Start: 2024-08-22 14:25:05 GMT [bookworm] 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 [bookworm-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/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/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 1.4.4~202408201135~1.4.3-10-g39df1906 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/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt roary=3.13.0+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp4gtkk8dz 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp4gtkk8dz 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp4gtkk8dz/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', 'update'] 0m1.8s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', 'update'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s INFO: Running scripts post_setup 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.0s 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' 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_setup_minimize'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_setup_minimize'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_setup_zz_backports'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_setup_zz_backports'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.1s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u7 install ok installed libc6:amd64 libc6 2.36-9+deb12u7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.26-1~deb12u2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.26-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat 0m4.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 0m4.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 0m4.5s INFO: Running scripts is_testable 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/is_testable_uninstallable'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/is_testable_uninstallable'] 0m4.5s INFO: Running scripts pre_test 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_test_exceptions'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_test_exceptions'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_test_root_password'] 0m4.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_test_root_password'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m4.9s 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 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m4.9s INFO: apt-cache knows about the following packages: roary 0m4.9s INFO: Running scripts pre_install 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_database-server'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_database-server'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_exceptions'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_exceptions'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_extras'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_extras'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'policy'] 0m5.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'policy'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'policy', 'roary'] 0m5.0s DUMP: roary: Installed: (none) Candidate: 3.13.0+dfsg-1 Version table: 3.13.0+dfsg-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'policy', 'roary'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', '-y', 'install', 'roary'] 0m42.9s 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 libclone-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 libgssapi-krb5-2 libharfbuzz0b libheap-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu72 libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblmdb0 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto7 libmbedtls14 libmbedx509-1 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnsl2 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 libpcre3 libperl5.36 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16 libproc2-0 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libregexp-ipv6-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-object-perl libsm6 libspiffy-perl libsqlite3-0 libssh2-1 libssl3 libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-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 libtiff6 libtimedate-perl libtingea0 libtirpc-common libtirpc3 libtk8.6 libtry-tiny-perl liburi-perl libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxrender1 libxss1 libxt6 mafft mcl media-types ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.36 perl-openssl-defaults prank procps python3 python3-minimal python3.11 python3.11-minimal r-base-core r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband 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-pkgconfig r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite 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 low-memory-monitor krb5-doc krb5-user 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 libsub-name-perl libbusiness-isbn-perl libauthen-ntlm-perl mcl-doc csh fish ksh tcsh zsh perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl debhelper python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binutils binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-callr r-cran-covr r-cran-crayon r-cran-digest r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-whoami r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-unitizer r-cran-profvis r-cran-rgeos r-cran-dbi r-cran-forcats r-cran-r.utils r-cran-rsqlite r-cran-stringr r-cran-waldo r-cran-magick r-cran-sf r-cran-lintr r-cran-tidyverse r-cran-bit64 r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-stringi r-cran-survival r-cran-units r-cran-vdiffr r-cran-testthat r-cran-fs r-cran-usethis r-cran-dichromat r-cran-bench r-cran-blob r-cran-brio r-cran-evaluate r-cran-hms r-cran-pkgbuild r-cran-pkgload r-cran-purrr r-cran-tidyr r-cran-pkgdown r-cran-zeallot readline-doc 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 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 krb5-locales 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-testthat r-cran-mockery r-cran-covr r-cran-ragg r-cran-dplyr r-cran-hexbin r-cran-hmisc r-cran-interp r-cran-knitr r-cran-mapproj r-cran-maps r-cran-maptools r-cran-multcomp r-cran-quantreg r-cran-rmarkdown r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 r-cran-crayon r-cran-lubridate r-cran-bit64 r-cran-hms r-cran-stringi r-cran-data.table r-cran-rsqlite r-cran-mockr r-cran-formattable r-cran-generics r-cran-waldo r-cran-dbi 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 libclone-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 libgssapi-krb5-2 libharfbuzz0b libheap-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu72 libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblmdb0 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto7 libmbedtls14 libmbedx509-1 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnsl2 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 libpcre3 libperl5.36 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16 libproc2-0 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libregexp-ipv6-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-object-perl libsm6 libspiffy-perl libsqlite3-0 libssh2-1 libssl3 libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-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 libtiff6 libtimedate-perl libtingea0 libtirpc-common libtirpc3 libtk8.6 libtry-tiny-perl liburi-perl libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxrender1 libxss1 libxt6 mafft mcl media-types ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.36 perl-openssl-defaults prank procps python3 python3-minimal python3.11 python3.11-minimal r-base-core r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband 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-pkgconfig r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr readline-common roary sensible-utils sysstat ucf unzip x11-common xdg-utils xz-utils zip 0 upgraded, 234 newly installed, 0 to remove and 0 not upgraded. Need to get 132 MB of archives. After this operation, 389 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7+deb12u1 [2815 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7+deb12u1 [4218 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7+deb12u1 [239 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.13-1~deb12u1 [2022 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6+deb12u2 [814 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6+deb12u2 [2067 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:16 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6+deb12u2 [1799 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6+deb12u2 [573 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:27 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 netbase all 6.4 [12.8 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.13-1~deb12u1 [1418 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 xz-utils amd64 5.4.1-0.2 [471 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 bedtools amd64 2.30.0+dfsg-3 [665 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:41 http://deb.debian.org/debian bookworm/main amd64 libdevel-stacktrace-perl all 2.0400-2 [26.8 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libtest-differences-perl all 0.69-1 [18.9 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 bioperl all 1.7.8-1 [246 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5+deb12u3 [398 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libarray-utils-perl all 0.5-3 [6184 B] Get:65 http://deb.debian.org/debian bookworm/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 libclass-c3-perl all 0.35-2 [21.0 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libparams-util-perl amd64 1.102-2+b1 [24.8 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libdata-optlist-perl all 0.113-1 [10.6 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 libclass-load-perl all 0.25-2 [15.3 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libclass-load-xs-perl amd64 0.10-2+b1 [14.0 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u6 [390 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:104 http://deb.debian.org/debian bookworm/main amd64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get:105 http://deb.debian.org/debian bookworm/main amd64 libmro-compat-perl all 0.15-2 [11.8 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get:107 http://deb.debian.org/debian bookworm/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get:113 http://deb.debian.org/debian bookworm/main amd64 liburi-perl all 5.17-1 [90.4 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:117 http://deb.debian.org/debian bookworm/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:118 http://deb.debian.org/debian bookworm/main amd64 libhttp-message-perl all 6.44-1 [81.7 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:122 http://deb.debian.org/debian bookworm/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get:123 http://deb.debian.org/debian bookworm/main amd64 libio-socket-ssl-perl all 2.081-2 [219 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 libnet-http-perl all 6.22-1 [25.3 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get:126 http://deb.debian.org/debian bookworm/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 libwww-perl all 6.68-1 [186 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 libdigest-md5-file-perl all 0.08-1.1 [9608 B] Get:129 http://deb.debian.org/debian bookworm/main amd64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get:130 http://deb.debian.org/debian bookworm/main amd64 libenv-path-perl all 0.19-4 [19.1 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 libsub-exporter-perl all 0.989-1 [50.5 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 libeval-closure-perl all 0.14-3 [11.2 kB] Get:133 http://deb.debian.org/debian bookworm/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:134 http://deb.debian.org/debian bookworm/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:135 http://deb.debian.org/debian bookworm/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 libfile-grep-perl all 0.02-3 [8352 B] Get:137 http://deb.debian.org/debian bookworm/main amd64 libfile-slurper-perl all 0.014-1 [8560 B] Get:138 http://deb.debian.org/debian bookworm/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get:140 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:143 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2+deb12u3 [1400 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 libheap-perl all 0.80-5 [34.3 kB] Get:145 http://deb.debian.org/debian bookworm/main amd64 libset-object-perl amd64 1.42-1+b2 [37.9 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 libgraph-perl all 1:0.9726-1 [110 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get:148 http://deb.debian.org/debian bookworm/main amd64 libio-all-perl all 0.87-2 [67.3 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 libparse-yapp-perl all 1.21-3 [42.5 kB] Get:150 http://deb.debian.org/debian bookworm/main amd64 libxml-parser-perl amd64 2.46-4 [201 kB] Get:151 http://deb.debian.org/debian bookworm/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 libgraph-readwrite-perl all 2.10-1 [45.2 kB] Get:153 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:154 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:155 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:156 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:158 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:159 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:160 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:161 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:162 http://deb.debian.org/debian bookworm/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get:163 http://deb.debian.org/debian bookworm/main amd64 liblog-log4perl-perl all 1.57-1 [367 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get:165 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get:166 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get:167 http://deb.debian.org/debian bookworm/main amd64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get:168 http://deb.debian.org/debian bookworm/main amd64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get:169 http://deb.debian.org/debian bookworm/main amd64 libpackage-stash-xs-perl amd64 0.30-1+b1 [19.8 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 libmoose-perl amd64 2.2203-1 [794 kB] Get:171 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:172 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:173 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:174 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:175 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:177 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:178 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 libperlio-utf8-strict-perl amd64 0.010-1 [11.4 kB] Get:180 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get:182 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:183 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 libtest-file-perl all 1.993-1 [24.5 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 libtest-files-perl all 0.15-1 [12.0 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 libtest-output-perl all 1.033-2 [16.1 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 libtext-csv-perl all 2.02-2 [110 kB] Get:188 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:190 http://deb.debian.org/debian bookworm/main amd64 libtingea0 amd64 21-361-2 [50.7 kB] Get:191 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:193 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:194 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:195 http://deb.debian.org/debian bookworm/main amd64 mafft amd64 7.505-1 [1078 kB] Get:196 http://deb.debian.org/debian bookworm/main amd64 mcl amd64 1:22-282+ds-2 [474 kB] Get:197 http://deb.debian.org/debian bookworm/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get:198 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+ amd64 2.12.0+ds-3+b1 [11.9 MB] Get:199 http://deb.debian.org/debian bookworm/main amd64 sysstat amd64 12.6.1-1 [596 kB] Get:200 http://deb.debian.org/debian bookworm/main amd64 parallel all 20221122+ds-2 [1873 kB] Get:201 http://deb.debian.org/debian bookworm/main amd64 prank amd64 0.0.170427+dfsg-3 [395 kB] Get:202 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get:203 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get:204 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:205 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get:206 http://deb.debian.org/debian bookworm/main amd64 r-cran-cli amd64 3.6.0-1 [1287 kB] Get:207 http://deb.debian.org/debian bookworm/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB] Get:208 http://deb.debian.org/debian bookworm/main amd64 r-cran-fansi amd64 1.0.4-1 [619 kB] Get:209 http://deb.debian.org/debian bookworm/main amd64 r-cran-farver amd64 2.1.1-1 [1404 kB] Get:210 http://deb.debian.org/debian bookworm/main amd64 r-cran-glue amd64 1.6.2-1 [152 kB] Get:211 http://deb.debian.org/debian bookworm/main amd64 r-cran-gtable all 0.3.1+dfsg-1 [165 kB] Get:212 http://deb.debian.org/debian bookworm/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:213 http://deb.debian.org/debian bookworm/main amd64 r-cran-rlang amd64 1.0.6-1 [1618 kB] Get:214 http://deb.debian.org/debian bookworm/main amd64 r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB] Get:215 http://deb.debian.org/debian bookworm/main amd64 r-cran-mass amd64 7.3-58.2-1 [1121 kB] Get:216 http://deb.debian.org/debian bookworm/main amd64 r-cran-lattice amd64 0.20-45-3 [1177 kB] Get:217 http://deb.debian.org/debian bookworm/main amd64 r-cran-nlme amd64 3.1.162-1 [2260 kB] Get:218 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrix amd64 1.5-3-1 [3822 kB] Get:219 http://deb.debian.org/debian bookworm/main amd64 r-cran-mgcv amd64 1.8-41-1 [3171 kB] Get:220 http://deb.debian.org/debian bookworm/main amd64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get:221 http://deb.debian.org/debian bookworm/main amd64 r-cran-munsell all 0.5.0-2 [236 kB] Get:222 http://deb.debian.org/debian bookworm/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:223 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:224 http://deb.debian.org/debian bookworm/main amd64 r-cran-viridislite all 0.4.1-1 [1299 kB] Get:225 http://deb.debian.org/debian bookworm/main amd64 r-cran-scales all 1.2.1-1 [614 kB] Get:226 http://deb.debian.org/debian bookworm/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:227 http://deb.debian.org/debian bookworm/main amd64 r-cran-utf8 amd64 1.2.3-1 [133 kB] Get:228 http://deb.debian.org/debian bookworm/main amd64 r-cran-vctrs amd64 0.5.2-1 [1371 kB] Get:229 http://deb.debian.org/debian bookworm/main amd64 r-cran-pillar all 1.8.1+dfsg-1 [463 kB] Get:230 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:231 http://deb.debian.org/debian bookworm/main amd64 r-cran-tibble amd64 3.1.8+dfsg-1 [513 kB] Get:232 http://deb.debian.org/debian bookworm/main amd64 r-cran-withr all 2.5.0-1 [236 kB] Get:233 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggplot2 all 3.4.1+dfsg-1 [3333 kB] Get:234 http://deb.debian.org/debian bookworm/main amd64 roary all 3.13.0+dfsg-1 [184 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 MB in 7s (17.9 MB/s) Selecting previously unselected package perl-modules-5.36. (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 ... 6093 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.36_5.36.0-7+deb12u1_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7+deb12u1) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.23-3_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-3) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Unpacking parallel (20221122+ds-2) ... Selecting previously unselected package prank. Preparing to unpack .../174-prank_0.0.170427+dfsg-3_amd64.deb ... Unpacking prank (0.0.170427+dfsg-3) ... Selecting previously unselected package zip. Preparing to unpack .../175-zip_3.0-13_amd64.deb ... Unpacking zip (3.0-13) ... Selecting previously unselected package unzip. Preparing to unpack .../176-unzip_6.0-28_amd64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../177-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package r-base-core. Preparing to unpack .../178-r-base-core_4.2.2.20221110-2_amd64.deb ... Unpacking r-base-core (4.2.2.20221110-2) ... 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Selecting previously unselected package r-cran-matrix. Preparing to unpack .../191-r-cran-matrix_1.5-3-1_amd64.deb ... Unpacking r-cran-matrix (1.5-3-1) ... Selecting previously unselected package r-cran-mgcv. Preparing to unpack .../192-r-cran-mgcv_1.8-41-1_amd64.deb ... Unpacking r-cran-mgcv (1.8-41-1) ... Selecting previously unselected package r-cran-labeling. Preparing to unpack .../193-r-cran-labeling_0.4.2-1_all.deb ... Unpacking r-cran-labeling (0.4.2-1) ... Selecting previously unselected package r-cran-munsell. Preparing to unpack .../194-r-cran-munsell_0.5.0-2_all.deb ... Unpacking r-cran-munsell (0.5.0-2) ... Selecting previously unselected package r-cran-r6. Preparing to unpack .../195-r-cran-r6_2.5.1-1_all.deb ... Unpacking r-cran-r6 (2.5.1-1) ... Selecting previously unselected package r-cran-rcolorbrewer. Preparing to unpack .../196-r-cran-rcolorbrewer_1.1-3-1_all.deb ... Unpacking r-cran-rcolorbrewer (1.1-3-1) ... 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Selecting previously unselected package r-cran-pkgconfig. Preparing to unpack .../203-r-cran-pkgconfig_2.0.3-2_all.deb ... Unpacking r-cran-pkgconfig (2.0.3-2) ... Selecting previously unselected package r-cran-tibble. Preparing to unpack .../204-r-cran-tibble_3.1.8+dfsg-1_amd64.deb ... Unpacking r-cran-tibble (3.1.8+dfsg-1) ... Selecting previously unselected package r-cran-withr. Preparing to unpack .../205-r-cran-withr_2.5.0-1_all.deb ... Unpacking r-cran-withr (2.5.0-1) ... Selecting previously unselected package r-cran-ggplot2. Preparing to unpack .../206-r-cran-ggplot2_3.4.1+dfsg-1_all.deb ... Unpacking r-cran-ggplot2 (3.4.1+dfsg-1) ... Selecting previously unselected package roary. Preparing to unpack .../207-roary_3.13.0+dfsg-1_all.deb ... Unpacking roary (3.13.0+dfsg-1) ... Setting up media-types (10.0.0) ... Setting up liblmdb0:amd64 (0.9.24-1) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up ncbi-data (6.1.20170106+dfsg1-10) ... Setting up libpixman-1-0:amd64 (0.42.2-1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up libdatrie1:amd64 (0.2.13-2+b1) ... Setting up libtext-glob-perl (0.11-3) ... Setting up libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... No schema files found: doing nothing. Setting up libtirpc-common (1.3.3+ds-1) ... Setting up unzip (6.0-28) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libsensors-config (1:3.6.0-7.1) ... Setting up libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libnumber-compare-perl (0.03-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up libpcre3:amd64 (2:8.39-15) ... Setting up zip (3.0-13) ... Setting up perl-modules-5.36 (5.36.0-7+deb12u1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libmbedcrypto7:amd64 (2.28.3-1) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up xz-utils (5.4.1-0.2) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libproc2-0:amd64 (2:4.0.2-3) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libsensors5:amd64 (1:3.6.0-7.1) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libtiff6:amd64 (4.5.0-6+deb12u1) ... Setting up procps (2:4.0.2-3) ... Setting up libtingea0:amd64 (21-361-2) ... Setting up libthai-data (0.1.29-1) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up fasttree (2.1.11-2) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up openssl (3.0.13-1~deb12u1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up readline-common (8.2-1.3) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up bedtools (2.30.0+dfsg-3) ... Setting up prank (0.0.170427+dfsg-3) ... Setting up libgdbm6:amd64 (1.23-3) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Setting up mcl (1:22-282+ds-2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libcurl4:amd64 (7.88.1-10+deb12u6) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up sysstat (12.6.1-1) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libpaper1:amd64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libpaper-utils (1.1.29) ... Setting up libcairo2:amd64 (1.16.0-7) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libpackage-stash-xs-perl:amd64 (0.30-1+b1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libalgorithm-c3-perl (0.11-2) ... Setting up libset-object-perl (1.42-1+b2) ... Setting up liblog-log4perl-perl (1.57-1) ... Setting up libfile-find-rule-perl (0.34-3) ... Setting up libperlio-utf8-strict-perl (0.010-1) ... Setting up libxml-writer-perl (0.900-2) ... Setting up libenv-path-perl (0.19-4) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Setting up libfile-grep-perl (0.02-3) ... Setting up libxt6:amd64 (1:1.2.1-1.1) ... Setting up libparams-util-perl (1.102-2+b1) ... Setting up parallel (20221122+ds-2) ... Setting up libspiffy-perl (0.46-1) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libdevel-globaldestruction-perl (0.14-4) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up liburi-perl (5.17-1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libtext-csv-perl (2.02-2) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ... Setting up cd-hit (4.8.1-4) ... Setting up libarray-utils-perl (0.5-3) ... Setting up libhttp-date-perl (6.05-2) ... Setting up libfile-slurper-perl (0.014-1) ... Setting up libfile-which-perl (1.27-2) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libparse-yapp-perl (1.21-3) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libtest-deep-perl (1.204-1) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:amd64 (0.46-1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libtest-file-perl (1.993-1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up libheap-perl (0.80-5) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up libnet-http-perl (6.22-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libexception-class-perl (1.45-1) ... Setting up libfindbin-libs-perl (3.0.2-1) ... Setting up libio-all-perl (0.87-2) ... Setting up libclass-c3-perl (0.35-2) ... Setting up libgraph-perl (1:0.9726-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up libsub-install-perl (0.929-1) ... Setting up libio-string-perl (1.08-4) ... Setting up libtest-exception-perl (0.43-3) ... Setting up libtext-diff-perl (1.45-2) ... Setting up r-base-core (4.2.2.20221110-2) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-gtable (0.3.1+dfsg-1) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up libdata-optlist-perl (0.113-1) ... Setting up libtest-output-perl (1.033-2) ... Setting up r-cran-lattice (0.20-45-3) ... Setting up r-cran-nlme (3.1.162-1) ... Setting up r-cran-farver (2.1.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up r-cran-viridislite (0.4.1-1) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libmro-compat-perl (0.15-2) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up libio-socket-ssl-perl (2.081-2) ... Setting up libsub-exporter-perl (0.989-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libeval-closure-perl (0.14-3) ... Setting up python3.11 (3.11.2-6+deb12u2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up r-cran-rlang (1.0.6-1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up r-cran-withr (2.5.0-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up r-cran-fansi (1.0.4-1) ... Setting up libtest-differences-perl (0.69-1) ... Setting up r-cran-mass (7.3-58.2-1) ... Setting up python3 (3.11.2-1+b1) ... Setting up r-cran-glue (1.6.2-1) ... Setting up libtest-files-perl (0.15-1) ... Setting up r-cran-cli (3.6.0-1) ... Setting up r-cran-lifecycle (1.0.3+dfsg-1) ... Setting up ncbi-blast+ (2.12.0+ds-3+b1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.3-1) ... Setting up r-cran-colorspace (2.1-0+dfsg-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up libdist-checkconflicts-perl (0.11-2) ... Setting up r-cran-matrix (1.5-3-1) ... Setting up r-cran-mgcv (1.8-41-1) ... Setting up r-cran-vctrs (0.5.2-1) ... Setting up r-cran-pillar (1.8.1+dfsg-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libtest-most-perl (0.38-1) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-tibble (3.1.8+dfsg-1) ... Setting up libmodule-runtime-conflicts-perl (0.003-2) ... Setting up libclass-load-perl (0.25-2) ... Setting up r-cran-scales (1.2.1-1) ... Setting up libpackage-deprecationmanager-perl (0.18-1) ... Setting up libdevel-overloadinfo-perl (0.007-1) ... Setting up libclass-load-xs-perl (0.10-2+b1) ... Setting up bioperl (1.7.8-1) ... Setting up r-cran-ggplot2 (3.4.1+dfsg-1) ... Setting up libmoose-perl:amd64 (2.2203-1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up libwww-perl (6.68-1) ... Setting up libdigest-md5-file-perl (0.08-1.1) ... Setting up libxml-parser-perl (2.46-4) ... Setting up libgraph-readwrite-perl (2.10-1) ... Setting up roary (3.13.0+dfsg-1) ... Processing triggers for libc-bin (2.36-9+deb12u7) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', '-y', 'install', 'roary'] 0m42.9s INFO: Running scripts post_install 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_install_exceptions'] 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_install_exceptions'] 0m42.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 0m43.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 0m43.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp4gtkk8dz to bookworm-next 0m43.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main deb http://security.debian.org bookworm-security main deb http://deb.debian.org/debian/ bookworm-updates main deb http://deb.debian.org/debian/ bookworm-proposed-updates main 0m43.8s INFO: Running scripts pre_distupgrade 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_distupgrade_exceptions'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_distupgrade_exceptions'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m43.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m43.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', 'update'] 0m45.8s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Get:2 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB] Get:3 http://security.debian.org bookworm-security InRelease [48.0 kB] Get:4 http://deb.debian.org/debian bookworm-proposed-updates InRelease [59.5 kB] Get:5 http://security.debian.org bookworm-security/main amd64 Packages [176 kB] Get:6 http://security.debian.org bookworm-security/main Translation-en [106 kB] Get:7 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [13.8 kB] Get:8 http://deb.debian.org/debian bookworm-updates/main Translation-en [16.0 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages [108 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main Translation-en [62.5 kB] Fetched 645 kB in 1s (693 kB/s) Reading package lists... 0m45.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', 'update'] 0m45.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', '-yf', 'dist-upgrade'] 0m48.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc6 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libssl3 libsystemd0 libudev1 openssl 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7825 kB of archives. After this operation, 5120 B of additional disk space will be used. Get:1 http://security.debian.org bookworm-security/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u2 [135 kB] Get:2 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6 amd64 2.36-9+deb12u8 [2754 kB] Get:3 http://security.debian.org bookworm-security/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u2 [332 kB] Get:4 http://security.debian.org bookworm-security/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u2 [32.6 kB] Get:5 http://security.debian.org bookworm-security/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u2 [78.7 kB] Get:6 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-bin amd64 2.36-9+deb12u8 [608 kB] Get:7 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libsystemd0 amd64 252.29-1~deb12u1 [332 kB] Get:8 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libudev1 amd64 252.29-1~deb12u1 [108 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libssl3 amd64 3.0.13-1~deb12u2 [2023 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 openssl amd64 3.0.13-1~deb12u2 [1421 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7825 kB in 0s (50.4 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 ... 19669 files and directories currently installed.) Preparing to unpack .../libc6_2.36-9+deb12u8_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc6:amd64 (2.36-9+deb12u8) ... (Reading database ... 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Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../3-libk5crypto3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../4-libssl3_3.0.13-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u2) over (3.0.13-1~deb12u1) ... Preparing to unpack .../5-openssl_3.0.13-1~deb12u2_amd64.deb ... Unpacking openssl (3.0.13-1~deb12u2) over (3.0.13-1~deb12u1) ... Setting up libssl3:amd64 (3.0.13-1~deb12u2) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Setting up openssl (3.0.13-1~deb12u2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', '-yf', 'dist-upgrade'] 0m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m49.2s DUMP: 8d734360ea7c957ed98a0e4620f217b3 - 0m49.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m49.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m49.4s 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 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m49.4s INFO: apt-cache knows about the following packages: roary 0m49.4s INFO: Running scripts pre_install 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_database-server'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_database-server'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_exceptions'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_exceptions'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_extras'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_extras'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_foreign_architecture'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_foreign_architecture'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'policy'] 0m49.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'policy'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'policy', 'roary'] 0m49.6s 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 bookworm/main amd64 Packages 100 /var/lib/dpkg/status 0m49.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'policy', 'roary'] 0m49.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', '-y', 'install', 'roary'] 0m50.1s 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. 0m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', '-y', 'install', 'roary'] 0m50.1s INFO: Running scripts post_install 0m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_install_exceptions'] 0m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_install_exceptions'] 0m50.1s INFO: Running scripts post_distupgrade 0m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_distupgrade_exceptions'] 0m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_distupgrade_exceptions'] 0m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_distupgrade_zz_backports'] 0m50.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_distupgrade_zz_backports'] 0m50.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 0m50.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 0m50.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 0m51.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 0m51.6s INFO: Running scripts pre_install 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_database-server'] 0m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_database-server'] 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_exceptions'] 0m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_exceptions'] 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_extras'] 0m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_extras'] 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_foreign_architecture'] 0m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_foreign_architecture'] 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'policy'] 0m51.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'policy'] 0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'policy', 'roary'] 0m51.8s 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 bookworm/main amd64 Packages 100 /var/lib/dpkg/status 0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-cache', 'policy', 'roary'] 0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', '-y', 'install', 'roary=3.13.0+dfsg-1'] 0m52.3s 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. 0m52.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', '-y', 'install', 'roary=3.13.0+dfsg-1'] 0m52.3s INFO: Running scripts post_install 0m52.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_install_exceptions'] 0m52.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_install_exceptions'] 0m52.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 0m53.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 0m53.3s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m53.3s INFO: /bin converted to /usr/bin by /usr merge 0m53.3s INFO: /lib converted to /usr/lib by /usr merge 0m53.3s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m53.3s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m53.3s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m53.3s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m53.3s INFO: /lib/systemd/system-sleep converted to /usr/lib/systemd/system-sleep by /usr merge 0m53.3s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m53.3s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m53.3s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m53.3s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m53.3s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m53.3s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m53.3s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m53.3s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m53.3s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m53.3s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m53.3s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m53.3s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m53.3s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m53.3s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m53.3s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m53.3s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m53.3s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m53.3s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m53.3s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m53.3s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m53.3s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m53.3s INFO: /sbin converted to /usr/sbin by /usr merge 0m54.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', '-ac', '--ignore-obsolete'] 0m56.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', '-ac', '--ignore-obsolete'] 0m56.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m56.6s DUMP: 0.15.6 0m56.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m56.6s INFO: Running adequate version 0.15.6 now. 0m56.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'roary'] 0m56.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'roary'] 0m56.8s INFO: Running scripts pre_remove 0m56.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m56.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m56.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m56.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m56.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_remove_exceptions'] 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/pre_remove_exceptions'] 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m1.6s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bedtools bedtools 2.30.0+dfsg-3 install ok installed bioperl bioperl 1.7.8-1 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed ca-certificates ca-certificates 20230311 install ok installed cd-hit cd-hit 4.8.1-4 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed fasttree fasttree 2.1.11-2 install ok installed findutils findutils 4.9.0-4 install ok installed fontconfig fontconfig 2.14.1-4 install ok installed fontconfig-config fontconfig-config 2.14.1-4 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-6 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libalgorithm-c3-perl libalgorithm-c3-perl 0.11-2 install ok installed libalgorithm-diff-perl libalgorithm-diff-perl 1.201-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libarray-utils-perl libarray-utils-perl 0.5-3 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libb-hooks-op-check-perl:amd64 libb-hooks-op-check-perl 0.22-2+b1 install ok installed libbio-perl-perl libbio-perl-perl 1.7.8-1 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b6 install ok installed libbsd0:amd64 libbsd0 0.11.7-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u8 install ok installed libc6:amd64 libc6 2.36-9+deb12u8 install ok installed libcairo2:amd64 libcairo2 1.16.0-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcapture-tiny-perl libcapture-tiny-perl 0.48-2 install ok installed libclass-c3-perl libclass-c3-perl 0.35-2 install ok installed libclass-data-inheritable-perl libclass-data-inheritable-perl 0.08-3 install ok installed libclass-load-perl libclass-load-perl 0.25-2 install ok installed libclass-load-xs-perl libclass-load-xs-perl 0.10-2+b1 install ok installed libclone-perl:amd64 libclone-perl 0.46-1 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libcurl4:amd64 libcurl4 7.88.1-10+deb12u6 install ok installed libdata-optlist-perl libdata-optlist-perl 0.113-1 install ok installed libdata-stag-perl libdata-stag-perl 0.14-3 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-2+b1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libdeflate0:amd64 libdeflate0 1.14-1 install ok installed libdevel-callchecker-perl:amd64 libdevel-callchecker-perl 0.008-2 install ok installed libdevel-globaldestruction-perl libdevel-globaldestruction-perl 0.14-4 install ok installed libdevel-overloadinfo-perl libdevel-overloadinfo-perl 0.007-1 install ok installed libdevel-stacktrace-perl libdevel-stacktrace-perl 2.0400-2 install ok installed libdigest-md5-file-perl libdigest-md5-file-perl 0.08-1.1 install ok installed libdist-checkconflicts-perl libdist-checkconflicts-perl 0.11-2 install ok installed libdynaloader-functions-perl libdynaloader-functions-perl 0.003-3 install ok installed libencode-locale-perl libencode-locale-perl 1.05-3 install ok installed libenv-path-perl libenv-path-perl 0.19-4 install ok installed libeval-closure-perl libeval-closure-perl 0.14-3 install ok installed libexception-class-perl libexception-class-perl 1.45-1 install ok installed libexpat1:amd64 libexpat1 2.5.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libfile-grep-perl libfile-grep-perl 0.02-3 install ok installed libfile-listing-perl libfile-listing-perl 6.15-1 install ok installed libfile-slurper-perl libfile-slurper-perl 0.014-1 install ok installed libfile-which-perl libfile-which-perl 1.27-2 install ok installed libfindbin-libs-perl libfindbin-libs-perl 3.0.2-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.14.1-4 install ok installed libfreetype6:amd64 libfreetype6 2.12.1+dfsg-5+deb12u3 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2.1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgfortran5:amd64 libgfortran5 12.2.0-14 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.74.6-2+deb12u3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgomp1:amd64 libgomp1 12.2.0-14 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgraph-perl libgraph-perl 1:0.9726-1 install ok installed libgraph-readwrite-perl libgraph-readwrite-perl 2.10-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2+deb12u2 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 6.0.0+dfsg-3 install ok installed libheap-perl libheap-perl 0.80-5 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libhtml-parser-perl:amd64 libhtml-parser-perl 3.81-1 install ok installed libhtml-tagset-perl libhtml-tagset-perl 3.20-6 install ok installed libhtml-tree-perl libhtml-tree-perl 5.07-3 install ok installed libhttp-cookies-perl libhttp-cookies-perl 6.10-1 install ok installed libhttp-date-perl libhttp-date-perl 6.05-2 install ok installed libhttp-message-perl libhttp-message-perl 6.44-1 install ok installed libhttp-negotiate-perl libhttp-negotiate-perl 6.01-2 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu72:amd64 libicu72 72.1-3 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libio-all-perl libio-all-perl 0.87-2 install ok installed libio-html-perl libio-html-perl 1.004-3 install ok installed libio-socket-ssl-perl libio-socket-ssl-perl 2.081-2 install ok installed libio-string-perl libio-string-perl 1.08-4 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-2+deb12u2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2+deb12u2 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2+deb12u2 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-2 install ok installed liblmdb0:amd64 liblmdb0 0.9.24-1 install ok installed liblog-log4perl-perl liblog-log4perl-perl 1.57-1 install ok installed liblwp-mediatypes-perl liblwp-mediatypes-perl 6.04-2 install ok installed liblwp-protocol-https-perl liblwp-protocol-https-perl 6.10-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.3-1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.3-1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.3-1 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmodule-implementation-perl libmodule-implementation-perl 0.09-2 install ok installed libmodule-runtime-conflicts-perl libmodule-runtime-conflicts-perl 0.003-2 install ok installed libmodule-runtime-perl libmodule-runtime-perl 0.016-2 install ok installed libmoose-perl:amd64 libmoose-perl 2.2203-1 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libmro-compat-perl libmro-compat-perl 0.15-2 install ok installed libncursesw6:amd64 libncursesw6 6.4-4 install ok installed libnet-http-perl libnet-http-perl 6.22-1 install ok installed libnet-ssleay-perl:amd64 libnet-ssleay-perl 1.92-2+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.52.0-1+deb12u1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpackage-deprecationmanager-perl libpackage-deprecationmanager-perl 0.18-1 install ok installed libpackage-stash-perl libpackage-stash-perl 0.40-1 install ok installed libpackage-stash-xs-perl:amd64 libpackage-stash-xs-perl 0.30-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.50.12+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.50.12+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.50.12+ds-1 install ok installed libpaper-utils libpaper-utils 1.1.29 install ok installed libpaper1:amd64 libpaper1 1.1.29 install ok installed libparams-classify-perl:amd64 libparams-classify-perl 0.015-2+b1 install ok installed libparams-util-perl libparams-util-perl 1.102-2+b1 install ok installed libparse-yapp-perl libparse-yapp-perl 1.21-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-15 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libperlio-utf8-strict-perl libperlio-utf8-strict-perl 0.010-1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.39-2 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.2-3 install ok installed libpsl5:amd64 libpsl5 0.21.2-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.2-1+b1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.2-6+deb12u2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.2-6+deb12u2 install ok installed libquadmath0:amd64 libquadmath0 12.2.0-14 install ok installed libreadline8:amd64 libreadline8 8.2-1.3 install ok installed libregexp-ipv6-perl libregexp-ipv6-perl 0.03-3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg-10 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg-10 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsensors-config libsensors-config 1:3.6.0-7.1 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-7.1 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libset-object-perl libset-object-perl 1.42-1+b2 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libspiffy-perl libspiffy-perl 0.46-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.40.1-2 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssh2-1:amd64 libssh2-1 1.10.0-3+b1 install ok installed libssl3:amd64 libssl3 3.0.13-1~deb12u2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsub-exporter-perl libsub-exporter-perl 0.989-1 install ok installed libsub-exporter-progressive-perl libsub-exporter-progressive-perl 0.001013-3 install ok installed libsub-install-perl libsub-install-perl 0.929-1 install ok installed libsub-uplevel-perl libsub-uplevel-perl 0.2800-3 install ok installed libsystemd0:amd64 libsystemd0 252.29-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.13+dfsg-2 install ok installed libtest-deep-perl libtest-deep-perl 1.204-1 install ok installed libtest-differences-perl libtest-differences-perl 0.69-1 install ok installed libtest-exception-perl libtest-exception-perl 0.43-3 install ok installed libtest-file-perl libtest-file-perl 1.993-1 install ok installed libtest-files-perl libtest-files-perl 0.15-1 install ok installed libtest-most-perl libtest-most-perl 0.38-1 install ok installed libtest-output-perl libtest-output-perl 1.033-2 install ok installed libtest-warn-perl libtest-warn-perl 0.37-2 install ok installed libtext-csv-perl libtext-csv-perl 2.02-2 install ok installed libtext-diff-perl libtext-diff-perl 1.45-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libthai-data libthai-data 0.1.29-1 install ok installed libthai0:amd64 libthai0 0.1.29-1 install ok installed libtiff6:amd64 libtiff6 4.5.0-6+deb12u1 install ok installed libtimedate-perl libtimedate-perl 2.3300-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libtingea0:amd64 libtingea0 21-361-2 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.13-2 install ok installed libtry-tiny-perl libtry-tiny-perl 0.31-2 install ok installed libudev1:amd64 libudev1 252.29-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed liburi-perl liburi-perl 5.17-1 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libwebp7:amd64 libwebp7 1.2.4-0.2+deb12u1 install ok installed libwww-perl libwww-perl 6.68-1 install ok installed libwww-robotrules-perl libwww-robotrules-perl 6.02-1 install ok installed libx11-6:amd64 libx11-6 2:1.8.4-2+deb12u2 install ok installed libx11-data libx11-data 2:1.8.4-2+deb12u2 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxft2:amd64 libxft2 2.3.6-1 install ok installed libxml-parser-perl libxml-parser-perl 2.46-4 install ok installed libxml-writer-perl libxml-writer-perl 0.900-2 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6:amd64 libxt6 1:1.2.1-1.1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mafft mafft 7.505-1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mcl mcl 1:22-282+ds-2 install ok installed media-types media-types 10.0.0 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncbi-blast+ ncbi-blast+ 2.12.0+ds-3+b1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-10 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.0.13-1~deb12u2 install ok installed parallel parallel 20221122+ds-2 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl perl 5.36.0-7+deb12u1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed perl-openssl-defaults:amd64 perl-openssl-defaults 7+b1 install ok installed prank prank 0.0.170427+dfsg-3 install ok installed procps procps 2:4.0.2-3 install ok installed python3 python3 3.11.2-1+b1 install ok installed python3-minimal python3-minimal 3.11.2-1+b1 install ok installed python3.11 python3.11 3.11.2-6+deb12u2 install ok installed python3.11-minimal python3.11-minimal 3.11.2-6+deb12u2 install ok installed r-base-core r-base-core 4.2.2.20221110-2 install ok installed r-cran-cli r-cran-cli 3.6.0-1 install ok installed r-cran-colorspace r-cran-colorspace 2.1-0+dfsg-1 install ok installed r-cran-fansi r-cran-fansi 1.0.4-1 install ok installed r-cran-farver r-cran-farver 2.1.1-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.4.1+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.6.2-1 install ok installed r-cran-gtable r-cran-gtable 0.3.1+dfsg-1 install ok installed r-cran-isoband r-cran-isoband 0.2.7-1 install ok installed r-cran-labeling r-cran-labeling 0.4.2-1 install ok installed r-cran-lattice r-cran-lattice 0.20-45-3 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.3+dfsg-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-mass r-cran-mass 7.3-58.2-1 install ok installed r-cran-matrix r-cran-matrix 1.5-3-1 install ok installed r-cran-mgcv r-cran-mgcv 1.8-41-1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-2 install ok installed r-cran-nlme r-cran-nlme 3.1.162-1 install ok installed r-cran-pillar r-cran-pillar 1.8.1+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-3-1 install ok installed r-cran-rlang r-cran-rlang 1.0.6-1 install ok installed r-cran-scales r-cran-scales 1.2.1-1 install ok installed r-cran-tibble r-cran-tibble 3.1.8+dfsg-1 install ok installed r-cran-utf8 r-cran-utf8 1.2.3-1 install ok installed r-cran-vctrs r-cran-vctrs 0.5.2-1 install ok installed r-cran-viridislite r-cran-viridislite 0.4.1-1 install ok installed r-cran-withr r-cran-withr 2.5.0-1 install ok installed readline-common readline-common 8.2-1.3 install ok installed roary roary 3.13.0+dfsg-1 install ok installed sed sed 4.9-1 install ok installed sensible-utils sensible-utils 0.0.17+nmu1 install ok installed sysstat sysstat 12.6.1-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed x11-common x11-common 1:7.7+23 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed xz-utils xz-utils 5.4.1-0.2 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', '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:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclone-perl:amd64', 'libcurl4:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfile-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', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmro-compat-perl', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libnumber-compare-perl', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libparse-yapp-perl', 'libpcre3:amd64', 'libperl5.36:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libregexp-ipv6-perl', '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', 'libssl3:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-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', 'libtiff6:amd64', 'libtimedate-perl', 'libtingea0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.36', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'r-base-core', 'r-cran-cli', 'r-cran-colorspace', 'r-cran-fansi', 'r-cran-farver', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-isoband', '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-pkgconfig', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rlang', 'r-cran-scales', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'readline-common', 'sensible-utils', 'sysstat', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip', 'roary'] 1m5.4s 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 libclone-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 libgssapi-krb5-2 libharfbuzz0b libheap-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu72 libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblmdb0 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto7 libmbedtls14 libmbedx509-1 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnsl2 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 libpcre3 libperl5.36 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16 libproc2-0 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libregexp-ipv6-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-object-perl libsm6 libspiffy-perl libsqlite3-0 libssh2-1 libssl3 libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-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 libtiff6 libtimedate-perl libtingea0 libtirpc-common libtirpc3 libtk8.6 libtry-tiny-perl liburi-perl libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxrender1 libxss1 libxt6 mafft mcl media-types ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.36 perl-openssl-defaults prank procps python3 python3-minimal python3.11 python3.11-minimal r-base-core r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband 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-pkgconfig r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr readline-common roary sensible-utils sysstat ucf unzip x11-common xdg-utils xz-utils zip 0 upgraded, 0 newly installed, 234 to remove and 0 not upgraded. After this operation, 389 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 ... 19669 files and directories currently installed.) Removing roary (3.13.0+dfsg-1) ... Removing bedtools (2.30.0+dfsg-3) ... Removing bioperl (1.7.8-1) ... Removing r-cran-ggplot2 (3.4.1+dfsg-1) ... Removing r-cran-mgcv (1.8-41-1) ... Removing r-cran-matrix (1.5-3-1) ... Removing r-cran-scales (1.2.1-1) ... Removing r-cran-rcolorbrewer (1.1-3-1) ... Removing r-cran-withr (2.5.0-1) ... Removing r-cran-viridislite (0.4.1-1) ... Removing libgraph-readwrite-perl (2.10-1) ... Removing libxml-parser-perl (2.46-4) ... Removing cd-hit (4.8.1-4) ... Removing fasttree (2.1.11-2) ... Removing libmoose-perl:amd64 (2.2203-1) ... Removing libdevel-overloadinfo-perl (0.007-1) ... Removing libmro-compat-perl (0.15-2) ... Removing libclass-c3-perl (0.35-2) ... Removing libalgorithm-c3-perl (0.11-2) ... Removing libtest-files-perl (0.15-1) ... Removing libtest-most-perl (0.38-1) ... Removing libtest-differences-perl (0.69-1) ... Removing libtext-diff-perl (1.45-2) ... Removing libalgorithm-diff-perl (1.201-1) ... Removing libarray-utils-perl (0.5-3) ... Removing libmodule-runtime-conflicts-perl (0.003-2) ... Removing libpackage-deprecationmanager-perl (0.18-1) ... Removing libbio-perl-perl (1.7.8-1) ... Removing libtest-output-perl (1.033-2) ... Removing libcapture-tiny-perl (0.48-2) ... Removing libexception-class-perl (1.45-1) ... Removing libclass-data-inheritable-perl (0.08-3) ... Removing libclass-load-xs-perl (0.10-2+b1) ... Removing libclass-load-perl (0.25-2) ... Removing libeval-closure-perl (0.14-3) ... Removing libsub-exporter-perl (0.989-1) ... Removing libdata-optlist-perl (0.113-1) ... Removing libdata-stag-perl (0.14-3) ... Removing libdevel-globaldestruction-perl (0.14-4) ... Removing libdevel-stacktrace-perl (2.0400-2) ... Removing libdigest-md5-file-perl (0.08-1.1) ... Removing libdist-checkconflicts-perl (0.11-2) ... Removing libenv-path-perl (0.19-4) ... Removing ncbi-blast+ (2.12.0+ds-3+b1) ... Removing python3 (3.11.2-1+b1) ... Removing python3.11 (3.11.2-6+deb12u2) ... Removing python3-minimal (3.11.2-1+b1) ... Removing python3.11-minimal (3.11.2-6+deb12u2) ... Removing libfile-find-rule-perl (0.34-3) ... Removing libfile-grep-perl (0.02-3) ... Removing libfile-slurper-perl (0.014-1) ... Removing libfile-which-perl (1.27-2) ... Removing libfindbin-libs-perl (3.0.2-1) ... Removing parallel (20221122+ds-2) ... 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 libio-all-perl (0.87-2) ... Removing libspiffy-perl (0.46-1) ... Removing mafft (7.505-1) ... Removing libtest-deep-perl (1.204-1) ... Removing libgraph-perl (1:0.9726-1) ... Removing libpython3-stdlib:amd64 (3.11.2-1+b1) ... Removing libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-2) ... Removing libheap-perl (0.80-5) ... Removing libio-string-perl (1.08-4) ... Removing liblmdb0:amd64 (0.9.24-1) ... Removing liblog-log4perl-perl (1.57-1) ... Removing libmbedtls14:amd64 (2.28.3-1) ... Removing libmbedx509-1:amd64 (2.28.3-1) ... Removing libmbedcrypto7:amd64 (2.28.3-1) ... Removing procps (2:4.0.2-3) ... Removing libncursesw6:amd64 (6.4-4) ... Removing libnumber-compare-perl (0.03-3) ... Removing libpackage-stash-xs-perl:amd64 (0.30-1+b1) ... Removing libparams-util-perl (1.102-2+b1) ... Removing libparse-yapp-perl (1.21-3) ... Removing libpcre3:amd64 (2:8.39-15) ... Removing libperlio-utf8-strict-perl (0.010-1) ... Removing libproc2-0:amd64 (2:4.0.2-3) ... Removing libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing sysstat (12.6.1-1) ... Removing libsensors5:amd64 (1:3.6.0-7.1) ... Removing libsensors-config (1:3.6.0-7.1) ... Removing libset-object-perl (1.42-1+b2) ... Removing libsqlite3-0:amd64 (3.40.1-2) ... Removing libsub-exporter-progressive-perl (0.001013-3) ... Removing libsub-install-perl (0.929-1) ... Removing libtest-warn-perl (0.37-2) ... Removing libtest-exception-perl (0.43-3) ... Removing libsub-uplevel-perl (0.2800-3) ... Removing libtest-file-perl (1.993-1) ... Removing libtext-csv-perl (2.02-2) ... Removing libtext-glob-perl (0.11-3) ... Removing mcl (1:22-282+ds-2) ... Removing libtingea0:amd64 (21-361-2) ... Removing libxml-writer-perl (0.900-2) ... Removing media-types (10.0.0) ... Removing ncbi-data (6.1.20170106+dfsg1-10) ... Removing prank (0.0.170427+dfsg-3) ... Removing r-cran-tibble (3.1.8+dfsg-1) ... Removing r-cran-pillar (1.8.1+dfsg-1) ... Removing r-cran-vctrs (0.5.2-1) ... Removing r-cran-lifecycle (1.0.3+dfsg-1) ... Removing r-cran-cli (3.6.0-1) ... Removing r-cran-munsell (0.5.0-2) ... Removing r-cran-colorspace (2.1-0+dfsg-1) ... Removing r-cran-fansi (1.0.4-1) ... Removing r-cran-farver (2.1.1-1) ... Removing r-cran-glue (1.6.2-1) ... Removing r-cran-gtable (0.3.1+dfsg-1) ... Removing r-cran-isoband (0.2.7-1) ... Removing r-cran-labeling (0.4.2-1) ... Removing r-cran-nlme (3.1.162-1) ... Removing r-cran-lattice (0.20-45-3) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-58.2-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rlang (1.0.6-1) ... Removing r-cran-utf8 (1.2.3-1) ... Removing xz-utils (5.4.1-0.2) ... Removing r-base-core (4.2.2.20221110-2) ... Removing libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Removing libpango-1.0-0:amd64 (1.50.12+ds-1) ... Removing fontconfig (2.14.1-4) ... Removing libtk8.6:amd64 (8.6.13-2) ... Removing libxft2:amd64 (2.3.6-1) ... Removing libcairo2:amd64 (1.16.0-7) ... Removing libfontconfig1:amd64 (2.14.1-4) ... Removing fontconfig-config (2.14.1-4) ... Removing fonts-dejavu-core (2.37-6) ... Removing libpackage-stash-perl (0.40-1) ... Removing libmodule-implementation-perl (0.09-2) ... Removing libmodule-runtime-perl (0.016-2) ... Removing libparams-classify-perl:amd64 (0.015-2+b1) ... Removing libdevel-callchecker-perl:amd64 (0.008-2) ... Removing libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing libcurl4:amd64 (7.88.1-10+deb12u6) ... Removing libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Removing libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Removing libbrotli1:amd64 (1.0.9-2+b6) ... Removing libxt6:amd64 (1:1.2.1-1.1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libthai0:amd64 (0.1.29-1) ... Removing libdatrie1:amd64 (0.2.13-2+b1) ... Removing libtiff6:amd64 (4.5.0-6+deb12u1) ... Removing libdeflate0:amd64 (1.14-1) ... Removing libdynaloader-functions-perl (0.003-3) ... Removing libexpat1:amd64 (2.5.0-1) ... Removing libfribidi0:amd64 (1.0.8-2.1) ... Removing libgfortran5:amd64 (12.2.0-14) ... Removing libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... Removing libgomp1:amd64 (12.2.0-14) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Removing libicu72:amd64 (72.1-3) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2) ... Removing libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Removing libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Removing liblerc4:amd64 (4.0.0+ds-2) ... Removing libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libpixman-1-0:amd64 (0.42.2-1) ... Removing libpng16-16:amd64 (1.6.39-2) ... Removing libpsl5:amd64 (0.21.2-1) ... Removing libquadmath0:amd64 (12.2.0-14) ... Removing libreadline8:amd64 (8.2-1.3) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg-10) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Removing libssh2-1:amd64 (1.10.0-3+b1) ... Removing libtcl8.6:amd64 (8.6.13+dfsg-2) ... Removing libthai-data (0.1.29-1) ... Removing libtirpc-common (1.3.3+ds-1) ... Removing libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing readline-common (8.2-1.3) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.17+nmu1) ... Removing unzip (6.0-28) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-13) ... Removing libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.7-2) ... Removing libx11-data (2:1.8.4-2+deb12u2) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing libwww-perl (6.68-1) ... Removing libhttp-negotiate-perl (6.01-2) ... Removing libfile-listing-perl (6.15-1) ... Removing libwww-robotrules-perl (6.02-1) ... Removing libhttp-cookies-perl (6.10-1) ... Removing libhtml-tree-perl (5.07-3) ... Removing libhtml-parser-perl:amd64 (3.81-1) ... Removing libhtml-tagset-perl (3.20-6) ... Removing liblwp-protocol-https-perl (6.10-1) ... Removing libio-socket-ssl-perl (2.081-2) ... Removing libnet-http-perl (6.22-1) ... Removing libnet-ssleay-perl:amd64 (1.92-2+b1) ... Removing perl-openssl-defaults:amd64 (7+b1) ... Removing libtry-tiny-perl (0.31-2) ... Removing netbase (6.4) ... Removing ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libhttp-message-perl (6.44-1) ... Removing libclone-perl:amd64 (0.46-1) ... Removing libencode-locale-perl (1.05-3) ... Removing libhttp-date-perl (6.05-2) ... Removing libio-html-perl (1.004-3) ... Removing liblwp-mediatypes-perl (6.04-2) ... Removing liburi-perl (5.17-1) ... Removing libregexp-ipv6-perl (0.03-3) ... Removing openssl (3.0.13-1~deb12u2) ... Removing libssl3:amd64 (3.0.13-1~deb12u2) ... Removing libtimedate-perl (2.3300-2) ... Removing perl (5.36.0-7+deb12u1) ... Removing libperl5.36:amd64 (5.36.0-7+deb12u1) ... Removing libgdbm-compat4:amd64 (1.23-3) ... Removing libgdbm6:amd64 (1.23-3) ... Removing perl-modules-5.36 (5.36.0-7+deb12u1) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 1m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', '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:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclone-perl:amd64', 'libcurl4:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfile-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', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmro-compat-perl', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libnumber-compare-perl', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libparse-yapp-perl', 'libpcre3:amd64', 'libperl5.36:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libregexp-ipv6-perl', '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', 'libssl3:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-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', 'libtiff6:amd64', 'libtimedate-perl', 'libtingea0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.36', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'r-base-core', 'r-cran-cli', 'r-cran-colorspace', 'r-cran-fansi', 'r-cran-farver', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-isoband', '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-pkgconfig', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rlang', 'r-cran-scales', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'readline-common', 'sensible-utils', 'sysstat', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip', 'roary'] 1m5.4s INFO: Running scripts post_remove 1m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_remove_exceptions'] 1m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_remove_exceptions'] 1m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', '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:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclone-perl:amd64', 'libcurl4:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfile-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', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmro-compat-perl', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libnumber-compare-perl', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libparse-yapp-perl', 'libpcre3:amd64', 'libperl5.36:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libregexp-ipv6-perl', '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', 'libssl3:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-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', 'libtiff6:amd64', 'libtimedate-perl', 'libtingea0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.36', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'r-base-core', 'r-cran-cli', 'r-cran-colorspace', 'r-cran-fansi', 'r-cran-farver', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-isoband', '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-pkgconfig', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rlang', 'r-cran-scales', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'readline-common', 'sensible-utils', 'sysstat', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip'] 1m6.8s 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 ... 6166 files and directories currently installed.) Purging configuration files for ca-certificates (20230311) ... 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 (2.14.1-4) ... Purging configuration files for fontconfig-config (2.14.1-4) ... Purging configuration files for fonts-dejavu-core (2.37-6) ... dpkg: warning: ignoring request to remove libalgorithm-c3-perl which isn't installed dpkg: warning: ignoring request to remove libalgorithm-diff-perl which isn't installed dpkg: warning: ignoring request to remove libarray-utils-perl which isn't installed dpkg: warning: ignoring request to remove libb-hooks-op-check-perl which isn't installed dpkg: warning: ignoring request to remove libbio-perl-perl which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcapture-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libclass-c3-perl which isn't installed dpkg: warning: ignoring request to remove libclass-data-inheritable-perl which isn't installed dpkg: warning: ignoring request to remove libclass-load-perl which isn't installed dpkg: warning: ignoring request to remove libclass-load-xs-perl which isn't installed dpkg: warning: ignoring request to remove libclone-perl which isn't installed dpkg: warning: ignoring request to remove 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 (2.74.6-2+deb12u3) ... 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 Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... 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 libicu72 which isn't installed dpkg: warning: ignoring request to remove libio-all-perl which isn't installed dpkg: warning: ignoring request to remove libio-html-perl which isn't installed dpkg: warning: ignoring request to remove libio-socket-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libio-string-perl which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove liblog-log4perl-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-mediatypes-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-protocol-https-perl which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1 which isn't installed dpkg: warning: ignoring request to remove 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 libmro-compat-perl 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 libnsl2 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 (1.1.29) ... dpkg: warning: ignoring request to remove libparams-classify-perl which isn't installed dpkg: warning: ignoring request to remove libparams-util-perl which isn't installed dpkg: warning: ignoring request to remove libparse-yapp-perl which isn't installed dpkg: warning: ignoring request to remove libpcre3 which isn't installed dpkg: warning: ignoring request to remove libperl5.36 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 libproc2-0 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 libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libregexp-ipv6-perl which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed Purging configuration files for libsensors-config (1:3.6.0-7.1) ... dpkg: warning: ignoring request to remove libsensors5 which isn't installed dpkg: warning: ignoring request to remove 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 libssl3 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-install-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 libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtimedate-perl which isn't installed dpkg: warning: ignoring request to remove libtingea0 which isn't installed Purging configuration files for libtirpc-common (1.3.3+ds-1) ... dpkg: warning: ignoring request to remove libtirpc3 which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove 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 libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwww-perl which isn't installed dpkg: warning: ignoring request to remove libwww-robotrules-perl which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libxml-writer-perl which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove 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 (10.0.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-10) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.0.13-1~deb12u2) ... Purging configuration files for parallel (20221122+ds-2) ... Purging configuration files for perl (5.36.0-7+deb12u1) ... dpkg: warning: ignoring request to remove perl-modules-5.36 which isn't installed dpkg: warning: ignoring request to remove perl-openssl-defaults which isn't installed dpkg: warning: ignoring request to remove prank which isn't installed Purging configuration files for procps (2:4.0.2-3) ... Purging configuration files for python3 (3.11.2-1+b1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.2-6+deb12u2) ... Purging configuration files for r-base-core (4.2.2.20221110-2) ... 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-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-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-pkgconfig 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-rlang which isn't installed dpkg: warning: ignoring request to remove r-cran-scales which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-cran-utf8 which isn't installed dpkg: warning: ignoring request to remove r-cran-vctrs which isn't installed dpkg: warning: ignoring request to remove r-cran-viridislite which isn't installed dpkg: warning: ignoring request to remove r-cran-withr which isn't installed Purging configuration files for readline-common (8.2-1.3) ... dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for sysstat (12.6.1-1) ... Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove xz-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 1m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', '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:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclone-perl:amd64', 'libcurl4:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfile-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', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmro-compat-perl', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libnumber-compare-perl', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libparse-yapp-perl', 'libpcre3:amd64', 'libperl5.36:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libregexp-ipv6-perl', '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', 'libssl3:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-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', 'libtiff6:amd64', 'libtimedate-perl', 'libtingea0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.36', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'r-base-core', 'r-cran-cli', 'r-cran-colorspace', 'r-cran-fansi', 'r-cran-farver', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-isoband', '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-pkgconfig', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rlang', 'r-cran-scales', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'readline-common', 'sensible-utils', 'sysstat', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip'] 1m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'dpkg', '--purge', 'roary'] 1m6.8s DUMP: dpkg: warning: ignoring request to remove roary which isn't installed 1m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'dpkg', '--purge', 'roary'] 1m6.8s INFO: Running scripts post_purge 1m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_purge_exceptions'] 1m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_purge_exceptions'] 1m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'dpkg', '--purge', '--pending'] 1m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'dpkg', '--purge', '--pending'] 1m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'dpkg', '--remove', '--pending'] 1m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'dpkg', '--remove', '--pending'] 1m6.8s INFO: Running scripts post_test 1m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_test_exceptions'] 1m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'tmp/scripts/post_test_exceptions'] 1m6.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 1m7.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 1m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'dpkg-divert', '--list'] 1m7.2s 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 1m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'dpkg-divert', '--list'] 1m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', 'clean'] 1m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz', 'apt-get', 'clean'] 1m7.3s DEBUG: Recording chroot state 1m8.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/shm'] 1m8.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/shm'] 1m8.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/console'] 1m8.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/console'] 1m8.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/ptmx'] 1m8.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/ptmx'] 1m8.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/pts'] 1m8.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/dev/pts'] 1m8.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/proc'] 1m8.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz/proc'] 1m8.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 1m8.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp4gtkk8dz'] 1m8.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp4gtkk8dz 1m8.6s INFO: PASS: Upgrading between Debian distributions. 1m8.6s INFO: PASS: All tests. 1m8.6s INFO: piuparts run ends. ret=0 End: 2024-08-22 14:26:14 GMT