Start: 2024-01-30 18:16:03 GMT 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-log-alternatives --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 --no-upgrade-test --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 1.2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --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 --no-upgrade-test --apt roary=3.13.0+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-27-amd64 #1 SMP Debian 5.10.205-2 (2023-12-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpu0mpi5z7 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpu0mpi5z7 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m2.0s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/proc'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/proc'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/pts'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/pts'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/ptmx'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/ptmx'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/console'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/console'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/shm'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/shm'] 0m2.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.1s DEBUG: Created policy-rc.d and chmodded it. 0m2.1s DEBUG: Created resolv.conf. 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmpu0mpi5z7/tmp/scripts/ 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpu0mpi5z7/tmp/scripts/ 0m2.1s INFO: Running scripts post_chroot_unpack 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-get', 'update'] 0m3.3s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-get', 'update'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-get', '-yf', 'dist-upgrade'] 0m3.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-get', '-yf', 'dist-upgrade'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.0s DUMP: c39ed9ca72afa1f69a1eea88b0965329 - 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.0s INFO: Running scripts post_setup 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_setup_dummy_users'] 0m5.1s 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 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_setup_dummy_users'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_setup_forbid_home'] 0m5.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_setup_forbid_home'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.2s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_setup_minimize'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_setup_minimize'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_setup_zz_backports'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_setup_zz_backports'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-get', 'clean'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-get', 'clean'] 0m5.2s DEBUG: Recording chroot state 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.7s 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+deb12u4 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 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+b1 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+deb12u3 install ok installed libc6:amd64 libc6 2.36-9+deb12u3 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+deb12u1 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+b1 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+b3 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+b1 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 252.19-1~deb12u1 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 252.19-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 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+b1 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 install ok installed tzdata tzdata 2023c-5+deb12u1 install ok installed usr-is-merged usr-is-merged 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg-divert', '--list'] 0m5.7s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg-divert', '--list'] 0m5.7s INFO: Running scripts is_testable 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/is_testable_uninstallable'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/is_testable_uninstallable'] 0m5.7s INFO: apt-cache does not know about any of the requested packages 0m5.7s INFO: Running scripts pre_test 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_test_exceptions'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_test_exceptions'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_test_root_password'] 0m5.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_test_root_password'] 0m5.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7'] 0m6.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7'] 0m6.6s DEBUG: No broken symlinks as far as we can find. 0m6.6s INFO: Running scripts pre_install 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_install_database-server'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_install_database-server'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_install_exceptions'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_install_exceptions'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_install_extras'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_install_extras'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_install_log_alternatives'] 0m6.6s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_install_log_alternatives'] 0m6.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7'] 0m6.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7'] 0m7.5s DEBUG: No broken symlinks as far as we can find. 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-cache', 'policy'] 0m8.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.4,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-cache', 'policy'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-cache', 'policy', 'roary'] 0m8.4s DUMP: roary: Installed: (none) Candidate: 3.13.0+dfsg-1 Version table: 3.13.0+dfsg-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-cache', 'policy', 'roary'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-get', '-y', 'install', 'roary=3.13.0+dfsg-1'] 0m48.5s 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 3.0.11-1~deb12u2 [2019 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 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 [2064 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 [1796 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 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 3.0.11-1~deb12u2 [1419 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 [399 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+deb12u4 [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 [1398 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 9s (14.4 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 ... 6101 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. Preparing to unpack .../2-libgdbm-compat4_1.23-3_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-3) ... Selecting previously unselected package libperl5.36:amd64. Preparing to unpack .../3-libperl5.36_5.36.0-7+deb12u1_amd64.deb ... Unpacking libperl5.36:amd64 (5.36.0-7+deb12u1) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.36.0-7+deb12u1_amd64.deb ... Unpacking perl (5.36.0-7+deb12u1) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../5-libssl3_3.0.11-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.11-1~deb12u2) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../6-libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../7-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../8-python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libssl3:amd64 (3.0.11-1~deb12u2) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8433 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../02-libncursesw6_6.4-4_amd64.deb ... 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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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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) ... 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 (3.0.11-1~deb12u2) ... 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) ... 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+deb12u4) ... 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) ... 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) ... 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+deb12u3) ... 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. 0m48.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-get', '-y', 'install', 'roary=3.13.0+dfsg-1'] 0m48.5s INFO: Running scripts post_install 0m48.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_install_exceptions'] 0m48.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_install_exceptions'] 0m48.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_install_log_alternatives'] 0m48.5s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=python3: piuparts=roary=3.13.0+dfsg-1: /usr/bin/update-alternatives --auto /usr/bin/python3 LOG-ALTERNATIVES: dpkg=libblas3: piuparts=roary=3.13.0+dfsg-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 LOG-ALTERNATIVES: dpkg=xz-utils: piuparts=roary=3.13.0+dfsg-1: /usr/bin/update-alternatives --install /usr/bin/lzma lzma /usr/bin/xz 20 --slave /usr/share/man/man1/lzma.1.gz lzma.1.gz /usr/share/man/man1/xz.1.gz --slave /usr/bin/unlzma unlzma /usr/bin/unxz --slave /usr/share/man/man1/unlzma.1.gz unlzma.1.gz /usr/share/man/man1/unxz.1.gz --slave /usr/bin/lzcat lzcat /usr/bin/xzcat --slave /usr/share/man/man1/lzcat.1.gz lzcat.1.gz /usr/share/man/man1/xzcat.1.gz --slave /usr/bin/lzmore lzmore /usr/bin/xzmore --slave /usr/share/man/man1/lzmore.1.gz lzmore.1.gz /usr/share/man/man1/xzmore.1.gz --slave /usr/bin/lzless lzless /usr/bin/xzless --slave /usr/share/man/man1/lzless.1.gz lzless.1.gz /usr/share/man/man1/xzless.1.gz --slave /usr/bin/lzdiff lzdiff /usr/bin/xzdiff --slave /usr/share/man/man1/lzdiff.1.gz lzdiff.1.gz /usr/share/man/man1/xzdiff.1.gz --slave /usr/bin/lzcmp lzcmp /usr/bin/xzcmp --slave /usr/share/man/man1/lzcmp.1.gz lzcmp.1.gz /usr/share/man/man1/xzcmp.1.gz --slave /usr/bin/lzgrep lzgrep /usr/bin/xzgrep --slave /usr/share/man/man1/lzgrep.1.gz lzgrep.1.gz /usr/share/man/man1/xzgrep.1.gz --slave /usr/bin/lzegrep lzegrep /usr/bin/xzegrep --slave /usr/share/man/man1/lzegrep.1.gz lzegrep.1.gz /usr/share/man/man1/xzegrep.1.gz --slave /usr/bin/lzfgrep lzfgrep /usr/bin/xzfgrep --slave /usr/share/man/man1/lzfgrep.1.gz lzfgrep.1.gz /usr/share/man/man1/xzfgrep.1.gz LOG-ALTERNATIVES: dpkg=procps: piuparts=roary=3.13.0+dfsg-1: /usr/bin/update-alternatives --remove w /usr/bin/w.procps LOG-ALTERNATIVES: dpkg=xdg-utils: piuparts=roary=3.13.0+dfsg-1: /usr/bin/update-alternatives --install /usr/bin/open open /usr/bin/xdg-open 50 --slave /usr/share/man/man1/open.1.gz open.1.gz /usr/share/man/man1/xdg-open.1.gz LOG-ALTERNATIVES: dpkg=liblapack3: piuparts=roary=3.13.0+dfsg-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 LOG-ALTERNATIVES: dpkg=sysstat: piuparts=roary=3.13.0+dfsg-1: /usr/bin/update-alternatives --display sar LOG-ALTERNATIVES: dpkg=sysstat: piuparts=roary=3.13.0+dfsg-1: /usr/bin/update-alternatives --install /usr/bin/sar sar /usr/bin/sar.sysstat 0 --slave /usr/share/man/man1/sar.1.gz sar.1.gz /usr/share/man/man1/sar.sysstat.1.gz LOG-ALTERNATIVES: dpkg=perl: piuparts=roary=3.13.0+dfsg-1: /usr/bin/update-alternatives --remove rename /usr/bin/prename 0m48.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_install_log_alternatives'] 0m48.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7'] 0m49.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7'] 0m50.9s DEBUG: No broken symlinks as far as we can find. 0m50.9s INFO: /bin converted to /usr/bin by /usr merge 0m50.9s INFO: /lib converted to /usr/lib by /usr merge 0m50.9s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m50.9s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m50.9s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m50.9s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m50.9s INFO: /lib/systemd/system-sleep converted to /usr/lib/systemd/system-sleep by /usr merge 0m50.9s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m50.9s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m50.9s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m50.9s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m50.9s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m50.9s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m50.9s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m50.9s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m50.9s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m50.9s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m50.9s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m50.9s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m50.9s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m50.9s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m50.9s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m50.9s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m50.9s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m50.9s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m50.9s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m50.9s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m50.9s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m50.9s INFO: /sbin converted to /usr/sbin by /usr merge 0m51.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', '-ac', '--ignore-obsolete'] 0m54.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', '-ac', '--ignore-obsolete'] 0m54.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m54.2s DUMP: 0.15.6 0m54.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m54.2s INFO: Running adequate version 0.15.6 now. 0m54.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'roary'] 0m54.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'roary'] 0m54.5s INFO: Running scripts pre_remove 0m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m54.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m54.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m59.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m59.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m59.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m59.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_remove_exceptions'] 0m59.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/pre_remove_exceptions'] 0m59.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m59.6s 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+deb12u4 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 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+b1 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+b1 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+deb12u3 install ok installed libc6:amd64 libc6 2.36-9+deb12u3 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+deb12u4 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 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 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u1 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+deb12u1 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+deb12u1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2+deb12u1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2+deb12u1 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+b1 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 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.2-6 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+b3 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+b1 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 3.0.11-1~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 252.19-1~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 252.19-1~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+b1 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+b1 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 3.0.11-1~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 install ok installed python3.11-minimal python3.11-minimal 3.11.2-6 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 install ok installed tzdata tzdata 2023c-5+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 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 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 0m59.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m59.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', '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'] 1m3.1s 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 ... 19676 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) ... Removing python3-minimal (3.11.2-1+b1) ... Removing python3.11-minimal (3.11.2-6) ... 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) ... 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) ... 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 libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Removing libfreetype6:amd64 (2.12.1+dfsg-5) ... Removing libcurl4:amd64 (7.88.1-10+deb12u4) ... 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) ... 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+deb12u1) ... 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+deb12u1) ... Removing libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2+deb12u1) ... 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 (3.0.11-1~deb12u2) ... Removing libssl3:amd64 (3.0.11-1~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+deb12u3) ... 1m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', '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'] 1m3.1s INFO: Running scripts post_remove 1m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_remove_exceptions'] 1m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_remove_exceptions'] 1m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', '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'] 1m4.5s 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 ... 6173 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) ... 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+deb12u1) ... 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) ... 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 (3.0.11-1~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) ... 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 1m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', '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'] 1m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg', '--purge', 'roary'] 1m4.5s DUMP: dpkg: warning: ignoring request to remove roary which isn't installed 1m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg', '--purge', 'roary'] 1m4.5s INFO: Running scripts post_purge 1m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_purge_exceptions'] 1m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_purge_exceptions'] 1m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg', '--purge', '--pending'] 1m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg', '--purge', '--pending'] 1m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg', '--remove', '--pending'] 1m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg', '--remove', '--pending'] 1m4.5s INFO: Running scripts post_test 1m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_test_exceptions'] 1m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'tmp/scripts/post_test_exceptions'] 1m4.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7'] 1m4.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7'] 1m5.5s DEBUG: No broken symlinks as far as we can find. 1m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg-divert', '--list'] 1m5.5s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 1m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'dpkg-divert', '--list'] 1m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-get', 'clean'] 1m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7', 'apt-get', 'clean'] 1m5.6s DEBUG: Recording chroot state 1m6.1s INFO: PASS: Installation and purging test. 1m6.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/shm'] 1m6.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/shm'] 1m6.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/console'] 1m6.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/console'] 1m6.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/ptmx'] 1m6.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/ptmx'] 1m6.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/pts'] 1m6.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/dev/pts'] 1m6.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/proc'] 1m6.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7/proc'] 1m6.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7'] 1m6.7s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpu0mpi5z7'] 1m6.7s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpu0mpi5z7 1m6.7s INFO: PASS: All tests. 1m6.7s INFO: piuparts run ends. ret=0 End: 2024-01-30 18:17:10 GMT