... Removing libfile-slurper-perl (0.012-1) ... Removing libfile-which-perl (1.23-1) ... Removing libfindbin-libs-perl (2.190.02-1) ... Removing parallel (20161222-1.1) ... 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 mafft (7.475-1) ... Removing libxml-writer-perl (0.900-1) ... Removing libgraph-perl (1:0.9716-2) ... Removing libheap-perl (0.80-3) ... Removing libio-all-perl (0.87-1) ... Removing libio-string-perl (1.08-3.1) ... Removing liblmdb0:amd64 (0.9.24-1) ... Removing liblog-log4perl-perl (1.54-1) ... 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 libpython3-stdlib:amd64 (3.9.2-3) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec3:amd64 (2.5.1-1) ... Removing procps (2:3.3.17-5) ... Removing libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Removing libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Removing libnumber-compare-perl (0.03-1.1) ... Removing libpackage-stash-xs-perl (0.29-1+b2) ... Removing libparams-util-perl (1.102-1+b1) ... Removing libparse-yapp-perl (1.21-2) ... Removing libperlio-utf8-strict-perl (0.008-1+b1) ... Removing libprocps8:amd64 (2:3.3.17-5) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing sysstat (12.5.2-2) ... Removing libsensors5:amd64 (1:3.6.0-7) ... Removing libsensors-config (1:3.6.0-7) ... Removing libset-object-perl (1.41-1) ... Removing libspiffy-perl (0.46-1) ... Removing libsqlite3-0:amd64 (3.34.1-3+deb11u1) ... Removing libsub-exporter-progressive-perl (0.001013-1) ... Removing libsub-identify-perl (0.14-1+b3) ... Removing libsub-install-perl (0.928-1.1) ... Removing libsub-name-perl (0.26-1+b1) ... Removing libtest-warn-perl (0.36-1) ... Removing libtest-exception-perl (0.43-1) ... Removing libsub-uplevel-perl (0.2800-1.1) ... Removing libtest-deep-perl (1.130-1) ... Removing libtest-file-perl (1.444-1) ... Removing libtext-csv-perl (2.00-1) ... Removing libtext-glob-perl (0.11-1) ... Removing mcl (1:14-137+ds-9+b1) ... Removing media-types (4.0.0) ... Removing ncbi-data (6.1.20170106+dfsg1-9) ... Removing prank (0.0.170427+dfsg-3) ... Removing r-cran-desc (1.2.0-3) ... Removing r-cran-rematch2 (2.1.2-2) ... Removing r-cran-tibble (3.0.6+dfsg-1) ... Removing r-cran-brio (1.1.1-1) ... Removing r-cran-callr (3.5.1-1) ... Removing r-cran-munsell (0.5.0-2) ... Removing r-cran-colorspace (2.0-0+dfsg-1) ... Removing r-cran-pillar (1.4.7-1) ... Removing r-cran-diffobj (0.3.2-1) ... Removing r-cran-crayon (1.4.0-1) ... Removing r-cran-vctrs (0.3.6-1) ... Removing r-cran-digest (0.6.27-1) ... Removing r-cran-ellipsis (0.3.1-1) ... Removing r-cran-evaluate (0.14-2) ... Removing r-cran-fansi (0.4.2-1) ... Removing r-cran-farver (2.0.3-1+b1) ... Removing r-cran-lifecycle (0.2.0-2) ... Removing r-cran-gtable (0.3.0+dfsg-2) ... Removing r-cran-jsonlite (1.7.2+dfsg-1) ... Removing r-cran-labeling (0.4.2-1) ... Removing r-cran-nlme (3.1.152-1) ... Removing r-cran-lattice (0.20-41-1+b1) ... Removing r-cran-magrittr (2.0.1-1) ... Removing r-cran-mass (7.3-53.1-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-praise (1.0.0-4) ... Removing r-cran-prettyunits (1.1.1-2) ... Removing r-cran-processx (3.4.5-1) ... Removing r-cran-ps (1.5.0-1) ... Removing r-cran-r6 (2.5.0-1) ... Removing r-cran-rlang (0.4.10-1) ... Removing r-cran-rprojroot (2.0.2-1) ... Removing r-cran-rstudioapi (0.13-1) ... Removing r-cran-utf8 (1.1.4-2) ... Removing r-cran-viridislite (0.3.0-4) ... Removing xz-utils (5.2.5-2.1~deb11u1) ... Removing libpackage-stash-perl (0.39-1) ... Removing libmodule-implementation-perl (0.09-1.1) ... Removing libmodule-runtime-perl (0.016-1) ... Removing libparams-classify-perl (0.015-1+b3) ... Removing libdevel-callchecker-perl (0.008-1+b2) ... Removing libb-hooks-op-check-perl (0.22-1+b3) ... Removing libdynaloader-functions-perl (0.003-1.1) ... Removing r-cran-cli (2.3.0-1) ... Removing r-cran-assertthat (0.2.1-2) ... Removing r-cran-glue (1.4.2-1) ... Removing r-base-core (4.0.4-1) ... Removing libpangocairo-1.0-0:amd64 (1.46.2-3) ... Removing libpangoft2-1.0-0:amd64 (1.46.2-3) ... Removing libpango-1.0-0:amd64 (1.46.2-3) ... Removing fontconfig (2.13.1-4.2) ... Removing libtk8.6:amd64 (8.6.11-2) ... Removing libxft2:amd64 (2.3.2-2) ... Removing libcairo2:amd64 (1.16.0-5) ... Removing libfontconfig1:amd64 (2.13.1-4.2) ... Removing fontconfig-config (2.13.1-4.2) ... Removing fonts-dejavu-core (2.37-2) ... Removing liblapack3:amd64 (3.9.0-3+deb11u1) ... Removing libblas3:amd64 (3.9.0-3+deb11u1) ... Removing libcurl4:amd64 (7.74.0-1.3+deb11u13) ... Removing libharfbuzz0b:amd64 (2.7.4-1) ... Removing libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Removing libbrotli1:amd64 (1.0.9-2+b2) ... Removing libxt6:amd64 (1:1.2.0-1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxcb-shm0:amd64 (1.14-3) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libthai0:amd64 (0.1.28-3) ... Removing libdatrie1:amd64 (0.2.13-1) ... Removing libtiff5:amd64 (4.2.0-1+deb11u5) ... Removing libdeflate0:amd64 (1.7-1) ... Removing libexpat1:amd64 (2.2.10-2+deb11u6) ... Removing libfribidi0:amd64 (1.0.8-2+deb11u1) ... Removing libgfortran5:amd64 (10.2.1-6) ... Removing libglib2.0-0:amd64 (2.66.8-1+deb11u4) ... Removing libgomp1:amd64 (10.2.1-6) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libicu67:amd64 (67.1-7) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.0.6-4) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing libnghttp2-14:amd64 (1.43.0-1+deb11u2) ... Removing libpaper-utils (1.1.28+b1) ... Removing libpaper1:amd64 (1.1.28+b1) ... Removing libpixman-1-0:amd64 (0.40.0-1.1~deb11u1) ... Removing libpng16-16:amd64 (1.6.37-3) ... Removing libpsl5:amd64 (0.21.0-1.2) ... Removing libquadmath0:amd64 (10.2.1-6) ... Removing libreadline8:amd64 (8.1-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing libssh2-1:amd64 (1.9.0-2+deb11u1) ... Removing libtcl8.6:amd64 (8.6.11+dfsg-1) ... Removing libthai-data (0.1.28-3) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libxcb-render0:amd64 (1.14-3) ... Removing libxext6:amd64 (2:1.3.3-1.1) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing readline-common (8.1-1) ... Removing ucf (3.0043) ... Removing sensible-utils (0.0.14) ... Removing unzip (6.0-26+deb11u1) ... Removing x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-12) ... Removing libx11-6:amd64 (2:1.7.2-1+deb11u2) ... Removing libxcb1:amd64 (1.14-3) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.3-1+deb11u1) ... Removing libmd0:amd64 (1.0.3-3) ... Removing libx11-data (2:1.7.2-1+deb11u2) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing libwww-perl (6.52-1) ... Removing libhttp-negotiate-perl (6.01-1) ... Removing libfile-listing-perl (6.14-1) ... Removing libhttp-cookies-perl (6.10-1) ... Removing libwww-robotrules-perl (6.02-1) ... Removing libhtml-tree-perl (5.07-2) ... Removing libhtml-parser-perl (3.75-1+b1) ... Removing libhtml-tagset-perl (3.20-4) ... Removing liblwp-protocol-https-perl (6.10-1) ... Removing libio-socket-ssl-perl (2.069-1) ... Removing libnet-http-perl (6.20-1) ... Removing libnet-ssleay-perl (1.88-3+b1) ... Removing libtry-tiny-perl (0.30-1) ... Removing netbase (6.3) ... Removing perl-openssl-defaults:amd64 (5) ... Removing ca-certificates (20210119) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libhttp-message-perl (6.28-1) ... Removing libencode-locale-perl (1.05-1.1) ... Removing libhttp-date-perl (6.05-1) ... Removing libio-html-perl (1.004-2) ... Removing liblwp-mediatypes-perl (6.04-1) ... Removing libtimedate-perl (2.3300-2) ... Removing liburi-perl (5.08-1) ... Removing openssl (1.1.1w-0+deb11u1) ... Removing perl (5.32.1-4+deb11u3) ... Removing libperl5.32:amd64 (5.32.1-4+deb11u3) ... Removing libgdbm-compat4:amd64 (1.19-2) ... Removing libgdbm6:amd64 (1.19-2) ... Removing perl-modules-5.32 (5.32.1-4+deb11u3) ... Processing triggers for libc-bin (2.31-13+deb11u11) ... 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', 'remove', '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:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libcurl4:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', '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:amd64', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu67: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', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmd0:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl', 'libmpdec3:amd64', 'libmro-compat-perl', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnghttp2-14:amd64', 'libnumber-compare-perl', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparams-util-perl', 'libparse-yapp-perl', 'libperl5.32:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-object-perl', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl', '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', 'libtext-glob-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtimedate-perl', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libwebp6: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:amd64', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.32', 'perl-openssl-defaults:amd64', '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', 'roary'] 0m41.3s INFO: Running scripts post_remove 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_remove_exceptions'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_remove_exceptions'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg', '--purge', '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:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libcurl4:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', '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:amd64', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu67: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', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmd0:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl', 'libmpdec3:amd64', 'libmro-compat-perl', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnghttp2-14:amd64', 'libnumber-compare-perl', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparams-util-perl', 'libparse-yapp-perl', 'libperl5.32:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-object-perl', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl', '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', 'libtext-glob-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtimedate-perl', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libwebp6: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:amd64', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.32', 'perl-openssl-defaults:amd64', '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'] 0m41.9s 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 ... 6749 files and directories currently installed.) Purging configuration files for ca-certificates (20210119) ... 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 (2.13.1-4.2) ... Purging configuration files for fontconfig-config (2.13.1-4.2) ... Purging configuration files for fonts-dejavu-core (2.37-2) ... dpkg: warning: while removing fonts-dejavu-core, directory '/usr/share/fonts/truetype/dejavu' not empty so not removed 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 libcurl4 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-find-rule-perl 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 libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.66.8-1+deb11u4) ... 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 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 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 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 libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libmd0 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 libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnumber-compare-perl 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 libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.28+b1) ... dpkg: warning: ignoring request to remove 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 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 libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libprocps8 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed Purging configuration files for libsensors-config (1:3.6.0-7) ... dpkg: warning: ignoring request to remove libsensors5 which isn't installed dpkg: warning: ignoring request to remove libset-object-perl 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 libssh2-1 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 libtext-glob-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 libtimedate-perl 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 libwebp6 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 libxt6 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 (4.0.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-9) ... Purging configuration files for netbase (6.3) ... Purging configuration files for openssl (1.1.1w-0+deb11u1) ... Purging configuration files for parallel (20161222-1.1) ... Purging configuration files for perl (5.32.1-4+deb11u3) ... dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed dpkg: warning: ignoring request to remove perl-openssl-defaults which isn't installed dpkg: warning: ignoring request to remove prank which isn't installed Purging configuration files for procps (2:3.3.17-5) ... Purging configuration files for python3 (3.9.2-3) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for r-base-core (4.0.4-1) ... dpkg: warning: ignoring request to remove r-cran-assertthat which isn't installed dpkg: warning: ignoring request to remove r-cran-brio which isn't installed dpkg: warning: ignoring request to remove r-cran-callr which isn't installed dpkg: warning: ignoring request to remove r-cran-cli which isn't installed dpkg: warning: ignoring request to remove r-cran-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-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 (8.1-1) ... dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for sysstat (12.5.2-2) ... Purging configuration files for ucf (3.0043) ... Purging configuration files for unzip (6.0-26+deb11u1) ... Purging configuration files for x11-common (1:7.7+22) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove xz-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 0m41.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg', '--purge', '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:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libcurl4:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', '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:amd64', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu67: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', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmd0:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl', 'libmpdec3:amd64', 'libmro-compat-perl', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnghttp2-14:amd64', 'libnumber-compare-perl', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparams-util-perl', 'libparse-yapp-perl', 'libperl5.32:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-object-perl', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl', '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', 'libtext-glob-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtimedate-perl', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libwebp6: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:amd64', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.32', 'perl-openssl-defaults:amd64', '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'] 0m41.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg', '--purge', 'roary'] 0m41.9s DUMP: dpkg: warning: ignoring request to remove roary which isn't installed 0m41.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg', '--purge', 'roary'] 0m41.9s INFO: Running scripts post_purge 0m41.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_purge_exceptions'] 0m41.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_purge_exceptions'] 0m41.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg', '--purge', '--pending'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg', '--purge', '--pending'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg', '--remove', '--pending'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg', '--remove', '--pending'] 0m42.0s INFO: Running scripts post_test 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_test_exceptions'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'tmp/scripts/post_test_exceptions'] 0m42.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m42.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg-divert', '--list'] 0m42.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'dpkg-divert', '--list'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', 'clean'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r', 'apt-get', 'clean'] 0m42.2s DEBUG: Recording chroot state 0m42.5s INFO: Warning: Package purging left files on system: /usr/local/share/fonts/ not owned /usr/local/share/fonts/.uuid not owned /usr/share/fonts/ owned by: fonts-dejavu-core /usr/share/fonts/.uuid not owned /usr/share/fonts/truetype/ owned by: fonts-dejavu-core /usr/share/fonts/truetype/.uuid not owned /usr/share/fonts/truetype/dejavu/ owned by: fonts-dejavu-core /usr/share/fonts/truetype/dejavu/.uuid not owned 0m42.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/shm'] 0m42.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/shm'] 0m42.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/console'] 0m42.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/console'] 0m42.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/ptmx'] 0m42.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/ptmx'] 0m42.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/pts'] 0m42.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/dev/pts'] 0m42.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/proc'] 0m42.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r/proc'] 0m42.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m42.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpgd_bfy2r'] 0m42.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpgd_bfy2r 0m42.9s INFO: PASS: Upgrading between Debian distributions. 0m42.9s INFO: PASS: All tests. 0m42.9s INFO: piuparts run ends. ret=0 End: 2024-10-08 05:08:06 GMT