Start: 2019-12-07 06:02:34 UTC [testing] Package: roary Version: 3.13.0+dfsg-1 Installed-Size: 670 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Description: high speed stand alone pan genome pipeline Homepage: http://sanger-pathogens.github.io/Roary/ Description-md5: 6d457fd706202fc2ef292eacf7b46029 Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing Section: science Priority: optional Filename: pool/main/r/roary/roary_3.13.0+dfsg-1_all.deb Size: 183740 MD5sum: 991a49663368c3a0a660af3107720dad SHA256: 1732e00b165a0cee53b42fb9b142ea5491cd7de00b91be2cc8709297d999de66 [sid] Package: roary Version: 3.13.0+dfsg-1 Installed-Size: 670 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Description: high speed stand alone pan genome pipeline Homepage: http://sanger-pathogens.github.io/Roary/ Description-md5: 6d457fd706202fc2ef292eacf7b46029 Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing Section: science Priority: optional Filename: pool/main/r/roary/roary_3.13.0+dfsg-1_all.deb Size: 183740 MD5sum: 991a49663368c3a0a660af3107720dad SHA256: 1732e00b165a0cee53b42fb9b142ea5491cd7de00b91be2cc8709297d999de66 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python2.7/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://mirror-ubc.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt roary=3.13.0+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.0.2~201909101611~1.0.1-11-g98f8c745 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://mirror-ubc.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt roary=3.13.0+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.19.0-6-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpt_pGAH 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpt_pGAH 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m3.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m3.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/proc'] 0m3.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/proc'] 0m3.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/pts'] 0m3.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/pts'] 0m3.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/ptmx'] 0m3.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/ptmx'] 0m3.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/console'] 0m3.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/console'] 0m3.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/shm'] 0m3.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/shm'] 0m3.3s DEBUG: sources.list: deb http://mirror-ubc.debian.org/debian/ bullseye main 0m3.4s DEBUG: Created policy-rc.d and chmodded it. 0m3.4s DEBUG: Created resolv.conf. 0m3.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpt_pGAH/tmp/scripts/ 0m3.4s INFO: Running scripts post_chroot_unpack 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', 'update'] 0m10.4s DUMP: Get:1 http://mirror-ubc.debian.org/debian bullseye InRelease [113 kB] Get:2 http://mirror-ubc.debian.org/debian bullseye/main amd64 Packages [7685 kB] Get:3 http://mirror-ubc.debian.org/debian bullseye/main Translation-en [5838 kB] Fetched 13.6 MB in 5s (2545 kB/s) Reading package lists... 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', 'update'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', '-yf', 'dist-upgrade'] 0m12.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: gcc-9-base libgcc1 libpcre2-8-0 libstdc++6 libsystemd0 libudev1 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1480 kB of archives. After this operation, 52.2 kB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsystemd0 amd64 244-3 [347 kB] Get:2 http://mirror-ubc.debian.org/debian bullseye/main amd64 gcc-9-base amd64 9.2.1-21 [194 kB] Get:3 http://mirror-ubc.debian.org/debian bullseye/main amd64 libstdc++6 amd64 9.2.1-21 [501 kB] Get:4 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgcc1 amd64 1:9.2.1-21 [40.5 kB] Get:5 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpcre2-8-0 amd64 10.34-3+b1 [235 kB] Get:6 http://mirror-ubc.debian.org/debian bullseye/main amd64 libudev1 amd64 244-3 [162 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1480 kB in 0s (28.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6533 files and directories currently installed.) Preparing to unpack .../libsystemd0_244-3_amd64.deb ... Unpacking libsystemd0:amd64 (244-3) over (243-8) ... Setting up libsystemd0:amd64 (244-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6533 files and directories currently installed.) Preparing to unpack .../gcc-9-base_9.2.1-21_amd64.deb ... Unpacking gcc-9-base:amd64 (9.2.1-21) over (9.2.1-19) ... Setting up gcc-9-base:amd64 (9.2.1-21) ... (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 ... 6533 files and directories currently installed.) Preparing to unpack .../libstdc++6_9.2.1-21_amd64.deb ... Unpacking libstdc++6:amd64 (9.2.1-21) over (9.2.1-19) ... Setting up libstdc++6:amd64 (9.2.1-21) ... (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 ... 6533 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a9.2.1-21_amd64.deb ... Unpacking libgcc1:amd64 (1:9.2.1-21) over (1:9.2.1-19) ... Setting up libgcc1:amd64 (1:9.2.1-21) ... (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 ... 6533 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.34-3+b1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.34-3+b1) over (10.32-5+b1) ... Setting up libpcre2-8-0:amd64 (10.34-3+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6533 files and directories currently installed.) Preparing to unpack .../libudev1_244-3_amd64.deb ... Unpacking libudev1:amd64 (244-3) over (243-8) ... Setting up libudev1:amd64 (244-3) ... Processing triggers for libc-bin (2.29-3) ... 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', '-yf', 'dist-upgrade'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m12.7s DUMP: bff4f221bc0753adae90fd186f2094aa - 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m12.7s INFO: Running scripts post_setup 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_setup_dummy_users'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_setup_dummy_users'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_setup_forbid_home'] 0m14.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_setup_forbid_home'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_setup_force-unsafe-io'] 0m14.3s 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' 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_setup_force-unsafe-io'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_setup_minimize'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_setup_minimize'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_setup_squeeze-backports'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_setup_squeeze-backports'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_setup_zz_backports'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_setup_zz_backports'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m14.4s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.4 install ok installed base-files base-files 11 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-5 install ok installed bsdutils bsdutils 1:2.34-0.1 install ok installed coreutils coreutils 8.30-3+b1 install ok installed dash dash 0.5.10.2-6 install ok installed debconf debconf 1.5.73 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.9 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.7 install ok installed e2fsprogs e2fsprogs 1.45.4-1 install ok installed fdisk fdisk 2.34-0.1 install ok installed findutils findutils 4.7.0-1 install ok installed gcc-9-base:amd64 gcc-9-base 9.2.1-21 install ok installed gpgv gpgv 2.2.17-3 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+b1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.57 install ok installed libacl1:amd64 libacl1 2.2.53-5 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-5 install ok installed libaudit-common libaudit-common 1:2.8.5-2 install ok installed libaudit1:amd64 libaudit1 1:2.8.5-2+b1 install ok installed libblkid1:amd64 libblkid1 2.34-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-2 install ok installed libc-bin libc-bin 2.29-3 install ok installed libc6:amd64 libc6 2.29-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.1+b1 install ok installed libcom-err2:amd64 libcom-err2 1.45.4-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.250 install ok installed libext2fs2:amd64 libext2fs2 1.45.4-1 install ok installed libfdisk1:amd64 libfdisk1 2.34-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:9.2.1-21 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.5-3 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4 install ok installed libgnutls30:amd64 libgnutls30 3.6.10-5 install ok installed libgpg-error0:amd64 libgpg-error0 1.36-7 install ok installed libhogweed5:amd64 libhogweed5 3.5.1+really3.5.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.2.0-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.2-2 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+b1 install ok installed libmount1:amd64 libmount1 2.34-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20191019-1 install ok installed libnettle7:amd64 libnettle7 3.5.1+really3.5.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.18.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.34-3+b1 install ok installed libpcre3:amd64 libpcre3 2:8.39-12+b1 install ok installed libseccomp2:amd64 libseccomp2 2.4.2-2 install ok installed libselinux1:amd64 libselinux1 2.9-3+b1 install ok installed libsemanage-common libsemanage-common 2.9-3 install ok installed libsemanage1:amd64 libsemanage1 2.9-3+b1 install ok installed libsepol1:amd64 libsepol1 2.9-2+b2 install ok installed libsmartcols1:amd64 libsmartcols1 2.34-0.1 install ok installed libss2:amd64 libss2 1.45.4-1 install ok installed libstdc++6:amd64 libstdc++6 9.2.1-21 install ok installed libsystemd0:amd64 libsystemd0 244-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.14-3 install ok installed libtinfo6:amd64 libtinfo6 6.1+20191019-1 install ok installed libudev1:amd64 libudev1 244-3 install ok installed libunistring2:amd64 libunistring2 0.9.10-2 install ok installed libuuid1:amd64 libuuid1 2.34-0.1 install ok installed libzstd1:amd64 libzstd1 1.4.4+dfsg-1 install ok installed login login 1:4.7-2 install ok installed logsave logsave 1.45.4-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.34-0.1 install ok installed ncurses-base ncurses-base 6.1+20191019-1 install ok installed ncurses-bin ncurses-bin 6.1+20191019-1 install ok installed passwd passwd 1:4.7-2 install ok installed perl-base perl-base 5.30.0-9 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-1 install ok installed tar tar 1.30+dfsg-6+b1 install ok installed tzdata tzdata 2019c-3 install ok installed util-linux util-linux 2.34-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+b1 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m14.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m15.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 0m15.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 0m15.7s INFO: Running scripts is_testable 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/is_testable_uninstallable'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/is_testable_uninstallable'] 0m15.7s INFO: Running scripts pre_test 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_test_exceptions'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_test_exceptions'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_test_root_password'] 0m15.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_test_root_password'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m16.2s DUMP: Package: roary Version: 3.13.0+dfsg-1 Installed-Size: 670 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Description-en: high speed stand alone pan genome pipeline Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes. Description-md5: 6d457fd706202fc2ef292eacf7b46029 Homepage: http://sanger-pathogens.github.io/Roary/ Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing Section: science Priority: optional Filename: pool/main/r/roary/roary_3.13.0+dfsg-1_all.deb Size: 183740 MD5sum: 991a49663368c3a0a660af3107720dad SHA256: 1732e00b165a0cee53b42fb9b142ea5491cd7de00b91be2cc8709297d999de66 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m16.2s INFO: apt-cache knows about the following packages: roary 0m16.2s INFO: Running scripts pre_install 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_database-server'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_database-server'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_exceptions'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_exceptions'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_extras'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_extras'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_foreign_architecture'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_foreign_architecture'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'policy'] 0m16.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian bullseye/main amd64 Packages release o=Debian,a=testing,n=bullseye,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'policy'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'policy', 'roary'] 0m16.5s DUMP: roary: Installed: (none) Candidate: 3.13.0+dfsg-1 Version table: 3.13.0+dfsg-1 500 500 http://mirror-ubc.debian.org/debian bullseye/main amd64 Packages 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'policy', 'roary'] 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', '-y', 'install', 'roary'] 1m16.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: bedtools bioperl ca-certificates cd-hit fasttree fontconfig fontconfig-config fonts-dejavu-core libalgorithm-c3-perl libalgorithm-diff-perl libarray-utils-perl libb-hooks-op-check-perl libbio-perl-perl libblas3 libbrotli1 libbsd0 libcairo2 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libcurl4 libdata-optlist-perl libdata-stag-perl libdatrie1 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 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu63 libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblmdb0 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmpdec2 libmro-compat-perl libncurses6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparse-yapp-perl libperl5.30 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16 libprocps7 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsm6 libspiffy-perl libsqlite3-0 libssh2-1 libssl1.1 libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-uplevel-perl libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl liburi-perl libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxrender1 libxss1 libxt6 littler mafft mcl mime-support ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.30 perl-openssl-defaults prank procps python3 python3-minimal python3.7 python3.7-minimal r-base-core r-cran-assertthat r-cran-cli r-cran-colorspace r-cran-crayon r-cran-digest r-cran-fansi r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-labeling r-cran-lattice r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-utf8 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 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 libauthen-ntlm-perl mcl-doc perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libb-debug-perl liblocale-codes-perl python3-doc python3-tk python3-venv python3.7-venv python3.7-doc binutils binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-webshot 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-knitr r-cran-rmarkdown r-cran-viridis r-cran-rstudioapi r-cran-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-quantreg r-cran-rpart r-cran-sf r-cran-svglite r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats r-cran-getopt r-cran-testthat r-cran-foreach r-cran-doparallel r-cran-iterators r-cran-inline r-cran-covr r-cran-dichromat r-cran-htmltools libgdal-dev readline-doc isag Recommended packages: bioperl-run perl-doc libcache-cache-perl libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl libxml-simple-perl libyaml-perl libace-perl liblist-moreutils-perl libxml-twig-perl libset-scalar-perl libalgorithm-diff-xs-perl bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraphviz-perl libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl libxml-dom-xpath-perl libxml-sax-perl libxml-sax-writer-perl libxml-libxml-perl libclass-c3-xs-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl libdevel-lexalias-perl libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl krb5-locales liblog-dispatch-perl libipc-shareable-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 bzip2 file psmisc r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-mockery r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-lubridate r-cran-domc r-cran-abind r-cran-rmarkdown r-cran-bit64 r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-data.table r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-mockr r-cran-dbi cron | cron-daemon libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: bedtools bioperl ca-certificates cd-hit fasttree fontconfig fontconfig-config fonts-dejavu-core libalgorithm-c3-perl libalgorithm-diff-perl libarray-utils-perl libb-hooks-op-check-perl libbio-perl-perl libblas3 libbrotli1 libbsd0 libcairo2 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libcurl4 libdata-optlist-perl libdata-stag-perl libdatrie1 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 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu63 libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblmdb0 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmpdec2 libmro-compat-perl libncurses6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparse-yapp-perl libperl5.30 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16 libprocps7 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsm6 libspiffy-perl libsqlite3-0 libssh2-1 libssl1.1 libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-uplevel-perl libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl liburi-perl libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxrender1 libxss1 libxt6 littler mafft mcl mime-support ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.30 perl-openssl-defaults prank procps python3 python3-minimal python3.7 python3.7-minimal r-base-core r-cran-assertthat r-cran-cli r-cran-colorspace r-cran-crayon r-cran-digest r-cran-fansi r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-labeling r-cran-lattice r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-utf8 r-cran-viridislite r-cran-withr readline-common roary sensible-utils sysstat ucf unzip x11-common xdg-utils xz-utils zip 0 upgraded, 235 newly installed, 0 to remove and 0 not upgraded. Need to get 119 MB of archives. After this operation, 369 MB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian bullseye/main amd64 perl-modules-5.30 all 5.30.0-9 [2803 kB] Get:2 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.18.1-5 [64.5 kB] Get:3 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.18.1-5 [44.2 kB] Get:4 http://mirror-ubc.debian.org/debian bullseye/main amd64 libperl5.30 amd64 5.30.0-9 [4008 kB] Get:5 http://mirror-ubc.debian.org/debian bullseye/main amd64 perl amd64 5.30.0-9 [290 kB] Get:6 http://mirror-ubc.debian.org/debian bullseye/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB] Get:7 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython3.7-minimal amd64 3.7.5-2 [590 kB] Get:8 http://mirror-ubc.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:9 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3.7-minimal amd64 3.7.5-2 [1812 kB] Get:10 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.7.5-1 [36.6 kB] Get:11 http://mirror-ubc.debian.org/debian bullseye/main amd64 mime-support all 3.64 [37.8 kB] Get:12 http://mirror-ubc.debian.org/debian bullseye/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:13 http://mirror-ubc.debian.org/debian bullseye/main amd64 readline-common all 8.0-3 [72.5 kB] Get:14 http://mirror-ubc.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.0-3 [160 kB] Get:15 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.30.1-1 [649 kB] Get:16 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython3.7-stdlib amd64 3.7.5-2 [1732 kB] Get:17 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3.7 amd64 3.7.5-2 [347 kB] Get:18 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.7.5-1 [20.1 kB] Get:19 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3 amd64 3.7.5-1 [61.5 kB] Get:20 http://mirror-ubc.debian.org/debian bullseye/main amd64 netbase all 5.7 [19.1 kB] Get:21 http://mirror-ubc.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.1+20191019-1 [102 kB] Get:22 http://mirror-ubc.debian.org/debian bullseye/main amd64 libprocps7 amd64 2:3.3.15-2+b1 [62.0 kB] Get:23 http://mirror-ubc.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.15-2+b1 [259 kB] Get:24 http://mirror-ubc.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:25 http://mirror-ubc.debian.org/debian bullseye/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:26 http://mirror-ubc.debian.org/debian bullseye/main amd64 xz-utils amd64 5.2.4-1+b1 [183 kB] Get:27 http://mirror-ubc.debian.org/debian bullseye/main amd64 bedtools amd64 2.27.1+dfsg-4 [593 kB] Get:28 http://mirror-ubc.debian.org/debian bullseye/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:29 http://mirror-ubc.debian.org/debian bullseye/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get:30 http://mirror-ubc.debian.org/debian bullseye/main amd64 libbio-perl-perl all 1.7.6-3 [2604 kB] Get:31 http://mirror-ubc.debian.org/debian bullseye/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:32 http://mirror-ubc.debian.org/debian bullseye/main amd64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get:33 http://mirror-ubc.debian.org/debian bullseye/main amd64 libexception-class-perl all 1.44-1 [32.3 kB] Get:34 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtest-deep-perl all 1.128-1 [48.8 kB] Get:35 http://mirror-ubc.debian.org/debian bullseye/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:36 http://mirror-ubc.debian.org/debian bullseye/main amd64 libalgorithm-diff-perl all 1.19.03-2 [47.9 kB] Get:37 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtext-diff-perl all 1.45-1 [27.7 kB] Get:38 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtest-differences-perl all 0.67-1 [18.7 kB] Get:39 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsub-uplevel-perl all 0.2800-1 [16.3 kB] Get:40 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtest-exception-perl all 0.43-1 [18.7 kB] Get:41 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtest-warn-perl all 0.36-1 [16.2 kB] Get:42 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtest-most-perl all 0.35-1 [24.5 kB] Get:43 http://mirror-ubc.debian.org/debian bullseye/main amd64 bioperl all 1.7.6-3 [249 kB] Get:44 http://mirror-ubc.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1d-2 [840 kB] Get:45 http://mirror-ubc.debian.org/debian bullseye/main amd64 ca-certificates all 20190110 [157 kB] Get:46 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgomp1 amd64 9.2.1-21 [88.1 kB] Get:47 http://mirror-ubc.debian.org/debian bullseye/main amd64 cd-hit amd64 4.8.1-2 [526 kB] Get:48 http://mirror-ubc.debian.org/debian bullseye/main amd64 fasttree amd64 2.1.11-1 [177 kB] Get:49 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-1 [292 kB] Get:50 http://mirror-ubc.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.1-2 [392 kB] Get:51 http://mirror-ubc.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:52 http://mirror-ubc.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get:53 http://mirror-ubc.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-2+b1 [347 kB] Get:54 http://mirror-ubc.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-2+b1 [405 kB] Get:55 http://mirror-ubc.debian.org/debian bullseye/main amd64 libalgorithm-c3-perl all 0.10-1 [12.0 kB] Get:56 http://mirror-ubc.debian.org/debian bullseye/main amd64 libarray-utils-perl all 0.5-1 [6254 B] Get:57 http://mirror-ubc.debian.org/debian bullseye/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b2 [11.3 kB] Get:58 http://mirror-ubc.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-1 [153 kB] Get:59 http://mirror-ubc.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.7-5+b1 [267 kB] Get:60 http://mirror-ubc.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:61 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get:62 http://mirror-ubc.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:63 http://mirror-ubc.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:64 http://mirror-ubc.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get:65 http://mirror-ubc.debian.org/debian bullseye/main amd64 libx11-data all 2:1.6.8-1 [298 kB] Get:66 http://mirror-ubc.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.6.8-1 [756 kB] Get:67 http://mirror-ubc.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get:68 http://mirror-ubc.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get:69 http://mirror-ubc.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:70 http://mirror-ubc.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:71 http://mirror-ubc.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-4 [689 kB] Get:72 http://mirror-ubc.debian.org/debian bullseye/main amd64 libclass-c3-perl all 0.34-1 [22.4 kB] Get:73 http://mirror-ubc.debian.org/debian bullseye/main amd64 libparams-util-perl amd64 1.07-3+b5 [22.9 kB] Get:74 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsub-install-perl all 0.928-1 [11.4 kB] Get:75 http://mirror-ubc.debian.org/debian bullseye/main amd64 libdata-optlist-perl all 0.110-1 [10.6 kB] Get:76 http://mirror-ubc.debian.org/debian bullseye/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get:77 http://mirror-ubc.debian.org/debian bullseye/main amd64 libdevel-callchecker-perl amd64 0.008-1+b1 [15.9 kB] Get:78 http://mirror-ubc.debian.org/debian bullseye/main amd64 libparams-classify-perl amd64 0.015-1+b2 [25.6 kB] Get:79 http://mirror-ubc.debian.org/debian bullseye/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:80 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:81 http://mirror-ubc.debian.org/debian bullseye/main amd64 libmodule-implementation-perl all 0.09-1 [12.9 kB] Get:82 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpackage-stash-perl all 0.38-1 [21.7 kB] Get:83 http://mirror-ubc.debian.org/debian bullseye/main amd64 libclass-load-perl all 0.25-1 [16.1 kB] Get:84 http://mirror-ubc.debian.org/debian bullseye/main amd64 libclass-load-xs-perl amd64 0.10-1+b4 [14.8 kB] Get:85 http://mirror-ubc.debian.org/debian bullseye/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:86 http://mirror-ubc.debian.org/debian bullseye/main amd64 libkrb5support0 amd64 1.17-6 [64.6 kB] Get:87 http://mirror-ubc.debian.org/debian bullseye/main amd64 libk5crypto3 amd64 1.17-6 [116 kB] Get:88 http://mirror-ubc.debian.org/debian bullseye/main amd64 libkrb5-3 amd64 1.17-6 [366 kB] Get:89 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgssapi-krb5-2 amd64 1.17-6 [156 kB] Get:90 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1 [69.0 kB] Get:91 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1 [106 kB] Get:92 http://mirror-ubc.debian.org/debian bullseye/main amd64 libldap-common all 2.4.48+dfsg-1 [90.8 kB] Get:93 http://mirror-ubc.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.48+dfsg-1+b2 [225 kB] Get:94 http://mirror-ubc.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.40.0-1 [85.0 kB] Get:95 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:96 http://mirror-ubc.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b1 [60.8 kB] Get:97 http://mirror-ubc.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:98 http://mirror-ubc.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.67.0-2 [321 kB] Get:99 http://mirror-ubc.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.12-3 [39.5 kB] Get:100 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:101 http://mirror-ubc.debian.org/debian bullseye/main amd64 libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get:102 http://mirror-ubc.debian.org/debian bullseye/main amd64 libmro-compat-perl all 0.13-1 [12.2 kB] Get:103 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsub-identify-perl amd64 0.14-1+b2 [12.0 kB] Get:104 http://mirror-ubc.debian.org/debian bullseye/main amd64 libdevel-overloadinfo-perl all 0.005-1 [7212 B] Get:105 http://mirror-ubc.debian.org/debian bullseye/main amd64 libencode-locale-perl all 1.05-1 [13.7 kB] Get:106 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:107 http://mirror-ubc.debian.org/debian bullseye/main amd64 libhttp-date-perl all 6.05-1 [10.4 kB] Get:108 http://mirror-ubc.debian.org/debian bullseye/main amd64 libfile-listing-perl all 6.04-1 [10.3 kB] Get:109 http://mirror-ubc.debian.org/debian bullseye/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get:110 http://mirror-ubc.debian.org/debian bullseye/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:111 http://mirror-ubc.debian.org/debian bullseye/main amd64 libhtml-parser-perl amd64 3.72-3+b4 [105 kB] Get:112 http://mirror-ubc.debian.org/debian bullseye/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get:113 http://mirror-ubc.debian.org/debian bullseye/main amd64 libio-html-perl all 1.001-1 [17.6 kB] Get:114 http://mirror-ubc.debian.org/debian bullseye/main amd64 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get:115 http://mirror-ubc.debian.org/debian bullseye/main amd64 libhttp-message-perl all 6.18-1 [77.8 kB] Get:116 http://mirror-ubc.debian.org/debian bullseye/main amd64 libhttp-cookies-perl all 6.07-1 [19.1 kB] Get:117 http://mirror-ubc.debian.org/debian bullseye/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get:118 http://mirror-ubc.debian.org/debian bullseye/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:119 http://mirror-ubc.debian.org/debian bullseye/main amd64 libnet-ssleay-perl amd64 1.88-2 [321 kB] Get:120 http://mirror-ubc.debian.org/debian bullseye/main amd64 libio-socket-ssl-perl all 2.066-1 [210 kB] Get:121 http://mirror-ubc.debian.org/debian bullseye/main amd64 libnet-http-perl all 6.19-1 [24.8 kB] Get:122 http://mirror-ubc.debian.org/debian bullseye/main amd64 liblwp-protocol-https-perl all 6.07-2 [9242 B] Get:123 http://mirror-ubc.debian.org/debian bullseye/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:124 http://mirror-ubc.debian.org/debian bullseye/main amd64 libwww-perl all 6.43-1 [191 kB] Get:125 http://mirror-ubc.debian.org/debian bullseye/main amd64 libdigest-md5-file-perl all 0.08-1 [10.6 kB] Get:126 http://mirror-ubc.debian.org/debian bullseye/main amd64 libdist-checkconflicts-perl all 0.11-1 [10.8 kB] Get:127 http://mirror-ubc.debian.org/debian bullseye/main amd64 libenv-path-perl all 0.19-2 [19.5 kB] Get:128 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsub-exporter-perl all 0.987-1 [47.2 kB] Get:129 http://mirror-ubc.debian.org/debian bullseye/main amd64 libeval-closure-perl all 0.14-1 [11.5 kB] Get:130 http://mirror-ubc.debian.org/debian bullseye/main amd64 libnumber-compare-perl all 0.03-1 [7642 B] Get:131 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtext-glob-perl all 0.10-1 [8362 B] Get:132 http://mirror-ubc.debian.org/debian bullseye/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:133 http://mirror-ubc.debian.org/debian bullseye/main amd64 libfile-grep-perl all 0.02-1 [7654 B] Get:134 http://mirror-ubc.debian.org/debian bullseye/main amd64 libfile-slurper-perl all 0.012-1 [8344 B] Get:135 http://mirror-ubc.debian.org/debian bullseye/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:136 http://mirror-ubc.debian.org/debian bullseye/main amd64 libfindbin-libs-perl all 2.190.02-1 [30.3 kB] Get:137 http://mirror-ubc.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.7-1.1 [64.1 kB] Get:138 http://mirror-ubc.debian.org/debian bullseye/main amd64 libquadmath0 amd64 9.2.1-21 [145 kB] Get:139 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgfortran5 amd64 9.2.1-21 [634 kB] Get:140 http://mirror-ubc.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.62.3-2 [1320 kB] Get:141 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgraph-perl all 1:0.9704-1 [119 kB] Get:142 http://mirror-ubc.debian.org/debian bullseye/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get:143 http://mirror-ubc.debian.org/debian bullseye/main amd64 libio-all-perl all 0.87-1 [66.7 kB] Get:144 http://mirror-ubc.debian.org/debian bullseye/main amd64 libparse-yapp-perl all 1.21-2 [46.9 kB] Get:145 http://mirror-ubc.debian.org/debian bullseye/main amd64 libxml-parser-perl amd64 2.46-1+b1 [207 kB] Get:146 http://mirror-ubc.debian.org/debian bullseye/main amd64 libxml-writer-perl all 0.625-1 [29.7 kB] Get:147 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgraph-readwrite-perl all 2.09-1 [44.7 kB] Get:148 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.13-11 [80.9 kB] Get:149 http://mirror-ubc.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.6.4-1 [1360 kB] Get:150 http://mirror-ubc.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+20 [252 kB] Get:151 http://mirror-ubc.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:152 http://mirror-ubc.debian.org/debian bullseye/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:153 http://mirror-ubc.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:154 http://mirror-ubc.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+b1 [134 kB] Get:155 http://mirror-ubc.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-1 [2168 kB] Get:156 http://mirror-ubc.debian.org/debian bullseye/main amd64 liblmdb0 amd64 0.9.22-1 [45.0 kB] Get:157 http://mirror-ubc.debian.org/debian bullseye/main amd64 liblog-log4perl-perl all 1.49-1 [377 kB] Get:158 http://mirror-ubc.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.3-1 [212 kB] Get:159 http://mirror-ubc.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.3-1 [104 kB] Get:160 http://mirror-ubc.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.3-1 [133 kB] Get:161 http://mirror-ubc.debian.org/debian bullseye/main amd64 libmodule-runtime-conflicts-perl all 0.003-1 [6882 B] Get:162 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsub-name-perl amd64 0.26-1 [13.5 kB] Get:163 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpackage-deprecationmanager-perl all 0.17-1 [16.4 kB] Get:164 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpackage-stash-xs-perl amd64 0.29-1+b1 [20.2 kB] Get:165 http://mirror-ubc.debian.org/debian bullseye/main amd64 libmoose-perl amd64 2.2012-2 [805 kB] Get:166 http://mirror-ubc.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get:167 http://mirror-ubc.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get:168 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.42.4-7 [186 kB] Get:169 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.42.4-7 [67.9 kB] Get:170 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.42.4-7 [55.5 kB] Get:171 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get:172 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get:173 http://mirror-ubc.debian.org/debian bullseye/main amd64 libperlio-utf8-strict-perl amd64 0.007-2+b2 [11.7 kB] Get:174 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsensors-config all 1:3.6.0-2 [32.0 kB] Get:175 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsensors5 amd64 1:3.6.0-2 [53.1 kB] Get:176 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:177 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.10+dfsg-1 [1007 kB] Get:178 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtest-file-perl all 1.443-1 [20.0 kB] Get:179 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtest-files-perl all 0.14-1 [11.2 kB] Get:180 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtest-output-perl all 1.031-1 [13.0 kB] Get:181 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtext-csv-perl all 2.00-1 [105 kB] Get:182 http://mirror-ubc.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2+b1 [261 kB] Get:183 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.1.0+git191117-1 [271 kB] Get:184 http://mirror-ubc.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:185 http://mirror-ubc.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:186 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.10-1 [773 kB] Get:187 http://mirror-ubc.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get:188 http://mirror-ubc.debian.org/debian bullseye/main amd64 zip amd64 3.0-11+b1 [234 kB] Get:189 http://mirror-ubc.debian.org/debian bullseye/main amd64 unzip amd64 6.0-25 [172 kB] Get:190 http://mirror-ubc.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-1 [73.3 kB] Get:191 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-base-core amd64 3.6.1-7 [24.6 MB] Get:192 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-littler amd64 0.3.9-1 [312 kB] Get:193 http://mirror-ubc.debian.org/debian bullseye/main amd64 littler all 0.3.9-1 [14.6 kB] Get:194 http://mirror-ubc.debian.org/debian bullseye/main amd64 mafft amd64 7.453-1 [1011 kB] Get:195 http://mirror-ubc.debian.org/debian bullseye/main amd64 mcl amd64 1:14-137+ds-4 [624 kB] Get:196 http://mirror-ubc.debian.org/debian bullseye/main amd64 ncbi-data all 6.1.20170106+dfsg1-7 [3555 kB] Get:197 http://mirror-ubc.debian.org/debian bullseye/main amd64 ncbi-blast+ amd64 2.8.1-2 [11.1 MB] Get:198 http://mirror-ubc.debian.org/debian bullseye/main amd64 sysstat amd64 12.1.7-1 [572 kB] Get:199 http://mirror-ubc.debian.org/debian bullseye/main amd64 parallel all 20161222-1.1 [306 kB] Get:200 http://mirror-ubc.debian.org/debian bullseye/main amd64 prank amd64 0.0.170427+dfsg-2 [375 kB] Get:201 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-assertthat all 0.2.1-1 [56.7 kB] Get:202 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-crayon all 1.3.4-4 [750 kB] Get:203 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-cli all 1.1.0-1 [175 kB] Get:204 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-colorspace amd64 1.4-1+dfsg-1 [1587 kB] Get:205 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-digest amd64 0.6.23-1 [181 kB] Get:206 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-fansi amd64 0.4.0-1 [339 kB] Get:207 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-gtable all 0.3.0+dfsg-1 [164 kB] Get:208 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-lazyeval amd64 0.2.2-1 [144 kB] Get:209 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-mass amd64 7.3-51.4-2 [1112 kB] Get:210 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-lattice amd64 0.20-38-1+b1 [1131 kB] Get:211 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-nlme amd64 3.1.142-1 [2241 kB] Get:212 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-matrix amd64 1.2-17-2 [3492 kB] Get:213 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-mgcv amd64 1.8-31-1 [2778 kB] Get:214 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-pkgkitten all 0.1.5-1 [23.8 kB] Get:215 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-rcpp amd64 1.0.3-1 [1955 kB] Get:216 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-plyr amd64 1.8.4-2+b1 [817 kB] Get:217 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-glue amd64 1.3.1-1 [157 kB] Get:218 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-magrittr all 1.5-5 [152 kB] Get:219 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-stringi amd64 1.4.3-1 [709 kB] Get:220 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-stringr all 1.4.0-1 [198 kB] Get:221 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-reshape2 amd64 1.4.3-2 [114 kB] Get:222 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-rlang amd64 0.4.1-1 [1102 kB] Get:223 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-labeling all 0.3-3 [61.4 kB] Get:224 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-munsell all 0.5.0-1 [235 kB] Get:225 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-r6 all 2.4.1-1 [79.4 kB] Get:226 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-rcolorbrewer all 1.1-2-2 [54.3 kB] Get:227 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-viridislite all 0.3.0-3 [59.2 kB] Get:228 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-scales amd64 1.0.0-2 [546 kB] Get:229 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-utf8 amd64 1.1.4-1+b1 [131 kB] Get:230 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-pillar all 1.3.1-1 [203 kB] Get:231 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-pkgconfig all 2.0.3-1 [19.7 kB] Get:232 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-tibble amd64 2.0.1-1 [656 kB] Get:233 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-withr all 2.1.2-3 [152 kB] Get:234 http://mirror-ubc.debian.org/debian bullseye/main amd64 r-cran-ggplot2 all 3.2.1+dfsg-1 [2882 kB] Get:235 http://mirror-ubc.debian.org/debian bullseye/main amd64 roary all 3.13.0+dfsg-1 [184 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 119 MB in 5s (22.4 MB/s) Selecting previously unselected package perl-modules-5.30. (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 ... 6535 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.30_5.30.0-9_all.deb ... Unpacking perl-modules-5.30 (5.30.0-9) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.18.1-5_amd64.deb ... Unpacking libgdbm6:amd64 (1.18.1-5) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Preparing to unpack .../180-parallel_20161222-1.1_all.deb ... 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 (20161222-1.1) ... Selecting previously unselected package prank. Preparing to unpack .../181-prank_0.0.170427+dfsg-2_amd64.deb ... Unpacking prank (0.0.170427+dfsg-2) ... Selecting previously unselected package r-cran-assertthat. Preparing to unpack .../182-r-cran-assertthat_0.2.1-1_all.deb ... Unpacking r-cran-assertthat (0.2.1-1) ... Selecting previously unselected package r-cran-crayon. Preparing to unpack .../183-r-cran-crayon_1.3.4-4_all.deb ... Unpacking r-cran-crayon (1.3.4-4) ... Selecting previously unselected package r-cran-cli. Preparing to unpack .../184-r-cran-cli_1.1.0-1_all.deb ... Unpacking r-cran-cli (1.1.0-1) ... Selecting previously unselected package r-cran-colorspace. 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Setting up x11-common (1:7.7+20) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libsensors-config (1:3.6.0-2) ... Setting up libnghttp2-14:amd64 (1.40.0-1) ... Setting up perl-openssl-defaults:amd64 (3) ... Setting up libgomp1:amd64 (9.2.1-21) ... Setting up libldap-common (2.4.48+dfsg-1) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libicu63:amd64 (63.2-2) ... Setting up libkrb5support0:amd64 (1.17-6) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1) ... Setting up zip (3.0-11+b1) ... Setting up libblas3:amd64 (3.9.0-1) ... 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 (1:1.5.2-2+b1) ... Setting up mcl (1:14-137+ds-4) ... 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Creating config file /etc/papersize with new version Setting up libpython3.7-stdlib:amd64 (3.7.5-2) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up perl (5.30.0-9) ... Setting up libpackage-stash-xs-perl (0.29-1+b1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libalgorithm-c3-perl (0.10-1) ... Setting up liblog-log4perl-perl (1.49-1) ... Setting up libperlio-utf8-strict-perl (0.007-2+b2) ... Setting up libxml-writer-perl (0.625-1) ... Setting up libenv-path-perl (0.19-2) ... Setting up libio-html-perl (1.001-1) ... Setting up libb-hooks-op-check-perl (0.22-1+b2) ... Setting up libfile-grep-perl (0.02-1) ... Setting up libxt6:amd64 (1:1.1.5-1+b3) ... Setting up libparams-util-perl (1.07-3+b5) ... Setting up parallel (20161222-1.1) ... Setting up libspiffy-perl (0.46-1) ... 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Setting up libdevel-callchecker-perl (0.008-1+b1) ... Setting up libcairo2:amd64 (1.16.0-4) ... Setting up libsub-install-perl (0.928-1) ... Setting up libnumber-compare-perl (0.03-1) ... Setting up ncbi-blast+ (2.8.1-2) ... Setting up libio-string-perl (1.08-3) ... Setting up libtest-exception-perl (0.43-1) ... Setting up libtext-diff-perl (1.45-1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up libdata-optlist-perl (0.110-1) ... Setting up libtest-output-perl (1.031-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdata-stag-perl (0.14-2) ... Setting up libhtml-parser-perl (3.72-3+b4) ... Setting up libbio-perl-perl (1.7.6-3) ... Setting up libmro-compat-perl (0.13-1) ... Setting up libpangoft2-1.0-0:amd64 (1.42.4-7) ... Setting up libio-socket-ssl-perl (2.066-1) ... Setting up libsub-exporter-perl (0.987-1) ... Setting up libpangocairo-1.0-0:amd64 (1.42.4-7) ... Setting up libhttp-message-perl (6.18-1) ... Setting up libeval-closure-perl (0.14-1) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up libhttp-cookies-perl (6.07-1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl (0.015-1+b2) ... Setting up libtest-differences-perl (0.67-1) ... Setting up libtest-files-perl (0.14-1) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up r-base-core (3.6.1-7) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.3.4-4) ... Setting up r-cran-gtable (0.3.0+dfsg-1) ... Setting up r-cran-labeling (0.3-3) ... Setting up libdist-checkconflicts-perl (0.11-1) ... Setting up r-cran-lattice (0.20-38-1+b1) ... Setting up r-cran-nlme (3.1.142-1) ... Setting up r-cran-viridislite (0.3.0-3) ... Setting up r-cran-lazyeval (0.2.2-1) ... Setting up r-cran-r6 (2.4.1-1) ... Setting up r-cran-pkgkitten (0.1.5-1) ... Setting up r-cran-magrittr (1.5-5) ... Setting up r-cran-littler (0.3.9-1) ... Setting up r-cran-rcpp (1.0.3-1) ... Setting up r-cran-rlang (0.4.1-1) ... Setting up r-cran-assertthat (0.2.1-1) ... Setting up littler (0.3.9-1) ... Setting up libmodule-implementation-perl (0.09-1) ... Setting up libtest-most-perl (0.35-1) ... Setting up r-cran-withr (2.1.2-3) ... Setting up libpackage-stash-perl (0.38-1) ... Setting up r-cran-digest (0.6.23-1) ... Setting up r-cran-fansi (0.4.0-1) ... Setting up r-cran-mass (7.3-51.4-2) ... Setting up libmodule-runtime-conflicts-perl (0.003-1) ... Setting up r-cran-glue (1.3.1-1) ... Setting up r-cran-cli (1.1.0-1) ... Setting up libclass-load-perl (0.25-1) ... Setting up r-cran-pkgconfig (2.0.3-1) ... Setting up r-cran-utf8 (1.1.4-1+b1) ... Setting up r-cran-colorspace (1.4-1+dfsg-1) ... Setting up r-cran-stringi (1.4.3-1) ... Setting up r-cran-plyr (1.8.4-2+b1) ... Setting up r-cran-rcolorbrewer (1.1-2-2) ... Setting up r-cran-matrix (1.2-17-2) ... Setting up r-cran-mgcv (1.8-31-1) ... Setting up libpackage-deprecationmanager-perl (0.17-1) ... Setting up libdevel-overloadinfo-perl (0.005-1) ... Setting up libclass-load-xs-perl (0.10-1+b4) ... Setting up r-cran-pillar (1.3.1-1) ... Setting up bioperl (1.7.6-3) ... Setting up r-cran-stringr (1.4.0-1) ... Setting up libmoose-perl (2.2012-2) ... Setting up r-cran-munsell (0.5.0-1) ... Setting up r-cran-tibble (2.0.1-1) ... Setting up r-cran-reshape2 (1.4.3-2) ... Setting up r-cran-scales (1.0.0-2) ... Setting up r-cran-ggplot2 (3.2.1+dfsg-1) ... Setting up liblwp-protocol-https-perl (6.07-2) ... Setting up libwww-perl (6.43-1) ... Setting up libdigest-md5-file-perl (0.08-1) ... Setting up libxml-parser-perl (2.46-1+b1) ... Setting up libgraph-readwrite-perl (2.09-1) ... Setting up roary (3.13.0+dfsg-1) ... Processing triggers for libc-bin (2.29-3) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 1m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', '-y', 'install', 'roary'] 1m16.9s INFO: Running scripts post_install 1m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_install_exceptions'] 1m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_install_exceptions'] 1m17.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 1m19.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 1m19.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpt_pGAH to sid 1m19.7s DEBUG: sources.list: deb http://mirror-ubc.debian.org/debian/ sid main 1m19.7s INFO: Running scripts pre_distupgrade 1m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_distupgrade_exceptions'] 1m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_distupgrade_exceptions'] 1m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', 'update'] 1m31.2s DUMP: Get:1 http://mirror-ubc.debian.org/debian sid InRelease [142 kB] Get:2 http://mirror-ubc.debian.org/debian sid/main amd64 Packages [8219 kB] Get:3 http://mirror-ubc.debian.org/debian sid/main Translation-en [6174 kB] Fetched 14.5 MB in 9s (1694 kB/s) Reading package lists... 1m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', 'update'] 1m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', '-yf', 'dist-upgrade'] 1m45.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libcrypt1 r-cran-backports r-cran-ellipsis r-cran-vctrs r-cran-zeallot The following packages will be upgraded: bedtools libc-bin libc6 libhttp-cookies-perl libpcre2-8-0 libpython3-stdlib libtasn1-6 ncbi-blast+ netbase python3 python3-minimal r-cran-matrix r-cran-pillar r-cran-rlang r-cran-tibble 15 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 22.1 MB of archives. After this operation, 1332 kB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.10-5 [84.8 kB] Get:2 http://mirror-ubc.debian.org/debian sid/main amd64 libc6 amd64 2.29-5 [2807 kB] Get:3 http://mirror-ubc.debian.org/debian sid/main amd64 libc-bin amd64 2.29-5 [793 kB] Get:4 http://mirror-ubc.debian.org/debian sid/main amd64 python3-minimal amd64 3.7.5-3 [36.8 kB] Get:5 http://mirror-ubc.debian.org/debian sid/main amd64 python3 amd64 3.7.5-3 [62.1 kB] Get:6 http://mirror-ubc.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.7.5-3 [20.2 kB] Get:7 http://mirror-ubc.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.34-5 [235 kB] Get:8 http://mirror-ubc.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.15.0-2 [53.9 kB] Get:9 http://mirror-ubc.debian.org/debian sid/main amd64 netbase all 5.8 [19.1 kB] Get:10 http://mirror-ubc.debian.org/debian sid/main amd64 bedtools amd64 2.29.0+dfsg-2 [705 kB] Get:11 http://mirror-ubc.debian.org/debian sid/main amd64 libhttp-cookies-perl all 6.08-1 [19.3 kB] Get:12 http://mirror-ubc.debian.org/debian sid/main amd64 ncbi-blast+ amd64 2.9.0-3 [11.2 MB] Get:13 http://mirror-ubc.debian.org/debian sid/main amd64 r-cran-backports amd64 1.1.5-1 [57.9 kB] Get:14 http://mirror-ubc.debian.org/debian sid/main amd64 r-cran-rlang amd64 0.4.2-1 [1110 kB] Get:15 http://mirror-ubc.debian.org/debian sid/main amd64 r-cran-ellipsis amd64 0.3.0-1 [30.4 kB] Get:16 http://mirror-ubc.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.2-18-1 [3500 kB] Get:17 http://mirror-ubc.debian.org/debian sid/main amd64 r-cran-zeallot all 0.1.0-2 [59.9 kB] Get:18 http://mirror-ubc.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.2.0-1+b1 [747 kB] Get:19 http://mirror-ubc.debian.org/debian sid/main amd64 r-cran-pillar all 1.4.2-1 [227 kB] Get:20 http://mirror-ubc.debian.org/debian sid/main amd64 r-cran-tibble amd64 2.1.3-1 [329 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 22.1 MB in 2s (12.9 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19988 files and directories currently installed.) Preparing to unpack .../libc6_2.29-5_amd64.deb ... Unpacking libc6:amd64 (2.29-5) over (2.29-3) ... Selecting previously unselected package libcrypt1:amd64. Preparing to unpack .../libcrypt1_1%3a4.4.10-5_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.10-5) ... Setting up libcrypt1:amd64 (1:4.4.10-5) ... Setting up libc6:amd64 (2.29-5) ... (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 ... 19992 files and directories currently installed.) Preparing to unpack .../libc-bin_2.29-5_amd64.deb ... Unpacking libc-bin (2.29-5) over (2.29-3) ... Setting up libc-bin (2.29-5) ... (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 ... 19992 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.7.5-3_amd64.deb ... Unpacking python3-minimal (3.7.5-3) over (3.7.5-1) ... Setting up python3-minimal (3.7.5-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19992 files and directories currently installed.) Preparing to unpack .../python3_3.7.5-3_amd64.deb ... Unpacking python3 (3.7.5-3) over (3.7.5-1) ... Preparing to unpack .../libpython3-stdlib_3.7.5-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.7.5-3) over (3.7.5-1) ... Preparing to unpack .../libpcre2-8-0_10.34-5_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.34-5) over (10.34-3+b1) ... Setting up libpcre2-8-0:amd64 (10.34-5) ... (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 ... 19991 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.15.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.15.0-2) over (4.14-3) ... Setting up libtasn1-6:amd64 (4.15.0-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19991 files and directories currently installed.) Preparing to unpack .../00-netbase_5.8_all.deb ... Unpacking netbase (5.8) over (5.7) ... Preparing to unpack .../01-bedtools_2.29.0+dfsg-2_amd64.deb ... Unpacking bedtools (2.29.0+dfsg-2) over (2.27.1+dfsg-4) ... Preparing to unpack .../02-libhttp-cookies-perl_6.08-1_all.deb ... Unpacking libhttp-cookies-perl (6.08-1) over (6.07-1) ... Preparing to unpack .../03-ncbi-blast+_2.9.0-3_amd64.deb ... Unpacking ncbi-blast+ (2.9.0-3) over (2.8.1-2) ... Selecting previously unselected package r-cran-backports. Preparing to unpack .../04-r-cran-backports_1.1.5-1_amd64.deb ... Unpacking r-cran-backports (1.1.5-1) ... Preparing to unpack .../05-r-cran-rlang_0.4.2-1_amd64.deb ... Unpacking r-cran-rlang (0.4.2-1) over (0.4.1-1) ... Selecting previously unselected package r-cran-ellipsis. Preparing to unpack .../06-r-cran-ellipsis_0.3.0-1_amd64.deb ... Unpacking r-cran-ellipsis (0.3.0-1) ... Preparing to unpack .../07-r-cran-matrix_1.2-18-1_amd64.deb ... Unpacking r-cran-matrix (1.2-18-1) over (1.2-17-2) ... Selecting previously unselected package r-cran-zeallot. Preparing to unpack .../08-r-cran-zeallot_0.1.0-2_all.deb ... Unpacking r-cran-zeallot (0.1.0-2) ... Selecting previously unselected package r-cran-vctrs. Preparing to unpack .../09-r-cran-vctrs_0.2.0-1+b1_amd64.deb ... Unpacking r-cran-vctrs (0.2.0-1+b1) ... Preparing to unpack .../10-r-cran-pillar_1.4.2-1_all.deb ... Unpacking r-cran-pillar (1.4.2-1) over (1.3.1-1) ... Preparing to unpack .../11-r-cran-tibble_2.1.3-1_amd64.deb ... Unpacking r-cran-tibble (2.1.3-1) over (2.0.1-1) ... Setting up r-cran-rlang (0.4.2-1) ... Setting up libhttp-cookies-perl (6.08-1) ... Setting up r-cran-backports (1.1.5-1) ... Setting up r-cran-zeallot (0.1.0-2) ... Setting up r-cran-matrix (1.2-18-1) ... Setting up netbase (5.8) ... Installing new version of config file /etc/services ... Setting up bedtools (2.29.0+dfsg-2) ... Setting up libpython3-stdlib:amd64 (3.7.5-3) ... Setting up r-cran-ellipsis (0.3.0-1) ... Setting up python3 (3.7.5-3) ... Setting up ncbi-blast+ (2.9.0-3) ... Setting up r-cran-vctrs (0.2.0-1+b1) ... Setting up r-cran-pillar (1.4.2-1) ... Setting up r-cran-tibble (2.1.3-1) ... Processing triggers for libc-bin (2.29-5) ... 1m45.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', '-yf', 'dist-upgrade'] 1m45.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m46.9s DUMP: ed5b3c45b56efda9e80f3fab85216cad - 1m46.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'show', '--no-all-versions', 'roary'] 1m48.0s DUMP: Package: roary Version: 3.13.0+dfsg-1 Installed-Size: 670 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Description-en: high speed stand alone pan genome pipeline Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes. Description-md5: 6d457fd706202fc2ef292eacf7b46029 Homepage: http://sanger-pathogens.github.io/Roary/ Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing Section: science Priority: optional Filename: pool/main/r/roary/roary_3.13.0+dfsg-1_all.deb Size: 183740 MD5sum: 991a49663368c3a0a660af3107720dad SHA256: 1732e00b165a0cee53b42fb9b142ea5491cd7de00b91be2cc8709297d999de66 1m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'show', '--no-all-versions', 'roary'] 1m48.0s INFO: apt-cache knows about the following packages: roary 1m48.0s INFO: Running scripts pre_install 1m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_database-server'] 1m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_database-server'] 1m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_exceptions'] 1m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_exceptions'] 1m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_extras'] 1m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_extras'] 1m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_foreign_architecture'] 1m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_foreign_architecture'] 1m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'policy'] 1m48.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 1m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'policy'] 1m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'policy', 'roary'] 1m48.3s DUMP: roary: Installed: 3.13.0+dfsg-1 Candidate: 3.13.0+dfsg-1 Version table: *** 3.13.0+dfsg-1 500 500 http://mirror-ubc.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m48.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'policy', 'roary'] 1m48.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', '-y', 'install', 'roary'] 1m49.7s DUMP: Reading package lists... Building dependency tree... Reading state information... roary is already the newest version (3.13.0+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m49.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', '-y', 'install', 'roary'] 1m49.7s INFO: Running scripts post_install 1m49.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_install_exceptions'] 1m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_install_exceptions'] 1m49.8s INFO: Running scripts post_distupgrade 1m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_distupgrade_exceptions'] 1m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_distupgrade_exceptions'] 1m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m49.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m49.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_distupgrade_zz_backports'] 1m49.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_distupgrade_zz_backports'] 1m49.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 1m52.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 1m52.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 1m54.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 1m54.0s INFO: Running scripts pre_install 1m54.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_database-server'] 1m54.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_database-server'] 1m54.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_exceptions'] 1m54.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_exceptions'] 1m54.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_extras'] 1m54.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_extras'] 1m54.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_foreign_architecture'] 1m54.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_foreign_architecture'] 1m54.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m54.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m54.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'policy'] 1m54.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 1m54.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'policy'] 1m54.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'policy', 'roary'] 1m54.3s DUMP: roary: Installed: 3.13.0+dfsg-1 Candidate: 3.13.0+dfsg-1 Version table: *** 3.13.0+dfsg-1 500 500 http://mirror-ubc.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m54.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-cache', 'policy', 'roary'] 1m54.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', '-y', 'install', 'roary=3.13.0+dfsg-1'] 1m55.2s DUMP: Reading package lists... Building dependency tree... Reading state information... roary is already the newest version (3.13.0+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', '-y', 'install', 'roary=3.13.0+dfsg-1'] 1m55.2s INFO: Running scripts post_install 1m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_install_exceptions'] 1m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_install_exceptions'] 1m55.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 1m57.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 1m59.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', '-ac', '--ignore-obsolete'] 2m2.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', '-ac', '--ignore-obsolete'] 2m2.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m2.8s DUMP: 0.15.2 2m2.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m2.8s INFO: Running adequate version 0.15.2 now. 2m2.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'roary'] 2m3.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'roary'] 2m3.1s INFO: Running scripts pre_remove 2m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_remove_exceptions'] 2m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/pre_remove_exceptions'] 2m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m10.1s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.4 install ok installed base-files base-files 11 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-5 install ok installed bedtools bedtools 2.29.0+dfsg-2 install ok installed bioperl bioperl 1.7.6-3 install ok installed bsdutils bsdutils 1:2.34-0.1 install ok installed ca-certificates ca-certificates 20190110 install ok installed cd-hit cd-hit 4.8.1-2 install ok installed coreutils coreutils 8.30-3+b1 install ok installed dash dash 0.5.10.2-6 install ok installed debconf debconf 1.5.73 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.9 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.7 install ok installed e2fsprogs e2fsprogs 1.45.4-1 install ok installed fasttree fasttree 2.1.11-1 install ok installed fdisk fdisk 2.34-0.1 install ok installed findutils findutils 4.7.0-1 install ok installed fontconfig fontconfig 2.13.1-2+b1 install ok installed fontconfig-config fontconfig-config 2.13.1-2 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-1 install ok installed gcc-9-base:amd64 gcc-9-base 9.2.1-21 install ok installed gpgv gpgv 2.2.17-3 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+b1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.57 install ok installed libacl1:amd64 libacl1 2.2.53-5 install ok installed libalgorithm-c3-perl libalgorithm-c3-perl 0.10-1 install ok installed libalgorithm-diff-perl libalgorithm-diff-perl 1.19.03-2 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.4 install ok installed libarray-utils-perl libarray-utils-perl 0.5-1 install ok installed libattr1:amd64 libattr1 1:2.4.48-5 install ok installed libaudit-common libaudit-common 1:2.8.5-2 install ok installed libaudit1:amd64 libaudit1 1:2.8.5-2+b1 install ok installed libb-hooks-op-check-perl libb-hooks-op-check-perl 0.22-1+b2 install ok installed libbio-perl-perl libbio-perl-perl 1.7.6-3 install ok installed libblas3:amd64 libblas3 3.9.0-1 install ok installed libblkid1:amd64 libblkid1 2.34-0.1 install ok installed libbrotli1:amd64 libbrotli1 1.0.7-5+b1 install ok installed libbsd0:amd64 libbsd0 0.10.0-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-2 install ok installed libc-bin libc-bin 2.29-5 install ok installed libc6:amd64 libc6 2.29-5 install ok installed libcairo2:amd64 libcairo2 1.16.0-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.1+b1 install ok installed libcapture-tiny-perl libcapture-tiny-perl 0.48-1 install ok installed libclass-c3-perl libclass-c3-perl 0.34-1 install ok installed libclass-data-inheritable-perl libclass-data-inheritable-perl 0.08-3 install ok installed libclass-load-perl libclass-load-perl 0.25-1 install ok installed libclass-load-xs-perl libclass-load-xs-perl 0.10-1+b4 install ok installed libcom-err2:amd64 libcom-err2 1.45.4-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.10-5 install ok installed libcurl4:amd64 libcurl4 7.67.0-2 install ok installed libdata-optlist-perl libdata-optlist-perl 0.110-1 install ok installed libdata-stag-perl libdata-stag-perl 0.14-2 install ok installed libdatrie1:amd64 libdatrie1 0.2.12-3 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.250 install ok installed libdevel-callchecker-perl libdevel-callchecker-perl 0.008-1+b1 install ok installed libdevel-globaldestruction-perl libdevel-globaldestruction-perl 0.14-1 install ok installed libdevel-overloadinfo-perl libdevel-overloadinfo-perl 0.005-1 install ok installed libdevel-stacktrace-perl libdevel-stacktrace-perl 2.0400-1 install ok installed libdigest-md5-file-perl libdigest-md5-file-perl 0.08-1 install ok installed libdist-checkconflicts-perl libdist-checkconflicts-perl 0.11-1 install ok installed libdynaloader-functions-perl libdynaloader-functions-perl 0.003-1 install ok installed libencode-locale-perl libencode-locale-perl 1.05-1 install ok installed libenv-path-perl libenv-path-perl 0.19-2 install ok installed libeval-closure-perl libeval-closure-perl 0.14-1 install ok installed libexception-class-perl libexception-class-perl 1.44-1 install ok installed libexpat1:amd64 libexpat1 2.2.9-1 install ok installed libext2fs2:amd64 libext2fs2 1.45.4-1 install ok installed libfdisk1:amd64 libfdisk1 2.34-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-1 install ok installed libfile-grep-perl libfile-grep-perl 0.02-1 install ok installed libfile-listing-perl libfile-listing-perl 6.04-1 install ok installed libfile-slurper-perl libfile-slurper-perl 0.012-1 install ok installed libfile-which-perl libfile-which-perl 1.23-1 install ok installed libfindbin-libs-perl libfindbin-libs-perl 2.190.02-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.13.1-2+b1 install ok installed libfreetype6:amd64 libfreetype6 2.10.1-2 install ok installed libfribidi0:amd64 libfribidi0 1.0.7-1.1 install ok installed libgcc1:amd64 libgcc1 1:9.2.1-21 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.5-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.18.1-5 install ok installed libgdbm6:amd64 libgdbm6 1.18.1-5 install ok installed libgfortran5:amd64 libgfortran5 9.2.1-21 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.62.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4 install ok installed libgnutls30:amd64 libgnutls30 3.6.10-5 install ok installed libgomp1:amd64 libgomp1 9.2.1-21 install ok installed libgpg-error0:amd64 libgpg-error0 1.36-7 install ok installed libgraph-perl libgraph-perl 1:0.9704-1 install ok installed libgraph-readwrite-perl libgraph-readwrite-perl 2.09-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.13-11 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.17-6 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 2.6.4-1 install ok installed libhogweed5:amd64 libhogweed5 3.5.1+really3.5.1-2 install ok installed libhtml-parser-perl libhtml-parser-perl 3.72-3+b4 install ok installed libhtml-tagset-perl libhtml-tagset-perl 3.20-4 install ok installed libhtml-tree-perl libhtml-tree-perl 5.07-2 install ok installed libhttp-cookies-perl libhttp-cookies-perl 6.08-1 install ok installed libhttp-date-perl libhttp-date-perl 6.05-1 install ok installed libhttp-message-perl libhttp-message-perl 6.18-1 install ok installed libhttp-negotiate-perl libhttp-negotiate-perl 6.01-1 install ok installed libice6:amd64 libice6 2:1.0.9-2 install ok installed libicu63:amd64 libicu63 63.2-2 install ok installed libidn2-0:amd64 libidn2-0 2.2.0-2 install ok installed libio-all-perl libio-all-perl 0.87-1 install ok installed libio-html-perl libio-html-perl 1.001-1 install ok installed libio-socket-ssl-perl libio-socket-ssl-perl 2.066-1 install ok installed libio-string-perl libio-string-perl 1.08-3 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:1.5.2-2+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.17-6 install ok installed libkeyutils1:amd64 libkeyutils1 1.6-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.17-6 install ok installed libkrb5support0:amd64 libkrb5support0 1.17-6 install ok installed liblapack3:amd64 liblapack3 3.9.0-1 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.48+dfsg-1+b2 install ok installed libldap-common libldap-common 2.4.48+dfsg-1 install ok installed liblmdb0:amd64 liblmdb0 0.9.22-1 install ok installed liblog-log4perl-perl liblog-log4perl-perl 1.49-1 install ok installed liblwp-mediatypes-perl liblwp-mediatypes-perl 6.04-1 install ok installed liblwp-protocol-https-perl liblwp-protocol-https-perl 6.07-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.2-2 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+b1 install ok installed libmbedcrypto3:amd64 libmbedcrypto3 2.16.3-1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.3-1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.3-1 install ok installed libmodule-implementation-perl libmodule-implementation-perl 0.09-1 install ok installed libmodule-runtime-conflicts-perl libmodule-runtime-conflicts-perl 0.003-1 install ok installed libmodule-runtime-perl libmodule-runtime-perl 0.016-1 install ok installed libmoose-perl libmoose-perl 2.2012-2 install ok installed libmount1:amd64 libmount1 2.34-0.1 install ok installed libmpdec2:amd64 libmpdec2 2.4.2-2 install ok installed libmro-compat-perl libmro-compat-perl 0.13-1 install ok installed libncurses6:amd64 libncurses6 6.1+20191019-1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20191019-1 install ok installed libnet-http-perl libnet-http-perl 6.19-1 install ok installed libnet-ssleay-perl libnet-ssleay-perl 1.88-2 install ok installed libnettle7:amd64 libnettle7 3.5.1+really3.5.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.40.0-1 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.18.1-2 install ok installed libpackage-deprecationmanager-perl libpackage-deprecationmanager-perl 0.17-1 install ok installed libpackage-stash-perl libpackage-stash-perl 0.38-1 install ok installed libpackage-stash-xs-perl libpackage-stash-xs-perl 0.29-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.42.4-7 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.42.4-7 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.42.4-7 install ok installed libpaper-utils libpaper-utils 1.1.28+b1 install ok installed libpaper1:amd64 libpaper1 1.1.28+b1 install ok installed libparams-classify-perl libparams-classify-perl 0.015-1+b2 install ok installed libparams-util-perl libparams-util-perl 1.07-3+b5 install ok installed libparse-yapp-perl libparse-yapp-perl 1.21-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.34-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12+b1 install ok installed libperl5.30:amd64 libperl5.30 5.30.0-9 install ok installed libperlio-utf8-strict-perl libperlio-utf8-strict-perl 0.007-2+b2 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.36.0-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.37-1 install ok installed libprocps7:amd64 libprocps7 2:3.3.15-2+b1 install ok installed libpsl5:amd64 libpsl5 0.20.2-2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.7.5-3 install ok installed libpython3.7-minimal:amd64 libpython3.7-minimal 3.7.5-2 install ok installed libpython3.7-stdlib:amd64 libpython3.7-stdlib 3.7.5-2 install ok installed libquadmath0:amd64 libquadmath0 9.2.1-21 install ok installed libreadline8:amd64 libreadline8 8.0-3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b1 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-1 install ok installed libseccomp2:amd64 libseccomp2 2.4.2-2 install ok installed libselinux1:amd64 libselinux1 2.9-3+b1 install ok installed libsemanage-common libsemanage-common 2.9-3 install ok installed libsemanage1:amd64 libsemanage1 2.9-3+b1 install ok installed libsensors-config libsensors-config 1:3.6.0-2 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-2 install ok installed libsepol1:amd64 libsepol1 2.9-2+b2 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.34-0.1 install ok installed libspiffy-perl libspiffy-perl 0.46-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.30.1-1 install ok installed libss2:amd64 libss2 1.45.4-1 install ok installed libssh2-1:amd64 libssh2-1 1.8.0-2.1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1d-2 install ok installed libstdc++6:amd64 libstdc++6 9.2.1-21 install ok installed libsub-exporter-perl libsub-exporter-perl 0.987-1 install ok installed libsub-exporter-progressive-perl libsub-exporter-progressive-perl 0.001013-1 install ok installed libsub-identify-perl libsub-identify-perl 0.14-1+b2 install ok installed libsub-install-perl libsub-install-perl 0.928-1 install ok installed libsub-name-perl libsub-name-perl 0.26-1 install ok installed libsub-uplevel-perl libsub-uplevel-perl 0.2800-1 install ok installed libsystemd0:amd64 libsystemd0 244-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.15.0-2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.10+dfsg-1 install ok installed libtest-deep-perl libtest-deep-perl 1.128-1 install ok installed libtest-differences-perl libtest-differences-perl 0.67-1 install ok installed libtest-exception-perl libtest-exception-perl 0.43-1 install ok installed libtest-file-perl libtest-file-perl 1.443-1 install ok installed libtest-files-perl libtest-files-perl 0.14-1 install ok installed libtest-most-perl libtest-most-perl 0.35-1 install ok installed libtest-output-perl libtest-output-perl 1.031-1 install ok installed libtest-warn-perl libtest-warn-perl 0.36-1 install ok installed libtext-csv-perl libtext-csv-perl 2.00-1 install ok installed libtext-diff-perl libtext-diff-perl 1.45-1 install ok installed libtext-glob-perl libtext-glob-perl 0.10-1 install ok installed libthai-data libthai-data 0.1.28-3 install ok installed libthai0:amd64 libthai0 0.1.28-3 install ok installed libtiff5:amd64 libtiff5 4.1.0+git191117-1 install ok installed libtimedate-perl libtimedate-perl 2.3000-2 install ok installed libtinfo6:amd64 libtinfo6 6.1+20191019-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.10-1 install ok installed libtry-tiny-perl libtry-tiny-perl 0.30-1 install ok installed libudev1:amd64 libudev1 244-3 install ok installed libunistring2:amd64 libunistring2 0.9.10-2 install ok installed liburi-perl liburi-perl 1.76-1 install ok installed libuuid1:amd64 libuuid1 2.34-0.1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2+b1 install ok installed libwww-perl libwww-perl 6.43-1 install ok installed libwww-robotrules-perl libwww-robotrules-perl 6.02-1 install ok installed libx11-6:amd64 libx11-6 2:1.6.8-1 install ok installed libx11-data libx11-data 2:1.6.8-1 install ok installed libxau6:amd64 libxau6 1:1.0.8-1+b2 install ok installed libxcb-render0:amd64 libxcb-render0 1.13.1-2 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.13.1-2 install ok installed libxcb1:amd64 libxcb1 1.13.1-2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.3-1+b2 install ok installed libxft2:amd64 libxft2 2.3.2-2 install ok installed libxml-parser-perl libxml-parser-perl 2.46-1+b1 install ok installed libxml-writer-perl libxml-writer-perl 0.625-1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6:amd64 libxt6 1:1.1.5-1+b3 install ok installed libzstd1:amd64 libzstd1 1.4.4+dfsg-1 install ok installed littler littler 0.3.9-1 install ok installed login login 1:4.7-2 install ok installed logsave logsave 1.45.4-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mafft mafft 7.453-1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mcl mcl 1:14-137+ds-4 install ok installed mime-support mime-support 3.64 install ok installed mount mount 2.34-0.1 install ok installed ncbi-blast+ ncbi-blast+ 2.9.0-3 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-7 install ok installed ncurses-base ncurses-base 6.1+20191019-1 install ok installed ncurses-bin ncurses-bin 6.1+20191019-1 install ok installed netbase netbase 5.8 install ok installed openssl openssl 1.1.1d-2 install ok installed parallel parallel 20161222-1.1 install ok installed passwd passwd 1:4.7-2 install ok installed perl perl 5.30.0-9 install ok installed perl-base perl-base 5.30.0-9 install ok installed perl-modules-5.30 perl-modules-5.30 5.30.0-9 install ok installed perl-openssl-defaults:amd64 perl-openssl-defaults 3 install ok installed prank prank 0.0.170427+dfsg-2 install ok installed procps procps 2:3.3.15-2+b1 install ok installed python3 python3 3.7.5-3 install ok installed python3-minimal python3-minimal 3.7.5-3 install ok installed python3.7 python3.7 3.7.5-2 install ok installed python3.7-minimal python3.7-minimal 3.7.5-2 install ok installed r-base-core r-base-core 3.6.1-7 install ok installed r-cran-assertthat r-cran-assertthat 0.2.1-1 install ok installed r-cran-backports r-cran-backports 1.1.5-1 install ok installed r-cran-cli r-cran-cli 1.1.0-1 install ok installed r-cran-colorspace r-cran-colorspace 1.4-1+dfsg-1 install ok installed r-cran-crayon r-cran-crayon 1.3.4-4 install ok installed r-cran-digest r-cran-digest 0.6.23-1 install ok installed r-cran-ellipsis r-cran-ellipsis 0.3.0-1 install ok installed r-cran-fansi r-cran-fansi 0.4.0-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.2.1+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.3.1-1 install ok installed r-cran-gtable r-cran-gtable 0.3.0+dfsg-1 install ok installed r-cran-labeling r-cran-labeling 0.3-3 install ok installed r-cran-lattice r-cran-lattice 0.20-38-1+b1 install ok installed r-cran-lazyeval r-cran-lazyeval 0.2.2-1 install ok installed r-cran-littler r-cran-littler 0.3.9-1 install ok installed r-cran-magrittr r-cran-magrittr 1.5-5 install ok installed r-cran-mass r-cran-mass 7.3-51.4-2 install ok installed r-cran-matrix r-cran-matrix 1.2-18-1 install ok installed r-cran-mgcv r-cran-mgcv 1.8-31-1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-1 install ok installed r-cran-nlme r-cran-nlme 3.1.142-1 install ok installed r-cran-pillar r-cran-pillar 1.4.2-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-1 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.1.5-1 install ok installed r-cran-plyr r-cran-plyr 1.8.4-2+b1 install ok installed r-cran-r6 r-cran-r6 2.4.1-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-2-2 install ok installed r-cran-rcpp r-cran-rcpp 1.0.3-1 install ok installed r-cran-reshape2 r-cran-reshape2 1.4.3-2 install ok installed r-cran-rlang r-cran-rlang 0.4.2-1 install ok installed r-cran-scales r-cran-scales 1.0.0-2 install ok installed r-cran-stringi r-cran-stringi 1.4.3-1 install ok installed r-cran-stringr r-cran-stringr 1.4.0-1 install ok installed r-cran-tibble r-cran-tibble 2.1.3-1 install ok installed r-cran-utf8 r-cran-utf8 1.1.4-1+b1 install ok installed r-cran-vctrs r-cran-vctrs 0.2.0-1+b1 install ok installed r-cran-viridislite r-cran-viridislite 0.3.0-3 install ok installed r-cran-withr r-cran-withr 2.1.2-3 install ok installed r-cran-zeallot r-cran-zeallot 0.1.0-2 install ok installed readline-common readline-common 8.0-3 install ok installed roary roary 3.13.0+dfsg-1 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.12+nmu1 install ok installed sysstat sysstat 12.1.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-1 install ok installed tar tar 1.30+dfsg-6+b1 install ok installed tzdata tzdata 2019c-3 install ok installed ucf ucf 3.0038+nmu1 install ok installed unzip unzip 6.0-25 install ok installed util-linux util-linux 2.34-0.1 install ok installed x11-common x11-common 1:7.7+20 install ok installed xdg-utils xdg-utils 1.1.3-1 install ok installed xz-utils xz-utils 5.2.4-1+b1 install ok installed zip zip 3.0-11+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+b1 2m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', 'remove', 'libgraph-readwrite-perl', 'libmbedx509-0:amd64', 'libgssapi-krb5-2:amd64', 'libssh2-1:amd64', 'libmbedcrypto3:amd64', 'fonts-dejavu-core', 'libsensors-config', 'r-cran-rlang', 'r-cran-reshape2', 'libmodule-runtime-conflicts-perl', 'littler', 'sensible-utils', 'librtmp1:amd64', 'libdist-checkconflicts-perl', 'libnet-ssleay-perl', 'libtest-output-perl', 'libgdbm6:amd64', 'libtiff5:amd64', 'libdatrie1:amd64', 'r-cran-labeling', 'fontconfig', 'libclass-c3-perl', 'libprocps7:amd64', 'libreadline8:amd64', 'libxcb1:amd64', 'libmro-compat-perl', 'r-cran-rcpp', 'libsub-uplevel-perl', 'unzip', 'libtext-glob-perl', 'libssl1.1:amd64', 'libpango-1.0-0:amd64', 'liburi-perl', 'libalgorithm-c3-perl', 'libkrb5-3:amd64', 'libtext-csv-perl', 'python3-minimal', 'ca-certificates', 'r-base-core', 'libtk8.6:amd64', 'libmpdec2:amd64', 'readline-common', 'r-cran-matrix', 'libfile-listing-perl', 'python3.7-minimal', 'python3', 'libbsd0:amd64', 'libtest-files-perl', 'libparse-yapp-perl', 'r-cran-plyr', 'libpackage-stash-perl', 'libk5crypto3:amd64', 'libpython3.7-minimal:amd64', 'libgomp1:amd64', 'libthai0:amd64', 'libtext-diff-perl', 'libpangocairo-1.0-0:amd64', 'mafft', 'libfile-slurper-perl', 'libgraphite2-3:amd64', 'libtest-warn-perl', 'libhtml-tree-perl', 'r-cran-rcolorbrewer', 'r-cran-digest', 'libio-socket-ssl-perl', 'libtcl8.6:amd64', 'libx11-6:amd64', 'libbio-perl-perl', 'libdigest-md5-file-perl', 'libsensors5:amd64', 'r-cran-nlme', 'libhtml-parser-perl', 'libcapture-tiny-perl', 'libpython3-stdlib:amd64', 'libgdbm-compat4:amd64', 'libwww-perl', 'libperlio-utf8-strict-perl', 'libpackage-stash-xs-perl', 'r-cran-magrittr', 'libpython3.7-stdlib:amd64', 'libdevel-stacktrace-perl', 'r-cran-tibble', 'libsub-exporter-perl', 'libquadmath0:amd64', 'libfile-find-rule-perl', 'libperl5.30:amd64', 'r-cran-scales', 'libparams-classify-perl', 'libpsl5:amd64', 'libxext6:amd64', 'prank', 'libdevel-overloadinfo-perl', 'libxdmcp6:amd64', 'libeval-closure-perl', 'r-cran-ellipsis', 'libfindbin-libs-perl', 'libicu63:amd64', 'libgraph-perl', 'libhttp-message-perl', 'libdata-stag-perl', 'liblog-log4perl-perl', 'libnghttp2-14:amd64', 'ncbi-data', 'cd-hit', 'libxau6:amd64', 'libtest-file-perl', 'perl-openssl-defaults:amd64', 'libfile-which-perl', 'r-cran-glue', 'libxml-parser-perl', 'r-cran-fansi', 'libxcb-shm0:amd64', 'fontconfig-config', 'libxft2:amd64', 'libmbedtls12:amd64', 'openssl', 'sysstat', 'libxcb-render0:amd64', 'libharfbuzz0b:amd64', 'libldap-2.4-2:amd64', 'libpaper1:amd64', 'libclass-load-xs-perl', 'r-cran-pkgconfig', 'r-cran-gtable', 'libhtml-tagset-perl', 'libpangoft2-1.0-0:amd64', 'libfreetype6:amd64', 'libencode-locale-perl', 'libtest-most-perl', 'r-cran-stringr', 'r-cran-pillar', 'libthai-data', 'r-cran-cli', 'ucf', 'libfontconfig1:amd64', 'xz-utils', 'r-cran-munsell', 'libsm6:amd64', 'r-cran-stringi', 'mime-support', 'bioperl', 'libsqlite3-0:amd64', 'zip', 'r-cran-mgcv', 'perl', 'libsub-identify-perl', 'libclass-data-inheritable-perl', 'netbase', 'libxss1:amd64', 'x11-common', 'libpaper-utils', 'libb-hooks-op-check-perl', 'r-cran-pkgkitten', 'mcl', 'r-cran-vctrs', 'r-cran-lazyeval', 'libspiffy-perl', 'libsub-install-perl', 'libjbig0:amd64', 'libbrotli1:amd64', 'libhttp-cookies-perl', 'libncurses6:amd64', 'libkrb5support0:amd64', 'xdg-utils', 'libtest-differences-perl', 'ncbi-blast+-', 'liblwp-mediatypes-perl', 'libice6:amd64', 'libxt6:amd64', 'libwww-robotrules-perl', 'libdevel-globaldestruction-perl', 'libjpeg62-turbo:amd64', 'libio-string-perl', 'libalgorithm-diff-perl', 'procps', 'r-cran-withr', 'libx11-data', 'libcairo2:amd64', 'libsub-exporter-progressive-perl', 'libhttp-negotiate-perl', 'libtest-deep-perl', 'r-cran-utf8', 'libarray-utils-perl', 'liblmdb0:amd64', 'libexception-class-perl', 'libpackage-deprecationmanager-perl', 'libblas3:amd64', 'libkeyutils1:amd64', 'libpixman-1-0:amd64', 'r-cran-zeallot', 'r-cran-assertthat', 'r-cran-r6', 'bedtools', 'libgfortran5:amd64', 'r-cran-colorspace', 'perl-modules-5.30', 'r-cran-crayon', 'libfile-grep-perl', 'libdata-optlist-perl', 'r-cran-mass', 'r-cran-backports', 'libnumber-compare-perl', 'libtimedate-perl', 'libnet-http-perl', 'libdynaloader-functions-perl', 'libio-html-perl', 'libmodule-runtime-perl', 'libcurl4:amd64', 'r-cran-littler', 'libsub-name-perl', 'r-cran-viridislite', 'liblapack3:amd64', 'libsasl2-modules-db:amd64', 'libexpat1:amd64', 'fasttree', 'libtry-tiny-perl', 'libclass-load-perl', 'libfribidi0:amd64', 'libxrender1:amd64', 'libpng16-16:amd64', 'liblwp-protocol-https-perl', 'r-cran-ggplot2', 'parallel', 'libmodule-implementation-perl', 'libio-all-perl', 'libldap-common', 'python3.7', 'libsasl2-2:amd64', 'libdevel-callchecker-perl', 'libtest-exception-perl', 'libhttp-date-perl', 'libenv-path-perl', 'libwebp6:amd64', 'libglib2.0-0:amd64', 'r-cran-lattice', 'libxml-writer-perl', 'libparams-util-perl', 'libmoose-perl', 'roary'] 2m16.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bedtools bioperl ca-certificates cd-hit fasttree fontconfig fontconfig-config fonts-dejavu-core libalgorithm-c3-perl libalgorithm-diff-perl libarray-utils-perl libb-hooks-op-check-perl libbio-perl-perl libblas3 libbrotli1 libbsd0 libcairo2 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libcurl4 libdata-optlist-perl libdata-stag-perl libdatrie1 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 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu63 libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblmdb0 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmpdec2 libmro-compat-perl libncurses6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparse-yapp-perl libperl5.30 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16 libprocps7 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsm6 libspiffy-perl libsqlite3-0 libssh2-1 libssl1.1 libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-uplevel-perl libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl liburi-perl libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxrender1 libxss1 libxt6 littler mafft mcl mime-support ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.30 perl-openssl-defaults prank procps python3 python3-minimal python3.7 python3.7-minimal r-base-core r-cran-assertthat r-cran-backports r-cran-cli r-cran-colorspace r-cran-crayon r-cran-digest r-cran-ellipsis r-cran-fansi r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-labeling r-cran-lattice r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-zeallot readline-common roary sensible-utils sysstat ucf unzip x11-common xdg-utils xz-utils zip 0 upgraded, 0 newly installed, 239 to remove and 0 not upgraded. After this operation, 370 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20279 files and directories currently installed.) Removing roary (3.13.0+dfsg-1) ... Removing bedtools (2.29.0+dfsg-2) ... Removing bioperl (1.7.6-3) ... Removing r-cran-ggplot2 (3.2.1+dfsg-1) ... Removing r-cran-mgcv (1.8-31-1) ... Removing r-cran-matrix (1.2-18-1) ... Removing r-cran-scales (1.0.0-2) ... Removing r-cran-reshape2 (1.4.3-2) ... Removing r-cran-rcolorbrewer (1.1-2-2) ... Removing r-cran-tibble (2.1.3-1) ... Removing r-cran-pillar (1.4.2-1) ... Removing r-cran-vctrs (0.2.0-1+b1) ... Removing r-cran-zeallot (0.1.0-2) ... Removing libgraph-readwrite-perl (2.09-1) ... Removing libxml-parser-perl (2.46-1+b1) ... Removing cd-hit (4.8.1-2) ... Removing fasttree (2.1.11-1) ... Removing libmoose-perl (2.2012-2) ... Removing libdevel-overloadinfo-perl (0.005-1) ... Removing libmro-compat-perl (0.13-1) ... Removing libclass-c3-perl (0.34-1) ... Removing libalgorithm-c3-perl (0.10-1) ... Removing libtest-files-perl (0.14-1) ... Removing libtest-most-perl (0.35-1) ... Removing libtest-differences-perl (0.67-1) ... Removing libtext-diff-perl (1.45-1) ... Removing libalgorithm-diff-perl (1.19.03-2) ... Removing libarray-utils-perl (0.5-1) ... Removing libmodule-runtime-conflicts-perl (0.003-1) ... Removing libpackage-deprecationmanager-perl (0.17-1) ... Removing libbio-perl-perl (1.7.6-3) ... Removing libtest-output-perl (1.031-1) ... Removing libcapture-tiny-perl (0.48-1) ... Removing libexception-class-perl (1.44-1) ... Removing libclass-data-inheritable-perl (0.08-3) ... Removing libclass-load-xs-perl (0.10-1+b4) ... Removing libclass-load-perl (0.25-1) ... Removing libeval-closure-perl (0.14-1) ... Removing libsub-exporter-perl (0.987-1) ... Removing libdata-optlist-perl (0.110-1) ... Removing libdata-stag-perl (0.14-2) ... Removing libdevel-globaldestruction-perl (0.14-1) ... Removing libdevel-stacktrace-perl (2.0400-1) ... Removing libdigest-md5-file-perl (0.08-1) ... Removing libdist-checkconflicts-perl (0.11-1) ... Removing libenv-path-perl (0.19-2) ... Removing ncbi-blast+ (2.9.0-3) ... Removing python3 (3.7.5-3) ... Removing python3-minimal (3.7.5-3) ... Removing python3.7 (3.7.5-2) ... Removing python3.7-minimal (3.7.5-2) ... Removing libfile-find-rule-perl (0.34-1) ... Removing libfile-grep-perl (0.02-1) ... Removing libfile-slurper-perl (0.012-1) ... Removing libfile-which-perl (1.23-1) ... Removing libfindbin-libs-perl (2.190.02-1) ... Removing parallel (20161222-1.1) ... Removing 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Removing 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Removing mafft (7.453-1) ... Removing libxml-writer-perl (0.625-1) ... Removing libgraph-perl (1:0.9704-1) ... Removing r-cran-stringr (1.4.0-1) ... Removing r-cran-stringi (1.4.3-1) ... Removing libio-all-perl (0.87-1) ... Removing libio-string-perl (1.08-3) ... Removing liblmdb0:amd64 (0.9.22-1) ... Removing liblog-log4perl-perl (1.49-1) ... Removing libmbedtls12:amd64 (2.16.3-1) ... Removing libmbedx509-0:amd64 (2.16.3-1) ... Removing libmbedcrypto3:amd64 (2.16.3-1) ... Removing libpython3-stdlib:amd64 (3.7.5-3) ... Removing libpython3.7-stdlib:amd64 (3.7.5-2) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec2:amd64 (2.4.2-2) ... Removing procps (2:3.3.15-2+b1) ... Removing libncurses6:amd64 (6.1+20191019-1) ... Removing libnumber-compare-perl (0.03-1) ... Removing libpackage-stash-xs-perl (0.29-1+b1) ... Removing libparams-util-perl (1.07-3+b5) ... Removing libparse-yapp-perl (1.21-2) ... Removing libperlio-utf8-strict-perl (0.007-2+b2) ... Removing libprocps7:amd64 (2:3.3.15-2+b1) ... Removing libpython3.7-minimal:amd64 (3.7.5-2) ... find: '/usr/lib/python3': No such file or directory Removing sysstat (12.1.7-1) ... Removing libsensors5:amd64 (1:3.6.0-2) ... Removing libsensors-config (1:3.6.0-2) ... Removing libspiffy-perl (0.46-1) ... Removing libsqlite3-0:amd64 (3.30.1-1) ... Removing libsub-exporter-progressive-perl (0.001013-1) ... Removing libsub-identify-perl (0.14-1+b2) ... Removing libsub-install-perl (0.928-1) ... Removing libsub-name-perl (0.26-1) ... Removing libtest-warn-perl (0.36-1) ... Removing libtest-exception-perl (0.43-1) ... Removing libsub-uplevel-perl (0.2800-1) ... Removing libtest-deep-perl (1.128-1) ... Removing libtest-file-perl (1.443-1) ... Removing libtext-csv-perl (2.00-1) ... Removing libtext-glob-perl (0.10-1) ... Removing littler (0.3.9-1) ... Removing mcl (1:14-137+ds-4) ... Removing mime-support (3.64) ... Removing ncbi-data (6.1.20170106+dfsg1-7) ... Removing prank (0.0.170427+dfsg-2) ... Removing r-cran-cli (1.1.0-1) ... Removing r-cran-assertthat (0.2.1-1) ... Removing r-cran-backports (1.1.5-1) ... Removing r-cran-munsell (0.5.0-1) ... Removing r-cran-colorspace (1.4-1+dfsg-1) ... Removing r-cran-crayon (1.3.4-4) ... Removing r-cran-digest (0.6.23-1) ... Removing r-cran-ellipsis (0.3.0-1) ... Removing r-cran-fansi (0.4.0-1) ... Removing r-cran-glue (1.3.1-1) ... Removing r-cran-gtable (0.3.0+dfsg-1) ... Removing r-cran-labeling (0.3-3) ... Removing r-cran-nlme (3.1.142-1) ... Removing r-cran-lattice (0.20-38-1+b1) ... Removing r-cran-lazyeval (0.2.2-1) ... Removing r-cran-magrittr (1.5-5) ... Removing r-cran-mass (7.3-51.4-2) ... Removing r-cran-pkgconfig (2.0.3-1) ... Removing r-cran-plyr (1.8.4-2+b1) ... Removing r-cran-r6 (2.4.1-1) ... Removing r-cran-rlang (0.4.2-1) ... Removing r-cran-utf8 (1.1.4-1+b1) ... Removing r-cran-viridislite (0.3.0-3) ... Removing r-cran-withr (2.1.2-3) ... Removing xz-utils (5.2.4-1+b1) ... Removing r-cran-rcpp (1.0.3-1) ... Removing libpackage-stash-perl (0.38-1) ... Removing libmodule-implementation-perl (0.09-1) ... Removing libmodule-runtime-perl (0.016-1) ... Removing libparams-classify-perl (0.015-1+b2) ... Removing libdevel-callchecker-perl (0.008-1+b1) ... Removing libb-hooks-op-check-perl (0.22-1+b2) ... Removing libdynaloader-functions-perl (0.003-1) ... Removing r-cran-littler (0.3.9-1) ... Removing r-cran-pkgkitten (0.1.5-1) ... Removing r-base-core (3.6.1-7) ... Removing libpangocairo-1.0-0:amd64 (1.42.4-7) ... Removing libpangoft2-1.0-0:amd64 (1.42.4-7) ... Removing libpango-1.0-0:amd64 (1.42.4-7) ... Removing fontconfig (2.13.1-2+b1) ... Removing libtk8.6:amd64 (8.6.10-1) ... Removing libxft2:amd64 (2.3.2-2) ... Removing libcairo2:amd64 (1.16.0-4) ... Removing libfontconfig1:amd64 (2.13.1-2+b1) ... Removing fontconfig-config (2.13.1-2) ... Removing fonts-dejavu-core (2.37-1) ... Removing liblapack3:amd64 (3.9.0-1) ... Removing libblas3:amd64 (3.9.0-1) ... Removing libcurl4:amd64 (7.67.0-2) ... Removing libbrotli1:amd64 (1.0.7-5+b1) ... Removing libxt6:amd64 (1:1.1.5-1+b3) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxcb-shm0:amd64 (1.13.1-2) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.9-2) ... Removing libthai0:amd64 (0.1.28-3) ... Removing libdatrie1:amd64 (0.2.12-3) ... Removing libexpat1:amd64 (2.2.9-1) ... Removing libharfbuzz0b:amd64 (2.6.4-1) ... Removing libfreetype6:amd64 (2.10.1-2) ... Removing libfribidi0:amd64 (1.0.7-1.1) ... Removing libgfortran5:amd64 (9.2.1-21) ... Removing libglib2.0-0:amd64 (2.62.3-2) ... Removing libgomp1:amd64 (9.2.1-21) ... Removing libgraphite2-3:amd64 (1.3.13-11) ... Removing libgssapi-krb5-2:amd64 (1.17-6) ... Removing libicu63:amd64 (63.2-2) ... Removing libtiff5:amd64 (4.1.0+git191117-1) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:1.5.2-2+b1) ... Removing libkrb5-3:amd64 (1.17-6) ... Removing libk5crypto3:amd64 (1.17-6) ... Removing libkrb5support0:amd64 (1.17-6) ... Removing libkeyutils1:amd64 (1.6-6) ... Removing libldap-2.4-2:amd64 (2.4.48+dfsg-1+b2) ... Removing libldap-common (2.4.48+dfsg-1) ... Removing libnghttp2-14:amd64 (1.40.0-1) ... Removing libpaper-utils (1.1.28+b1) ... Removing libpaper1:amd64 (1.1.28+b1) ... Removing libpixman-1-0:amd64 (0.36.0-1) ... Removing libpng16-16:amd64 (1.6.37-1) ... Removing libpsl5:amd64 (0.20.2-2) ... Removing libquadmath0:amd64 (9.2.1-21) ... Removing libreadline8:amd64 (8.0-3) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b1) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-1) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-1) ... Removing libssh2-1:amd64 (1.8.0-2.1) ... Removing libtcl8.6:amd64 (8.6.10+dfsg-1) ... Removing libthai-data (0.1.28-3) ... Removing libwebp6:amd64 (0.6.1-2+b1) ... Removing libxcb-render0:amd64 (1.13.1-2) ... Removing libxext6:amd64 (2:1.3.3-1+b2) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing readline-common (8.0-3) ... Removing ucf (3.0038+nmu1) ... Removing sensible-utils (0.0.12+nmu1) ... Removing unzip (6.0-25) ... Removing x11-common (1:7.7+20) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-1) ... Removing zip (3.0-11+b1) ... Removing libx11-6:amd64 (2:1.6.8-1) ... Removing libxcb1:amd64 (1.13.1-2) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.10.0-1) ... Removing libx11-data (2:1.6.8-1) ... Removing libxau6:amd64 (1:1.0.8-1+b2) ... Removing libwww-perl (6.43-1) ... Removing libhttp-negotiate-perl (6.01-1) ... Removing libfile-listing-perl (6.04-1) ... Removing libhttp-cookies-perl (6.08-1) ... Removing libwww-robotrules-perl (6.02-1) ... Removing libhtml-tree-perl (5.07-2) ... Removing libhtml-parser-perl (3.72-3+b4) ... Removing libhtml-tagset-perl (3.20-4) ... Removing liblwp-protocol-https-perl (6.07-2) ... Removing libio-socket-ssl-perl (2.066-1) ... Removing libnet-http-perl (6.19-1) ... Removing libnet-ssleay-perl (1.88-2) ... Removing perl-openssl-defaults:amd64 (3) ... Removing libtry-tiny-perl (0.30-1) ... Removing netbase (5.8) ... Removing ca-certificates (20190110) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libhttp-message-perl (6.18-1) ... Removing libencode-locale-perl (1.05-1) ... Removing libhttp-date-perl (6.05-1) ... Removing liburi-perl (1.76-1) ... Removing libio-html-perl (1.001-1) ... Removing liblwp-mediatypes-perl (6.04-1) ... Removing openssl (1.1.1d-2) ... Removing libssl1.1:amd64 (1.1.1d-2) ... Removing libtimedate-perl (2.3000-2) ... Removing perl (5.30.0-9) ... Removing libperl5.30:amd64 (5.30.0-9) ... Removing libgdbm-compat4:amd64 (1.18.1-5) ... Removing libgdbm6:amd64 (1.18.1-5) ... Removing perl-modules-5.30 (5.30.0-9) ... Processing triggers for libc-bin (2.29-5) ... 2m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', 'remove', 'libgraph-readwrite-perl', 'libmbedx509-0:amd64', 'libgssapi-krb5-2:amd64', 'libssh2-1:amd64', 'libmbedcrypto3:amd64', 'fonts-dejavu-core', 'libsensors-config', 'r-cran-rlang', 'r-cran-reshape2', 'libmodule-runtime-conflicts-perl', 'littler', 'sensible-utils', 'librtmp1:amd64', 'libdist-checkconflicts-perl', 'libnet-ssleay-perl', 'libtest-output-perl', 'libgdbm6:amd64', 'libtiff5:amd64', 'libdatrie1:amd64', 'r-cran-labeling', 'fontconfig', 'libclass-c3-perl', 'libprocps7:amd64', 'libreadline8:amd64', 'libxcb1:amd64', 'libmro-compat-perl', 'r-cran-rcpp', 'libsub-uplevel-perl', 'unzip', 'libtext-glob-perl', 'libssl1.1:amd64', 'libpango-1.0-0:amd64', 'liburi-perl', 'libalgorithm-c3-perl', 'libkrb5-3:amd64', 'libtext-csv-perl', 'python3-minimal', 'ca-certificates', 'r-base-core', 'libtk8.6:amd64', 'libmpdec2:amd64', 'readline-common', 'r-cran-matrix', 'libfile-listing-perl', 'python3.7-minimal', 'python3', 'libbsd0:amd64', 'libtest-files-perl', 'libparse-yapp-perl', 'r-cran-plyr', 'libpackage-stash-perl', 'libk5crypto3:amd64', 'libpython3.7-minimal:amd64', 'libgomp1:amd64', 'libthai0:amd64', 'libtext-diff-perl', 'libpangocairo-1.0-0:amd64', 'mafft', 'libfile-slurper-perl', 'libgraphite2-3:amd64', 'libtest-warn-perl', 'libhtml-tree-perl', 'r-cran-rcolorbrewer', 'r-cran-digest', 'libio-socket-ssl-perl', 'libtcl8.6:amd64', 'libx11-6:amd64', 'libbio-perl-perl', 'libdigest-md5-file-perl', 'libsensors5:amd64', 'r-cran-nlme', 'libhtml-parser-perl', 'libcapture-tiny-perl', 'libpython3-stdlib:amd64', 'libgdbm-compat4:amd64', 'libwww-perl', 'libperlio-utf8-strict-perl', 'libpackage-stash-xs-perl', 'r-cran-magrittr', 'libpython3.7-stdlib:amd64', 'libdevel-stacktrace-perl', 'r-cran-tibble', 'libsub-exporter-perl', 'libquadmath0:amd64', 'libfile-find-rule-perl', 'libperl5.30:amd64', 'r-cran-scales', 'libparams-classify-perl', 'libpsl5:amd64', 'libxext6:amd64', 'prank', 'libdevel-overloadinfo-perl', 'libxdmcp6:amd64', 'libeval-closure-perl', 'r-cran-ellipsis', 'libfindbin-libs-perl', 'libicu63:amd64', 'libgraph-perl', 'libhttp-message-perl', 'libdata-stag-perl', 'liblog-log4perl-perl', 'libnghttp2-14:amd64', 'ncbi-data', 'cd-hit', 'libxau6:amd64', 'libtest-file-perl', 'perl-openssl-defaults:amd64', 'libfile-which-perl', 'r-cran-glue', 'libxml-parser-perl', 'r-cran-fansi', 'libxcb-shm0:amd64', 'fontconfig-config', 'libxft2:amd64', 'libmbedtls12:amd64', 'openssl', 'sysstat', 'libxcb-render0:amd64', 'libharfbuzz0b:amd64', 'libldap-2.4-2:amd64', 'libpaper1:amd64', 'libclass-load-xs-perl', 'r-cran-pkgconfig', 'r-cran-gtable', 'libhtml-tagset-perl', 'libpangoft2-1.0-0:amd64', 'libfreetype6:amd64', 'libencode-locale-perl', 'libtest-most-perl', 'r-cran-stringr', 'r-cran-pillar', 'libthai-data', 'r-cran-cli', 'ucf', 'libfontconfig1:amd64', 'xz-utils', 'r-cran-munsell', 'libsm6:amd64', 'r-cran-stringi', 'mime-support', 'bioperl', 'libsqlite3-0:amd64', 'zip', 'r-cran-mgcv', 'perl', 'libsub-identify-perl', 'libclass-data-inheritable-perl', 'netbase', 'libxss1:amd64', 'x11-common', 'libpaper-utils', 'libb-hooks-op-check-perl', 'r-cran-pkgkitten', 'mcl', 'r-cran-vctrs', 'r-cran-lazyeval', 'libspiffy-perl', 'libsub-install-perl', 'libjbig0:amd64', 'libbrotli1:amd64', 'libhttp-cookies-perl', 'libncurses6:amd64', 'libkrb5support0:amd64', 'xdg-utils', 'libtest-differences-perl', 'ncbi-blast+-', 'liblwp-mediatypes-perl', 'libice6:amd64', 'libxt6:amd64', 'libwww-robotrules-perl', 'libdevel-globaldestruction-perl', 'libjpeg62-turbo:amd64', 'libio-string-perl', 'libalgorithm-diff-perl', 'procps', 'r-cran-withr', 'libx11-data', 'libcairo2:amd64', 'libsub-exporter-progressive-perl', 'libhttp-negotiate-perl', 'libtest-deep-perl', 'r-cran-utf8', 'libarray-utils-perl', 'liblmdb0:amd64', 'libexception-class-perl', 'libpackage-deprecationmanager-perl', 'libblas3:amd64', 'libkeyutils1:amd64', 'libpixman-1-0:amd64', 'r-cran-zeallot', 'r-cran-assertthat', 'r-cran-r6', 'bedtools', 'libgfortran5:amd64', 'r-cran-colorspace', 'perl-modules-5.30', 'r-cran-crayon', 'libfile-grep-perl', 'libdata-optlist-perl', 'r-cran-mass', 'r-cran-backports', 'libnumber-compare-perl', 'libtimedate-perl', 'libnet-http-perl', 'libdynaloader-functions-perl', 'libio-html-perl', 'libmodule-runtime-perl', 'libcurl4:amd64', 'r-cran-littler', 'libsub-name-perl', 'r-cran-viridislite', 'liblapack3:amd64', 'libsasl2-modules-db:amd64', 'libexpat1:amd64', 'fasttree', 'libtry-tiny-perl', 'libclass-load-perl', 'libfribidi0:amd64', 'libxrender1:amd64', 'libpng16-16:amd64', 'liblwp-protocol-https-perl', 'r-cran-ggplot2', 'parallel', 'libmodule-implementation-perl', 'libio-all-perl', 'libldap-common', 'python3.7', 'libsasl2-2:amd64', 'libdevel-callchecker-perl', 'libtest-exception-perl', 'libhttp-date-perl', 'libenv-path-perl', 'libwebp6:amd64', 'libglib2.0-0:amd64', 'r-cran-lattice', 'libxml-writer-perl', 'libparams-util-perl', 'libmoose-perl', 'roary'] 2m16.7s INFO: Running scripts post_remove 2m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_remove_exceptions'] 2m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_remove_exceptions'] 2m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg', '--purge', 'libgraph-readwrite-perl', 'libmbedx509-0:amd64', 'libgssapi-krb5-2:amd64', 'libssh2-1:amd64', 'libmbedcrypto3:amd64', 'fonts-dejavu-core', 'libsensors-config', 'r-cran-rlang', 'r-cran-reshape2', 'libmodule-runtime-conflicts-perl', 'littler', 'sensible-utils', 'librtmp1:amd64', 'libdist-checkconflicts-perl', 'libnet-ssleay-perl', 'libtest-output-perl', 'libgdbm6:amd64', 'libtiff5:amd64', 'libdatrie1:amd64', 'r-cran-labeling', 'fontconfig', 'libclass-c3-perl', 'libprocps7:amd64', 'libreadline8:amd64', 'libxcb1:amd64', 'libmro-compat-perl', 'r-cran-rcpp', 'libsub-uplevel-perl', 'unzip', 'libtext-glob-perl', 'libssl1.1:amd64', 'libpango-1.0-0:amd64', 'liburi-perl', 'libalgorithm-c3-perl', 'libkrb5-3:amd64', 'libtext-csv-perl', 'python3-minimal', 'ca-certificates', 'r-base-core', 'libtk8.6:amd64', 'libmpdec2:amd64', 'readline-common', 'r-cran-matrix', 'libfile-listing-perl', 'python3.7-minimal', 'python3', 'libbsd0:amd64', 'libtest-files-perl', 'libparse-yapp-perl', 'r-cran-plyr', 'libpackage-stash-perl', 'libk5crypto3:amd64', 'libpython3.7-minimal:amd64', 'libgomp1:amd64', 'libthai0:amd64', 'libtext-diff-perl', 'libpangocairo-1.0-0:amd64', 'mafft', 'libfile-slurper-perl', 'libgraphite2-3:amd64', 'libtest-warn-perl', 'libhtml-tree-perl', 'r-cran-rcolorbrewer', 'r-cran-digest', 'libio-socket-ssl-perl', 'libtcl8.6:amd64', 'libx11-6:amd64', 'libbio-perl-perl', 'libdigest-md5-file-perl', 'libsensors5:amd64', 'r-cran-nlme', 'libhtml-parser-perl', 'libcapture-tiny-perl', 'libpython3-stdlib:amd64', 'libgdbm-compat4:amd64', 'libwww-perl', 'libperlio-utf8-strict-perl', 'libpackage-stash-xs-perl', 'r-cran-magrittr', 'libpython3.7-stdlib:amd64', 'libdevel-stacktrace-perl', 'r-cran-tibble', 'libsub-exporter-perl', 'libquadmath0:amd64', 'libfile-find-rule-perl', 'libperl5.30:amd64', 'r-cran-scales', 'libparams-classify-perl', 'libpsl5:amd64', 'libxext6:amd64', 'prank', 'libdevel-overloadinfo-perl', 'libxdmcp6:amd64', 'libeval-closure-perl', 'r-cran-ellipsis', 'libfindbin-libs-perl', 'libicu63:amd64', 'libgraph-perl', 'libhttp-message-perl', 'libdata-stag-perl', 'liblog-log4perl-perl', 'libnghttp2-14:amd64', 'ncbi-data', 'cd-hit', 'libxau6:amd64', 'libtest-file-perl', 'perl-openssl-defaults:amd64', 'libfile-which-perl', 'r-cran-glue', 'libxml-parser-perl', 'r-cran-fansi', 'libxcb-shm0:amd64', 'fontconfig-config', 'libxft2:amd64', 'libmbedtls12:amd64', 'openssl', 'sysstat', 'libxcb-render0:amd64', 'libharfbuzz0b:amd64', 'libldap-2.4-2:amd64', 'libpaper1:amd64', 'libclass-load-xs-perl', 'r-cran-pkgconfig', 'r-cran-gtable', 'libhtml-tagset-perl', 'libpangoft2-1.0-0:amd64', 'libfreetype6:amd64', 'libencode-locale-perl', 'libtest-most-perl', 'r-cran-stringr', 'r-cran-pillar', 'libthai-data', 'r-cran-cli', 'ucf', 'libfontconfig1:amd64', 'xz-utils', 'r-cran-munsell', 'libsm6:amd64', 'r-cran-stringi', 'mime-support', 'bioperl', 'libsqlite3-0:amd64', 'zip', 'r-cran-mgcv', 'perl', 'libsub-identify-perl', 'libclass-data-inheritable-perl', 'netbase', 'libxss1:amd64', 'x11-common', 'libpaper-utils', 'libb-hooks-op-check-perl', 'r-cran-pkgkitten', 'mcl', 'r-cran-vctrs', 'r-cran-lazyeval', 'libspiffy-perl', 'libsub-install-perl', 'libjbig0:amd64', 'libbrotli1:amd64', 'libhttp-cookies-perl', 'libncurses6:amd64', 'libkrb5support0:amd64', 'xdg-utils', 'libtest-differences-perl', 'ncbi-blast+', 'liblwp-mediatypes-perl', 'libice6:amd64', 'libxt6:amd64', 'libwww-robotrules-perl', 'libdevel-globaldestruction-perl', 'libjpeg62-turbo:amd64', 'libio-string-perl', 'libalgorithm-diff-perl', 'procps', 'r-cran-withr', 'libx11-data', 'libcairo2:amd64', 'libsub-exporter-progressive-perl', 'libhttp-negotiate-perl', 'libtest-deep-perl', 'r-cran-utf8', 'libarray-utils-perl', 'liblmdb0:amd64', 'libexception-class-perl', 'libpackage-deprecationmanager-perl', 'libblas3:amd64', 'libkeyutils1:amd64', 'libpixman-1-0:amd64', 'r-cran-zeallot', 'r-cran-assertthat', 'r-cran-r6', 'bedtools', 'libgfortran5:amd64', 'r-cran-colorspace', 'perl-modules-5.30', 'r-cran-crayon', 'libfile-grep-perl', 'libdata-optlist-perl', 'r-cran-mass', 'r-cran-backports', 'libnumber-compare-perl', 'libtimedate-perl', 'libnet-http-perl', 'libdynaloader-functions-perl', 'libio-html-perl', 'libmodule-runtime-perl', 'libcurl4:amd64', 'r-cran-littler', 'libsub-name-perl', 'r-cran-viridislite', 'liblapack3:amd64', 'libsasl2-modules-db:amd64', 'libexpat1:amd64', 'fasttree', 'libtry-tiny-perl', 'libclass-load-perl', 'libfribidi0:amd64', 'libxrender1:amd64', 'libpng16-16:amd64', 'liblwp-protocol-https-perl', 'r-cran-ggplot2', 'parallel', 'libmodule-implementation-perl', 'libio-all-perl', 'libldap-common', 'python3.7', 'libsasl2-2:amd64', 'libdevel-callchecker-perl', 'libtest-exception-perl', 'libhttp-date-perl', 'libenv-path-perl', 'libwebp6:amd64', 'libglib2.0-0:amd64', 'r-cran-lattice', 'libxml-writer-perl', 'libparams-util-perl', 'libmoose-perl'] 2m20.3s DUMP: dpkg: warning: ignoring request to remove libgraph-readwrite-perl which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed (Reading database ... 6616 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.17-6) ... dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed Purging configuration files for fonts-dejavu-core (2.37-1) ... dpkg: warning: while removing fonts-dejavu-core, directory '/usr/share/fonts/truetype/dejavu' not empty so not removed Purging configuration files for libsensors-config (1:3.6.0-2) ... dpkg: warning: ignoring request to remove r-cran-rlang which isn't installed dpkg: warning: ignoring request to remove r-cran-reshape2 which isn't installed dpkg: warning: ignoring request to remove libmodule-runtime-conflicts-perl which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libdist-checkconflicts-perl which isn't installed dpkg: warning: ignoring request to remove libnet-ssleay-perl which isn't installed dpkg: warning: ignoring request to remove libtest-output-perl which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove r-cran-labeling which isn't installed Purging configuration files for fontconfig (2.13.1-2+b1) ... dpkg: warning: ignoring request to remove libclass-c3-perl which isn't installed dpkg: warning: ignoring request to remove libprocps7 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libmro-compat-perl which isn't installed dpkg: warning: ignoring request to remove r-cran-rcpp which isn't installed dpkg: warning: ignoring request to remove libsub-uplevel-perl which isn't installed Purging configuration files for unzip (6.0-25) ... dpkg: warning: ignoring request to remove libtext-glob-perl which isn't installed Purging configuration files for libssl1.1:amd64 (1.1.1d-2) ... dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove liburi-perl which isn't installed dpkg: warning: ignoring request to remove libalgorithm-c3-perl which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libtext-csv-perl which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed Purging configuration files for ca-certificates (20190110) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for r-base-core (3.6.1-7) ... dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libmpdec2 which isn't installed Purging configuration files for readline-common (8.0-3) ... dpkg: warning: ignoring request to remove r-cran-matrix which isn't installed dpkg: warning: ignoring request to remove libfile-listing-perl which isn't installed Purging configuration files for python3.7-minimal (3.7.5-2) ... Purging configuration files for python3 (3.7.5-3) ... dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libtest-files-perl which isn't installed dpkg: warning: ignoring request to remove libparse-yapp-perl which isn't installed dpkg: warning: ignoring request to remove r-cran-plyr which isn't installed dpkg: warning: ignoring request to remove libpackage-stash-perl which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed Purging configuration files for libpython3.7-minimal:amd64 (3.7.5-2) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtext-diff-perl which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove mafft which isn't installed dpkg: warning: ignoring request to remove libfile-slurper-perl which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libtest-warn-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tree-perl 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-digest which isn't installed dpkg: warning: ignoring request to remove libio-socket-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libbio-perl-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 libsensors5 which isn't installed dpkg: warning: ignoring request to remove r-cran-nlme which isn't installed dpkg: warning: ignoring request to remove libhtml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libcapture-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libwww-perl which isn't installed dpkg: warning: ignoring request to remove libperlio-utf8-strict-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 r-cran-magrittr which isn't installed dpkg: warning: ignoring request to remove libpython3.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libdevel-stacktrace-perl which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove libsub-exporter-perl which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libfile-find-rule-perl which isn't installed dpkg: warning: ignoring request to remove libperl5.30 which isn't installed dpkg: warning: ignoring request to remove r-cran-scales which isn't installed dpkg: warning: ignoring request to remove libparams-classify-perl which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove prank which isn't installed dpkg: warning: ignoring request to remove libdevel-overloadinfo-perl which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libeval-closure-perl which isn't installed dpkg: warning: ignoring request to remove r-cran-ellipsis which isn't installed dpkg: warning: ignoring request to remove libfindbin-libs-perl which isn't installed dpkg: warning: ignoring request to remove libicu63 which isn't installed dpkg: warning: ignoring request to remove libgraph-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-message-perl which isn't installed dpkg: warning: ignoring request to remove libdata-stag-perl which isn't installed dpkg: warning: ignoring request to remove liblog-log4perl-perl which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-7) ... dpkg: warning: ignoring request to remove cd-hit which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libtest-file-perl which isn't installed dpkg: warning: ignoring request to remove perl-openssl-defaults which isn't installed dpkg: warning: ignoring request to remove libfile-which-perl which isn't installed dpkg: warning: ignoring request to remove r-cran-glue which isn't installed dpkg: warning: ignoring request to remove libxml-parser-perl which isn't installed dpkg: warning: ignoring request to remove r-cran-fansi which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed Purging configuration files for fontconfig-config (2.13.1-2) ... dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libmbedtls12 which isn't installed Purging configuration files for openssl (1.1.1d-2) ... Purging configuration files for sysstat (12.1.7-1) ... dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed Purging configuration files for libpaper1:amd64 (1.1.28+b1) ... dpkg: warning: ignoring request to remove libclass-load-xs-perl 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-gtable which isn't installed dpkg: warning: ignoring request to remove libhtml-tagset-perl which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libencode-locale-perl which isn't installed dpkg: warning: ignoring request to remove libtest-most-perl which isn't installed dpkg: warning: ignoring request to remove r-cran-stringr which isn't installed dpkg: warning: ignoring request to remove r-cran-pillar which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove r-cran-cli which isn't installed Purging configuration files for ucf (3.0038+nmu1) ... dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove xz-utils which isn't installed dpkg: warning: ignoring request to remove r-cran-munsell which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove r-cran-stringi which isn't installed Purging configuration files for mime-support (3.64) ... dpkg: warning: ignoring request to remove bioperl which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed dpkg: warning: ignoring request to remove r-cran-mgcv which isn't installed Purging configuration files for perl (5.30.0-9) ... dpkg: warning: ignoring request to remove libsub-identify-perl which isn't installed dpkg: warning: ignoring request to remove libclass-data-inheritable-perl which isn't installed Purging configuration files for netbase (5.8) ... dpkg: warning: ignoring request to remove libxss1 which isn't installed Purging configuration files for x11-common (1:7.7+20) ... dpkg: warning: ignoring request to remove libpaper-utils 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 r-cran-pkgkitten which isn't installed dpkg: warning: ignoring request to remove mcl 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-lazyeval which isn't installed dpkg: warning: ignoring request to remove libspiffy-perl which isn't installed dpkg: warning: ignoring request to remove libsub-install-perl which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libhttp-cookies-perl which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove libtest-differences-perl which isn't installed dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed dpkg: warning: ignoring request to remove liblwp-mediatypes-perl which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libxt6 which isn't installed dpkg: warning: ignoring request to remove libwww-robotrules-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-globaldestruction-perl which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libio-string-perl which isn't installed dpkg: warning: ignoring request to remove libalgorithm-diff-perl which isn't installed Purging configuration files for procps (2:3.3.15-2+b1) ... dpkg: warning: ignoring request to remove r-cran-withr which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libsub-exporter-progressive-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-negotiate-perl which isn't installed dpkg: warning: ignoring request to remove libtest-deep-perl which isn't installed dpkg: warning: ignoring request to remove r-cran-utf8 which isn't installed dpkg: warning: ignoring request to remove libarray-utils-perl which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove libexception-class-perl which isn't installed dpkg: warning: ignoring request to remove libpackage-deprecationmanager-perl which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove r-cran-zeallot which isn't installed dpkg: warning: ignoring request to remove r-cran-assertthat which isn't installed dpkg: warning: ignoring request to remove r-cran-r6 which isn't installed dpkg: warning: ignoring request to remove bedtools which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove r-cran-colorspace which isn't installed dpkg: warning: ignoring request to remove perl-modules-5.30 which isn't installed dpkg: warning: ignoring request to remove r-cran-crayon which isn't installed dpkg: warning: ignoring request to remove libfile-grep-perl which isn't installed dpkg: warning: ignoring request to remove libdata-optlist-perl 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-backports which isn't installed dpkg: warning: ignoring request to remove libnumber-compare-perl which isn't installed dpkg: warning: ignoring request to remove libtimedate-perl which isn't installed dpkg: warning: ignoring request to remove libnet-http-perl which isn't installed dpkg: warning: ignoring request to remove libdynaloader-functions-perl which isn't installed dpkg: warning: ignoring request to remove libio-html-perl which isn't installed dpkg: warning: ignoring request to remove libmodule-runtime-perl which isn't installed dpkg: warning: ignoring request to remove libcurl4 which isn't installed dpkg: warning: ignoring request to remove r-cran-littler which isn't installed dpkg: warning: ignoring request to remove libsub-name-perl which isn't installed dpkg: warning: ignoring request to remove r-cran-viridislite which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove fasttree which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libclass-load-perl which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove liblwp-protocol-https-perl which isn't installed dpkg: warning: ignoring request to remove r-cran-ggplot2 which isn't installed Purging configuration files for parallel (20161222-1.1) ... dpkg: warning: ignoring request to remove libmodule-implementation-perl which isn't installed dpkg: warning: ignoring request to remove libio-all-perl which isn't installed Purging configuration files for libldap-common (2.4.48+dfsg-1) ... dpkg: warning: ignoring request to remove python3.7 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libdevel-callchecker-perl which isn't installed dpkg: warning: ignoring request to remove libtest-exception-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-date-perl which isn't installed dpkg: warning: ignoring request to remove libenv-path-perl which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.62.3-2) ... dpkg: warning: ignoring request to remove r-cran-lattice which isn't installed dpkg: warning: ignoring request to remove libxml-writer-perl which isn't installed dpkg: warning: ignoring request to remove libparams-util-perl which isn't installed dpkg: warning: ignoring request to remove libmoose-perl which isn't installed 2m20.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg', '--purge', 'libgraph-readwrite-perl', 'libmbedx509-0:amd64', 'libgssapi-krb5-2:amd64', 'libssh2-1:amd64', 'libmbedcrypto3:amd64', 'fonts-dejavu-core', 'libsensors-config', 'r-cran-rlang', 'r-cran-reshape2', 'libmodule-runtime-conflicts-perl', 'littler', 'sensible-utils', 'librtmp1:amd64', 'libdist-checkconflicts-perl', 'libnet-ssleay-perl', 'libtest-output-perl', 'libgdbm6:amd64', 'libtiff5:amd64', 'libdatrie1:amd64', 'r-cran-labeling', 'fontconfig', 'libclass-c3-perl', 'libprocps7:amd64', 'libreadline8:amd64', 'libxcb1:amd64', 'libmro-compat-perl', 'r-cran-rcpp', 'libsub-uplevel-perl', 'unzip', 'libtext-glob-perl', 'libssl1.1:amd64', 'libpango-1.0-0:amd64', 'liburi-perl', 'libalgorithm-c3-perl', 'libkrb5-3:amd64', 'libtext-csv-perl', 'python3-minimal', 'ca-certificates', 'r-base-core', 'libtk8.6:amd64', 'libmpdec2:amd64', 'readline-common', 'r-cran-matrix', 'libfile-listing-perl', 'python3.7-minimal', 'python3', 'libbsd0:amd64', 'libtest-files-perl', 'libparse-yapp-perl', 'r-cran-plyr', 'libpackage-stash-perl', 'libk5crypto3:amd64', 'libpython3.7-minimal:amd64', 'libgomp1:amd64', 'libthai0:amd64', 'libtext-diff-perl', 'libpangocairo-1.0-0:amd64', 'mafft', 'libfile-slurper-perl', 'libgraphite2-3:amd64', 'libtest-warn-perl', 'libhtml-tree-perl', 'r-cran-rcolorbrewer', 'r-cran-digest', 'libio-socket-ssl-perl', 'libtcl8.6:amd64', 'libx11-6:amd64', 'libbio-perl-perl', 'libdigest-md5-file-perl', 'libsensors5:amd64', 'r-cran-nlme', 'libhtml-parser-perl', 'libcapture-tiny-perl', 'libpython3-stdlib:amd64', 'libgdbm-compat4:amd64', 'libwww-perl', 'libperlio-utf8-strict-perl', 'libpackage-stash-xs-perl', 'r-cran-magrittr', 'libpython3.7-stdlib:amd64', 'libdevel-stacktrace-perl', 'r-cran-tibble', 'libsub-exporter-perl', 'libquadmath0:amd64', 'libfile-find-rule-perl', 'libperl5.30:amd64', 'r-cran-scales', 'libparams-classify-perl', 'libpsl5:amd64', 'libxext6:amd64', 'prank', 'libdevel-overloadinfo-perl', 'libxdmcp6:amd64', 'libeval-closure-perl', 'r-cran-ellipsis', 'libfindbin-libs-perl', 'libicu63:amd64', 'libgraph-perl', 'libhttp-message-perl', 'libdata-stag-perl', 'liblog-log4perl-perl', 'libnghttp2-14:amd64', 'ncbi-data', 'cd-hit', 'libxau6:amd64', 'libtest-file-perl', 'perl-openssl-defaults:amd64', 'libfile-which-perl', 'r-cran-glue', 'libxml-parser-perl', 'r-cran-fansi', 'libxcb-shm0:amd64', 'fontconfig-config', 'libxft2:amd64', 'libmbedtls12:amd64', 'openssl', 'sysstat', 'libxcb-render0:amd64', 'libharfbuzz0b:amd64', 'libldap-2.4-2:amd64', 'libpaper1:amd64', 'libclass-load-xs-perl', 'r-cran-pkgconfig', 'r-cran-gtable', 'libhtml-tagset-perl', 'libpangoft2-1.0-0:amd64', 'libfreetype6:amd64', 'libencode-locale-perl', 'libtest-most-perl', 'r-cran-stringr', 'r-cran-pillar', 'libthai-data', 'r-cran-cli', 'ucf', 'libfontconfig1:amd64', 'xz-utils', 'r-cran-munsell', 'libsm6:amd64', 'r-cran-stringi', 'mime-support', 'bioperl', 'libsqlite3-0:amd64', 'zip', 'r-cran-mgcv', 'perl', 'libsub-identify-perl', 'libclass-data-inheritable-perl', 'netbase', 'libxss1:amd64', 'x11-common', 'libpaper-utils', 'libb-hooks-op-check-perl', 'r-cran-pkgkitten', 'mcl', 'r-cran-vctrs', 'r-cran-lazyeval', 'libspiffy-perl', 'libsub-install-perl', 'libjbig0:amd64', 'libbrotli1:amd64', 'libhttp-cookies-perl', 'libncurses6:amd64', 'libkrb5support0:amd64', 'xdg-utils', 'libtest-differences-perl', 'ncbi-blast+', 'liblwp-mediatypes-perl', 'libice6:amd64', 'libxt6:amd64', 'libwww-robotrules-perl', 'libdevel-globaldestruction-perl', 'libjpeg62-turbo:amd64', 'libio-string-perl', 'libalgorithm-diff-perl', 'procps', 'r-cran-withr', 'libx11-data', 'libcairo2:amd64', 'libsub-exporter-progressive-perl', 'libhttp-negotiate-perl', 'libtest-deep-perl', 'r-cran-utf8', 'libarray-utils-perl', 'liblmdb0:amd64', 'libexception-class-perl', 'libpackage-deprecationmanager-perl', 'libblas3:amd64', 'libkeyutils1:amd64', 'libpixman-1-0:amd64', 'r-cran-zeallot', 'r-cran-assertthat', 'r-cran-r6', 'bedtools', 'libgfortran5:amd64', 'r-cran-colorspace', 'perl-modules-5.30', 'r-cran-crayon', 'libfile-grep-perl', 'libdata-optlist-perl', 'r-cran-mass', 'r-cran-backports', 'libnumber-compare-perl', 'libtimedate-perl', 'libnet-http-perl', 'libdynaloader-functions-perl', 'libio-html-perl', 'libmodule-runtime-perl', 'libcurl4:amd64', 'r-cran-littler', 'libsub-name-perl', 'r-cran-viridislite', 'liblapack3:amd64', 'libsasl2-modules-db:amd64', 'libexpat1:amd64', 'fasttree', 'libtry-tiny-perl', 'libclass-load-perl', 'libfribidi0:amd64', 'libxrender1:amd64', 'libpng16-16:amd64', 'liblwp-protocol-https-perl', 'r-cran-ggplot2', 'parallel', 'libmodule-implementation-perl', 'libio-all-perl', 'libldap-common', 'python3.7', 'libsasl2-2:amd64', 'libdevel-callchecker-perl', 'libtest-exception-perl', 'libhttp-date-perl', 'libenv-path-perl', 'libwebp6:amd64', 'libglib2.0-0:amd64', 'r-cran-lattice', 'libxml-writer-perl', 'libparams-util-perl', 'libmoose-perl'] 2m20.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg', '--purge', 'roary'] 2m20.3s DUMP: dpkg: warning: ignoring request to remove roary which isn't installed 2m20.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg', '--purge', 'roary'] 2m20.3s INFO: Running scripts post_purge 2m20.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_purge_exceptions'] 2m20.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_purge_exceptions'] 2m20.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg', '--purge', '--pending'] 2m20.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg', '--purge', '--pending'] 2m20.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg', '--remove', '--pending'] 2m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg', '--remove', '--pending'] 2m20.4s INFO: Running scripts post_test 2m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_test_exceptions'] 2m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'tmp/scripts/post_test_exceptions'] 2m20.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 2m21.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 2m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg-divert', '--list'] 2m21.4s 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 2m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'dpkg-divert', '--list'] 2m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', 'clean'] 2m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_pGAH', 'apt-get', 'clean'] 2m21.5s DEBUG: Recording chroot state 2m23.3s INFO: Warning: Package purging left files on system: /usr/local/share/fonts/ not owned /usr/local/share/fonts/.uuid not owned /usr/share/fonts/ owned by: fonts-dejavu-core /usr/share/fonts/.uuid not owned /usr/share/fonts/truetype/ owned by: fonts-dejavu-core /usr/share/fonts/truetype/.uuid not owned /usr/share/fonts/truetype/dejavu/ owned by: fonts-dejavu-core /usr/share/fonts/truetype/dejavu/.uuid not owned 2m24.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/shm'] 2m24.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/shm'] 2m24.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/console'] 2m24.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/console'] 2m24.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/ptmx'] 2m24.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/ptmx'] 2m24.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/pts'] 2m24.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/dev/pts'] 2m24.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/proc'] 2m24.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_pGAH/proc'] 2m24.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 2m24.7s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpt_pGAH'] 2m24.7s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpt_pGAH 2m24.7s INFO: PASS: Upgrading between Debian distributions. 2m24.7s INFO: PASS: All tests. 2m24.7s INFO: piuparts run ends. ret=0 End: 2019-12-07 06:04:59 UTC