Start: 2023-04-03 10:48:07 GMT [stretch] Package: roary Version: 3.8.0+dfsg-1 Installed-Size: 634 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl, libarray-utils-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_3.8.0+dfsg-1_all.deb Size: 170134 MD5sum: d2b5bd8c3cf60d6fabc08169c52a4d40 SHA256: 062eece678b4556ee0de3961c4789d1b51e2e860d582d72e19aedd6f8beef3db [stretch-backports] Package: roary Version: 3.12.0+dfsg-2~bpo9+1 Installed-Size: 659 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl, 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 Section: science Priority: optional Filename: pool/main/r/roary/roary_3.12.0+dfsg-2~bpo9+1_all.deb Size: 176386 MD5sum: 5595abf6ba7a149a2b3d103d3aa0a77f SHA256: ff2b00abf705066759c33acf4ff4cae99e281997e1789b34ac85534b8a117e59 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d stretch-backports -B /srv/piuparts.debian.org/slave/refchroot/stretch2bpo/reference-chroot-metadata.dat --apt 'roary=3.12.0+dfsg-2~bpo9+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 1.1.5 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 --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d stretch-backports -B /srv/piuparts.debian.org/slave/refchroot/stretch2bpo/reference-chroot-metadata.dat --apt 'roary=3.12.0+dfsg-2~bpo9+1' 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpfk7gzh7f 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpfk7gzh7f 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m2.1s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/proc'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/proc'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/pts'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/pts'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/ptmx'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/ptmx'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/console'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/console'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/shm'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/shm'] 0m2.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m2.1s DEBUG: Created policy-rc.d and chmodded it. 0m2.1s DEBUG: Created resolv.conf. 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpfk7gzh7f/tmp/scripts/ 0m2.1s INFO: Running scripts post_chroot_unpack 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', 'update'] 0m3.0s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', 'update'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', '-yf', 'dist-upgrade'] 0m3.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', '-yf', 'dist-upgrade'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.6s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.6s INFO: Running scripts post_setup 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_setup_dummy_users'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_setup_dummy_users'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_setup_forbid_home'] 0m4.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_setup_forbid_home'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_setup_minimize'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_setup_minimize'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2bpo/reference-chroot-metadata.dat 0m4.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m4.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m4.9s INFO: Running scripts is_testable 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/is_testable_uninstallable'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/is_testable_uninstallable'] 0m4.9s INFO: Running scripts pre_test 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_test_exceptions'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_test_exceptions'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_test_root_password'] 0m5.0s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_test_root_password'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m5.2s DUMP: Package: roary Version: 3.8.0+dfsg-1 Installed-Size: 634 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl, libarray-utils-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_3.8.0+dfsg-1_all.deb Size: 170134 MD5sum: d2b5bd8c3cf60d6fabc08169c52a4d40 SHA256: 062eece678b4556ee0de3961c4789d1b51e2e860d582d72e19aedd6f8beef3db 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m5.2s INFO: apt-cache knows about the following packages: roary 0m5.2s INFO: Running scripts pre_install 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'policy'] 0m5.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'policy'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'policy', 'roary'] 0m5.3s DUMP: roary: Installed: (none) Candidate: 3.8.0+dfsg-1 Version table: 3.8.0+dfsg-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'policy', 'roary'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', '-y', 'install', 'roary'] 0m27.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bedtools bioperl ca-certificates cd-hit fasttree fontconfig fontconfig-config fonts-dejavu-core libalgorithm-c3-perl libalgorithm-diff-perl libarray-utils-perl libbio-perl-perl libblas-common libblas3 libbsd0 libcairo2 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libcurl3 libdata-optlist-perl libdata-stag-perl libdatrie1 libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdist-checkconflicts-perl libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libffi6 libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-slurper-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libgdbm3 libgfortran3 libglib2.0-0 libgmp10 libgnutls30 libgomp1 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhogweed4 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu57 libidn11 libidn2-0 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 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncurses5 libnet-http-perl libnet-ssleay-perl libnettle6 libnghttp2-14 libnumber-compare-perl libp11-kit0 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 libperl5.24 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16 libprocps6 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libscalar-list-utils-perl libsensors4 libsm6 libspiffy-perl libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-uplevel-perl libtasn1-6 libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-simple-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl libunistring0 liburi-perl 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 lsb-base mafft mcl mime-support ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.24 perl-openssl-defaults prank procps python python-minimal python2.7 python2.7-minimal r-base-core r-cran-assertthat r-cran-colorspace r-cran-dichromat r-cran-digest r-cran-ggplot2 r-cran-gtable r-cran-labeling r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-munsell r-cran-pkgkitten r-cran-plyr r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble readline-common sysstat tzdata ucf unzip x11-common xdg-utils xz-utils zip Suggested packages: filo groff-base libxml-sax-expatxs-perl gnutls-bin 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 python-doc python-tk python2.7-doc binutils binfmt-support ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-hexbin r-cran-hmisc r-cran-lattice r-cran-mapproj r-cran-maps r-cran-maptools r-cran-mgcv r-cran-multcomp r-cran-nlme r-cran-testthat r-cran-quantreg r-cran-knitr r-cran-rpart r-cran-getopt r-cran-abind r-cran-foreach r-cran-doparallel r-cran-iterators r-cran-inline r-cran-htmltools r-cran-htmlwidgets readline-doc isag gvfs-bin 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 libhtml-form-perl libhttp-daemon-perl libmailtools-perl blast2 lynx ruby bzip2 file rename psmisc r-recommended r-base-dev r-doc-html r-cran-crayon 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 libbio-perl-perl libblas-common libblas3 libbsd0 libcairo2 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libcurl3 libdata-optlist-perl libdata-stag-perl libdatrie1 libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdist-checkconflicts-perl libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libffi6 libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-slurper-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libgdbm3 libgfortran3 libglib2.0-0 libgmp10 libgnutls30 libgomp1 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhogweed4 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu57 libidn11 libidn2-0 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 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncurses5 libnet-http-perl libnet-ssleay-perl libnettle6 libnghttp2-14 libnumber-compare-perl libp11-kit0 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 libperl5.24 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16 libprocps6 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libscalar-list-utils-perl libsensors4 libsm6 libspiffy-perl libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-uplevel-perl libtasn1-6 libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-simple-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl libunistring0 liburi-perl 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 lsb-base mafft mcl mime-support ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.24 perl-openssl-defaults prank procps python python-minimal python2.7 python2.7-minimal r-base-core r-cran-assertthat r-cran-colorspace r-cran-dichromat r-cran-digest r-cran-ggplot2 r-cran-gtable r-cran-labeling r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-munsell r-cran-pkgkitten r-cran-plyr r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble readline-common roary sysstat tzdata ucf unzip x11-common xdg-utils xz-utils zip 0 upgraded, 222 newly installed, 0 to remove and 0 not upgraded. Need to get 101 MB of archives. After this operation, 328 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 perl-modules-5.24 all 5.24.1-3+deb9u7 [2723 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 libgdbm3 amd64 1.8.3-14 [30.0 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 libperl5.24 amd64 5.24.1-3+deb9u7 [3527 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 perl amd64 5.24.1-3+deb9u7 [218 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u3 [389 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u3 [1382 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u3 [83.7 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 python amd64 2.7.13-2 [154 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 libpng16-16 amd64 1.6.28-1+deb9u1 [280 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libfreetype6 amd64 2.6.3-3.2+deb9u1 [438 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 ucf all 3.0036 [70.2 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 fontconfig-config all 2.11.0-6.7 [271 kB] Get:24 http://deb.debian.org/debian stretch/main amd64 libfontconfig1 amd64 2.11.0-6.7+b1 [331 kB] Get:25 http://deb.debian.org/debian stretch/main amd64 fontconfig amd64 2.11.0-6.7+b1 [404 kB] Get:26 http://deb.debian.org/debian stretch/main amd64 libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:27 http://deb.debian.org/debian stretch/main amd64 libbsd0 amd64 0.8.3-1 [83.0 kB] Get:28 http://deb.debian.org/debian stretch/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:29 http://deb.debian.org/debian stretch/main amd64 libxcb1 amd64 1.12-1 [133 kB] Get:30 http://deb.debian.org/debian stretch/main amd64 libx11-data all 2:1.6.4-3+deb9u1 [287 kB] Get:31 http://deb.debian.org/debian stretch/main amd64 libx11-6 amd64 2:1.6.4-3+deb9u1 [748 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 lsb-base all 9.20161125 [27.9 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 x11-common all 1:7.7+19 [251 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 libxss1 amd64 1:1.2.2-1 [17.5 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 tzdata all 2020a-0+deb9u1 [278 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 libprocps6 amd64 2:3.3.12-3+deb9u1 [58.5 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 libssl1.0.2 amd64 1.0.2u-1~deb9u1 [1304 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 netbase all 5.4 [19.1 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 libncurses5 amd64 6.0+20161126-1+deb9u2 [93.4 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 procps amd64 2:3.3.12-3+deb9u1 [250 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:43 http://deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b2 [192 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b2 [136 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:46 http://deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB] Get:47 http://deb.debian.org/debian stretch/main amd64 libtasn1-6 amd64 4.10-1.1+deb9u1 [50.6 kB] Get:48 http://deb.debian.org/debian stretch/main amd64 libgnutls30 amd64 3.5.8-5+deb9u5 [896 kB] Get:49 http://deb.debian.org/debian stretch/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:50 http://deb.debian.org/debian stretch/main amd64 libkrb5support0 amd64 1.15-1+deb9u1 [61.9 kB] Get:51 http://deb.debian.org/debian stretch/main amd64 libk5crypto3 amd64 1.15-1+deb9u1 [119 kB] Get:52 http://deb.debian.org/debian stretch/main amd64 libkrb5-3 amd64 1.15-1+deb9u1 [311 kB] Get:53 http://deb.debian.org/debian stretch/main amd64 libgssapi-krb5-2 amd64 1.15-1+deb9u1 [155 kB] Get:54 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [68.4 kB] Get:55 http://deb.debian.org/debian stretch/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [105 kB] Get:56 http://deb.debian.org/debian stretch/main amd64 libldap-common all 2.4.44+dfsg-5+deb9u4 [85.7 kB] Get:57 http://deb.debian.org/debian stretch/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u4 [219 kB] Get:58 http://deb.debian.org/debian stretch/main amd64 xz-utils amd64 5.2.2-1.2+b1 [266 kB] Get:59 http://deb.debian.org/debian stretch/main amd64 bedtools amd64 2.26.0+dfsg-3 [584 kB] Get:60 http://deb.debian.org/debian stretch/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:61 http://deb.debian.org/debian stretch/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get:62 http://deb.debian.org/debian stretch/main amd64 libbio-perl-perl all 1.7.1-2 [4605 kB] Get:63 http://deb.debian.org/debian stretch/main amd64 bioperl all 1.7.1-2 [422 kB] Get:64 http://deb.debian.org/debian stretch/main amd64 openssl amd64 1.1.0l-1~deb9u1 [749 kB] Get:65 http://deb.debian.org/debian stretch/main amd64 ca-certificates all 20200601~deb9u1 [160 kB] Get:66 http://deb.debian.org/debian stretch/main amd64 libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:67 http://deb.debian.org/debian stretch/main amd64 cd-hit amd64 4.6.6-2 [852 kB] Get:68 http://deb.debian.org/debian stretch/main amd64 libalgorithm-c3-perl all 0.10-1 [12.0 kB] Get:69 http://deb.debian.org/debian stretch/main amd64 libalgorithm-diff-perl all 1.19.03-1 [48.7 kB] Get:70 http://deb.debian.org/debian stretch/main amd64 libarray-utils-perl all 0.5-1 [6254 B] Get:71 http://deb.debian.org/debian stretch/main amd64 libblas-common amd64 3.7.0-2 [14.2 kB] Get:72 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:73 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:74 http://deb.debian.org/debian stretch/main amd64 libblas3 amd64 3.7.0-2 [155 kB] Get:75 http://deb.debian.org/debian stretch/main amd64 libpixman-1-0 amd64 0.34.0-1 [530 kB] Get:76 http://deb.debian.org/debian stretch/main amd64 libxcb-render0 amd64 1.12-1 [105 kB] Get:77 http://deb.debian.org/debian stretch/main amd64 libxcb-shm0 amd64 1.12-1 [95.9 kB] Get:78 http://deb.debian.org/debian stretch/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:79 http://deb.debian.org/debian stretch/main amd64 libcairo2 amd64 1.14.8-1 [771 kB] Get:80 http://deb.debian.org/debian stretch/main amd64 libcapture-tiny-perl all 0.44-1 [25.4 kB] Get:81 http://deb.debian.org/debian stretch/main amd64 libclass-c3-perl all 0.32-1 [22.1 kB] Get:82 http://deb.debian.org/debian stretch/main amd64 libclass-data-inheritable-perl all 0.08-2 [9296 B] Get:83 http://deb.debian.org/debian stretch/main amd64 libparams-util-perl amd64 1.07-3+b1 [22.7 kB] Get:84 http://deb.debian.org/debian stretch/main amd64 libsub-install-perl all 0.928-1 [11.4 kB] Get:85 http://deb.debian.org/debian stretch/main amd64 libdata-optlist-perl all 0.110-1 [10.6 kB] Get:86 http://deb.debian.org/debian stretch/main amd64 libparams-classify-perl amd64 0.013-6+b1 [24.4 kB] Get:87 http://deb.debian.org/debian stretch/main amd64 libmodule-runtime-perl all 0.014-2 [18.0 kB] Get:88 http://deb.debian.org/debian stretch/main amd64 libtry-tiny-perl all 0.28-1 [22.7 kB] Get:89 http://deb.debian.org/debian stretch/main amd64 libmodule-implementation-perl all 0.09-1 [12.9 kB] Get:90 http://deb.debian.org/debian stretch/main amd64 libpackage-stash-perl all 0.37-1 [20.8 kB] Get:91 http://deb.debian.org/debian stretch/main amd64 libclass-load-perl all 0.23-1 [15.9 kB] Get:92 http://deb.debian.org/debian stretch/main amd64 libclass-load-xs-perl amd64 0.09-2+b1 [14.4 kB] Get:93 http://deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:94 http://deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:95 http://deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:96 http://deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB] Get:97 http://deb.debian.org/debian stretch/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:98 http://deb.debian.org/debian stretch/main amd64 libssh2-1 amd64 1.7.0-1+deb9u1 [139 kB] Get:99 http://deb.debian.org/debian stretch/main amd64 libcurl3 amd64 7.52.1-5+deb9u10 [292 kB] Get:100 http://deb.debian.org/debian stretch/main amd64 libdatrie1 amd64 0.2.10-4+b1 [36.4 kB] Get:101 http://deb.debian.org/debian stretch/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:102 http://deb.debian.org/debian stretch/main amd64 libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get:103 http://deb.debian.org/debian stretch/main amd64 libmro-compat-perl all 0.12-1 [13.2 kB] Get:104 http://deb.debian.org/debian stretch/main amd64 libsub-identify-perl amd64 0.12-2+b1 [11.5 kB] Get:105 http://deb.debian.org/debian stretch/main amd64 libdevel-overloadinfo-perl all 0.004-1 [7270 B] Get:106 http://deb.debian.org/debian stretch/main amd64 libdevel-stacktrace-perl all 2.0200-1 [27.3 kB] Get:107 http://deb.debian.org/debian stretch/main amd64 libdist-checkconflicts-perl all 0.11-1 [10.8 kB] Get:108 http://deb.debian.org/debian stretch/main amd64 libencode-locale-perl all 1.05-1 [13.7 kB] Get:109 http://deb.debian.org/debian stretch/main amd64 libenv-path-perl all 0.19-1 [22.0 kB] Get:110 http://deb.debian.org/debian stretch/main amd64 libsub-exporter-perl all 0.986-1 [49.9 kB] Get:111 http://deb.debian.org/debian stretch/main amd64 libeval-closure-perl all 0.14-1 [11.5 kB] Get:112 http://deb.debian.org/debian stretch/main amd64 libexception-class-perl all 1.42-1 [31.5 kB] Get:113 http://deb.debian.org/debian stretch/main amd64 libnumber-compare-perl all 0.03-1 [7642 B] Get:114 http://deb.debian.org/debian stretch/main amd64 libtext-glob-perl all 0.10-1 [8362 B] Get:115 http://deb.debian.org/debian stretch/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:116 http://deb.debian.org/debian stretch/main amd64 libfile-grep-perl all 0.02-1 [7654 B] Get:117 http://deb.debian.org/debian stretch/main amd64 libtimedate-perl all 2.3000-2+deb9u1 [37.9 kB] Get:118 http://deb.debian.org/debian stretch/main amd64 libhttp-date-perl all 6.02-1 [10.7 kB] Get:119 http://deb.debian.org/debian stretch/main amd64 libfile-listing-perl all 6.04-1 [10.3 kB] Get:120 http://deb.debian.org/debian stretch/main amd64 libfile-slurper-perl all 0.009-1 [7850 B] Get:121 http://deb.debian.org/debian stretch/main amd64 libfile-which-perl all 1.21-1 [14.3 kB] Get:122 http://deb.debian.org/debian stretch/main amd64 libfindbin-libs-perl all 2.150-1 [28.7 kB] Get:123 http://deb.debian.org/debian stretch/main amd64 libglib2.0-0 amd64 2.50.3-2+deb9u2 [2692 kB] Get:124 http://deb.debian.org/debian stretch/main amd64 libgraph-perl all 1:0.96-2 [126 kB] Get:125 http://deb.debian.org/debian stretch/main amd64 libscalar-list-utils-perl amd64 1:1.47-1 [54.4 kB] Get:126 http://deb.debian.org/debian stretch/main amd64 libspiffy-perl all 0.41-1 [26.1 kB] Get:127 http://deb.debian.org/debian stretch/main amd64 libio-all-perl all 0.86-2 [73.4 kB] Get:128 http://deb.debian.org/debian stretch/main amd64 libparse-yapp-perl all 1.05-12 [50.5 kB] Get:129 http://deb.debian.org/debian stretch/main amd64 liburi-perl all 1.71-1 [88.6 kB] Get:130 http://deb.debian.org/debian stretch/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:131 http://deb.debian.org/debian stretch/main amd64 libhtml-parser-perl amd64 3.72-3 [104 kB] Get:132 http://deb.debian.org/debian stretch/main amd64 libhtml-tree-perl all 5.03-2 [210 kB] Get:133 http://deb.debian.org/debian stretch/main amd64 libio-html-perl all 1.001-1 [17.6 kB] Get:134 http://deb.debian.org/debian stretch/main amd64 liblwp-mediatypes-perl all 6.02-1 [22.1 kB] Get:135 http://deb.debian.org/debian stretch/main amd64 libhttp-message-perl all 6.11-1 [75.9 kB] Get:136 http://deb.debian.org/debian stretch/main amd64 libhttp-cookies-perl all 6.01-1 [17.4 kB] Get:137 http://deb.debian.org/debian stretch/main amd64 libhttp-negotiate-perl all 6.00-2 [13.6 kB] Get:138 http://deb.debian.org/debian stretch/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:139 http://deb.debian.org/debian stretch/main amd64 libnet-ssleay-perl amd64 1.80-1 [285 kB] Get:140 http://deb.debian.org/debian stretch/main amd64 libio-socket-ssl-perl all 2.044-1 [195 kB] Get:141 http://deb.debian.org/debian stretch/main amd64 libnet-http-perl all 6.12-1 [23.8 kB] Get:142 http://deb.debian.org/debian stretch/main amd64 liblwp-protocol-https-perl all 6.06-2 [9582 B] Get:143 http://deb.debian.org/debian stretch/main amd64 libwww-robotrules-perl all 6.01-1 [14.3 kB] Get:144 http://deb.debian.org/debian stretch/main amd64 libwww-perl all 6.15-1 [195 kB] Get:145 http://deb.debian.org/debian stretch/main amd64 libxml-parser-perl amd64 2.44-2+b1 [212 kB] Get:146 http://deb.debian.org/debian stretch/main amd64 libxml-writer-perl all 0.625-1 [29.7 kB] Get:147 http://deb.debian.org/debian stretch/main amd64 libgraph-readwrite-perl all 2.09-1 [44.7 kB] Get:148 http://deb.debian.org/debian stretch/main amd64 libgraphite2-3 amd64 1.3.10-1 [84.2 kB] Get:149 http://deb.debian.org/debian stretch/main amd64 libharfbuzz0b amd64 1.4.2-1 [671 kB] Get:150 http://deb.debian.org/debian stretch/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:151 http://deb.debian.org/debian stretch/main amd64 libicu57 amd64 57.1-6+deb9u4 [7699 kB] Get:152 http://deb.debian.org/debian stretch/main amd64 libjpeg62-turbo amd64 1:1.5.1-2 [134 kB] Get:153 http://deb.debian.org/debian stretch/main amd64 liblapack3 amd64 3.7.0-2 [2141 kB] Get:154 http://deb.debian.org/debian stretch/main amd64 liblog-log4perl-perl all 1.48-1+deb9u1 [376 kB] Get:155 http://deb.debian.org/debian stretch/main amd64 libmodule-runtime-conflicts-perl all 0.003-1 [6882 B] Get:156 http://deb.debian.org/debian stretch/main amd64 libsub-name-perl amd64 0.21-1 [13.1 kB] Get:157 http://deb.debian.org/debian stretch/main amd64 libpackage-deprecationmanager-perl all 0.17-1 [16.4 kB] Get:158 http://deb.debian.org/debian stretch/main amd64 libpackage-stash-xs-perl amd64 0.28-3+b1 [17.9 kB] Get:159 http://deb.debian.org/debian stretch/main amd64 libmoose-perl amd64 2.1807-1 [801 kB] Get:160 http://deb.debian.org/debian stretch/main amd64 libthai-data all 0.1.26-1 [166 kB] Get:161 http://deb.debian.org/debian stretch/main amd64 libthai0 amd64 0.1.26-1 [52.1 kB] Get:162 http://deb.debian.org/debian stretch/main amd64 libpango-1.0-0 amd64 1.40.5-1 [320 kB] Get:163 http://deb.debian.org/debian stretch/main amd64 libpangoft2-1.0-0 amd64 1.40.5-1 [205 kB] Get:164 http://deb.debian.org/debian stretch/main amd64 libpangocairo-1.0-0 amd64 1.40.5-1 [193 kB] Get:165 http://deb.debian.org/debian stretch/main amd64 libpaper1 amd64 1.1.24+nmu5 [21.6 kB] Get:166 http://deb.debian.org/debian stretch/main amd64 libpaper-utils amd64 1.1.24+nmu5 [17.6 kB] Get:167 http://deb.debian.org/debian stretch/main amd64 libperlio-utf8-strict-perl amd64 0.006-1+b2 [11.3 kB] Get:168 http://deb.debian.org/debian stretch/main amd64 libsensors4 amd64 1:3.4.0-4 [53.3 kB] Get:169 http://deb.debian.org/debian stretch/main amd64 libsm6 amd64 2:1.2.2-1+b3 [33.3 kB] Get:170 http://deb.debian.org/debian stretch/main amd64 libsub-uplevel-perl all 0.2600-1 [16.1 kB] Get:171 http://deb.debian.org/debian stretch/main amd64 libtcl8.6 amd64 8.6.6+dfsg-1+b1 [985 kB] Get:172 http://deb.debian.org/debian stretch/main amd64 libtest-deep-perl all 1.126-1 [48.4 kB] Get:173 http://deb.debian.org/debian stretch/main amd64 libtext-diff-perl all 1.44-1 [27.4 kB] Get:174 http://deb.debian.org/debian stretch/main amd64 libtest-differences-perl all 0.64-1 [18.0 kB] Get:175 http://deb.debian.org/debian stretch/main amd64 libtest-exception-perl all 0.43-1 [18.7 kB] Get:176 http://deb.debian.org/debian stretch/main amd64 libtest-file-perl all 1.442-1 [19.8 kB] Get:177 http://deb.debian.org/debian stretch/main amd64 libtest-files-perl all 0.14-1 [11.2 kB] Get:178 http://deb.debian.org/debian stretch/main amd64 libtest-warn-perl all 0.32-1 [15.1 kB] Get:179 http://deb.debian.org/debian stretch/main amd64 libtest-simple-perl all 1.302075-1 [298 kB] Get:180 http://deb.debian.org/debian stretch/main amd64 libtest-most-perl all 0.35-1 [24.5 kB] Get:181 http://deb.debian.org/debian stretch/main amd64 libtest-output-perl all 1.03-1 [13.9 kB] Get:182 http://deb.debian.org/debian stretch/main amd64 libtext-csv-perl all 1.33-2 [50.5 kB] Get:183 http://deb.debian.org/debian stretch/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:184 http://deb.debian.org/debian stretch/main amd64 libtiff5 amd64 4.0.8-2+deb9u5 [239 kB] Get:185 http://deb.debian.org/debian stretch/main amd64 libxft2 amd64 2.3.2-1+b2 [56.5 kB] Get:186 http://deb.debian.org/debian stretch/main amd64 libtk8.6 amd64 8.6.6-1+b1 [754 kB] Get:187 http://deb.debian.org/debian stretch/main amd64 libxt6 amd64 1:1.1.5-1 [188 kB] Get:188 http://deb.debian.org/debian stretch/main amd64 zip amd64 3.0-11+b1 [234 kB] Get:189 http://deb.debian.org/debian stretch/main amd64 unzip amd64 6.0-21+deb9u2 [172 kB] Get:190 http://deb.debian.org/debian stretch/main amd64 xdg-utils all 1.1.1-1+deb9u2 [71.5 kB] Get:191 http://deb.debian.org/debian stretch/main amd64 r-base-core amd64 3.3.3-1 [21.2 MB] Get:192 http://deb.debian.org/debian stretch/main amd64 r-cran-littler amd64 0.3.1-1 [59.1 kB] Get:193 http://deb.debian.org/debian stretch/main amd64 littler all 0.3.1-1 [11.7 kB] Get:194 http://deb.debian.org/debian stretch/main amd64 mafft amd64 7.307-1 [889 kB] Get:195 http://deb.debian.org/debian stretch/main amd64 mcl amd64 1:14-137-1+b1 [619 kB] Get:196 http://deb.debian.org/debian stretch/main amd64 ncbi-data all 6.1.20170106+dfsg1-0+deb9u1 [3555 kB] Get:197 http://deb.debian.org/debian stretch/main amd64 ncbi-blast+ amd64 2.6.0-1 [9591 kB] Get:198 http://deb.debian.org/debian stretch/main amd64 prank amd64 0.0.150803-2 [374 kB] Get:199 http://deb.debian.org/debian stretch/main amd64 r-cran-assertthat all 0.1-1 [43.3 kB] Get:200 http://deb.debian.org/debian stretch/main amd64 r-cran-colorspace amd64 1.3-2-1 [388 kB] Get:201 http://deb.debian.org/debian stretch/main amd64 r-cran-dichromat all 2.0.0-3 [146 kB] Get:202 http://deb.debian.org/debian stretch/main amd64 r-cran-digest amd64 0.6.11-1 [112 kB] Get:203 http://deb.debian.org/debian stretch/main amd64 r-cran-gtable all 0.2.0-1 [65.1 kB] Get:204 http://deb.debian.org/debian stretch/main amd64 r-cran-mass amd64 7.3-45-1 [1017 kB] Get:205 http://deb.debian.org/debian stretch/main amd64 r-cran-pkgkitten all 0.1.4-1 [18.7 kB] Get:206 http://deb.debian.org/debian stretch/main amd64 r-cran-rcpp amd64 0.12.9-1 [2168 kB] Get:207 http://deb.debian.org/debian stretch/main amd64 r-cran-plyr amd64 1.8.4-1 [727 kB] Get:208 http://deb.debian.org/debian stretch/main amd64 r-cran-stringi amd64 1.1.2-1 [606 kB] Get:209 http://deb.debian.org/debian stretch/main amd64 r-cran-magrittr amd64 1.5-3 [147 kB] Get:210 http://deb.debian.org/debian stretch/main amd64 r-cran-stringr all 1.1.0-1 [117 kB] Get:211 http://deb.debian.org/debian stretch/main amd64 r-cran-reshape2 amd64 1.4.2-1 [87.5 kB] Get:212 http://deb.debian.org/debian stretch/main amd64 r-cran-rcolorbrewer all 1.1-2-1 [26.0 kB] Get:213 http://deb.debian.org/debian stretch/main amd64 r-cran-munsell all 0.4.3-1 [127 kB] Get:214 http://deb.debian.org/debian stretch/main amd64 r-cran-labeling all 0.3-1 [39.9 kB] Get:215 http://deb.debian.org/debian stretch/main amd64 r-cran-scales amd64 0.4.1-1 [200 kB] Get:216 http://deb.debian.org/debian stretch/main amd64 r-cran-lazyeval amd64 0.2.0-1 [112 kB] Get:217 http://deb.debian.org/debian stretch/main amd64 r-cran-tibble amd64 1.2-1 [121 kB] Get:218 http://deb.debian.org/debian stretch/main amd64 r-cran-ggplot2 all 2.2.1-2 [2658 kB] Get:219 http://deb.debian.org/debian stretch/main amd64 sysstat amd64 11.4.3-2 [360 kB] Get:220 http://deb.debian.org/debian stretch/main amd64 parallel all 20161222-1 [307 kB] Get:221 http://deb.debian.org/debian stretch/main amd64 fasttree amd64 2.1.9-1 [132 kB] Get:222 http://deb.debian.org/debian stretch/main amd64 roary all 3.8.0+dfsg-1 [170 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 101 MB in 1s (61.0 MB/s) Selecting previously unselected package perl-modules-5.24. (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 ... 4411 files and directories currently installed.) Preparing to unpack .../00-perl-modules-5.24_5.24.1-3+deb9u7_all.deb ... Unpacking perl-modules-5.24 (5.24.1-3+deb9u7) ... Selecting previously unselected package libgdbm3:amd64. Preparing to unpack .../01-libgdbm3_1.8.3-14_amd64.deb ... Unpacking libgdbm3:amd64 (1.8.3-14) ... Selecting previously unselected package libperl5.24:amd64. 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 7061 files and directories currently installed.) Preparing to unpack .../000-python_2.7.13-2_amd64.deb ... Unpacking python (2.7.13-2) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../001-libpng16-16_1.6.28-1+deb9u1_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.28-1+deb9u1) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../002-libfreetype6_2.6.3-3.2+deb9u1_amd64.deb ... Unpacking libfreetype6:amd64 (2.6.3-3.2+deb9u1) ... Selecting previously unselected package ucf. Preparing to unpack .../003-ucf_3.0036_all.deb ... Moving old data out of the way Unpacking ucf (3.0036) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../004-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../005-fontconfig-config_2.11.0-6.7_all.deb ... Unpacking fontconfig-config (2.11.0-6.7) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../006-libfontconfig1_2.11.0-6.7+b1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.11.0-6.7+b1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../007-fontconfig_2.11.0-6.7+b1_amd64.deb ... Unpacking fontconfig (2.11.0-6.7+b1) ... Selecting previously unselected package libxau6:amd64. 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Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Unpacking parallel (20161222-1) ... Selecting previously unselected package fasttree. Preparing to unpack .../203-fasttree_2.1.9-1_amd64.deb ... Unpacking fasttree (2.1.9-1) ... Selecting previously unselected package roary. Preparing to unpack .../204-roary_3.8.0+dfsg-1_all.deb ... Unpacking roary (3.8.0+dfsg-1) ... Setting up libquadmath0:amd64 (6.3.0-18+deb9u1) ... Setting up libncurses5:amd64 (6.0+20161126-1+deb9u2) ... Setting up libgomp1:amd64 (6.3.0-18+deb9u1) ... Setting up readline-common (7.0-3) ... Setting up prank (0.0.150803-2) ... Setting up perl-modules-5.24 (5.24.1-3+deb9u7) ... Setting up libgdbm3:amd64 (1.8.3-14) ... Setting up libperl5.24:amd64 (5.24.1-3+deb9u7) ... Setting up libnettle6:amd64 (3.3-1+b2) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u3) ... 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Setting up libpixman-1-0:amd64 (0.34.0-1) ... Setting up libblas3 (3.7.0-2) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libssh2-1:amd64 (1.7.0-1+deb9u1) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up fasttree (2.1.9-1) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up liburi-perl (1.71-1) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Setting up xz-utils (5.2.2-1.2+b1) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode Setting up libscalar-list-utils-perl (1:1.47-1) ... Setting up openssl (1.1.0l-1~deb9u1) ... Setting up mcl (1:14-137-1+b1) ... Setting up libfile-grep-perl (0.02-1) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up libio-string-perl (1.08-3) ... Setting up libalgorithm-diff-perl (1.19.03-1) ... Setting up libsensors4:amd64 (1:3.4.0-4) ... Setting up libnet-http-perl (6.12-1) ... Setting up libnumber-compare-perl (0.03-1) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up libtcl8.6:amd64 (8.6.6+dfsg-1+b1) ... Setting up libthai-data (0.1.26-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up libsub-uplevel-perl (0.2600-1) ... Setting up libparams-util-perl (1.07-3+b1) ... Setting up x11-common (1:7.7+19) ... 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 xdg-utils (1.1.1-1+deb9u2) ... Setting up libsub-name-perl (0.21-1) ... Setting up ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 126 added, 0 removed; done. Setting up libtext-csv-perl (1.33-2) ... Setting up libparams-classify-perl (0.013-6+b1) ... 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Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libtry-tiny-perl (0.28-1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up libpaper-utils (1.1.24+nmu5) ... Setting up fontconfig-config (2.11.0-6.7) ... Setting up liblog-log4perl-perl (1.48-1+deb9u1) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up sysstat (11.4.3-2) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up libclass-data-inheritable-perl (0.08-2) ... Setting up libbio-perl-perl (1.7.1-2) ... Setting up libfile-which-perl (1.21-1) ... Setting up libencode-locale-perl (1.05-1) ... Setting up libtimedate-perl (2.3000-2+deb9u1) ... Setting up libgraph-perl (1:0.96-2) ... Setting up perl-openssl-defaults:amd64 (3) ... Setting up libmodule-runtime-perl (0.014-2) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up libdevel-stacktrace-perl (2.0200-1) ... Setting up liblapack3 (3.7.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libtext-diff-perl (1.44-1) ... Setting up libtest-exception-perl (0.43-1) ... Setting up libglib2.0-0:amd64 (2.50.3-2+deb9u2) ... No schema files found: doing nothing. Setting up libcapture-tiny-perl (0.44-1) ... Setting up libio-html-perl (1.001-1) ... Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up libperlio-utf8-strict-perl (0.006-1+b2) ... Setting up libharfbuzz0b:amd64 (1.4.2-1) ... Setting up libthai0:amd64 (0.1.26-1) ... Setting up libmro-compat-perl (0.12-1) ... Setting up libtest-simple-perl (1.302075-1) ... Setting up libarray-utils-perl (0.5-1) ... Setting up libsub-identify-perl (0.12-2+b1) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u1) ... Setting up libxml-writer-perl (0.625-1) ... Setting up libtest-file-perl (1.442-1) ... Setting up libio-all-perl (0.86-2) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up libsub-exporter-perl (0.986-1) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up libhtml-parser-perl (3.72-3) ... Setting up bioperl (1.7.1-2) ... Setting up libdevel-globaldestruction-perl (0.14-1) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up libeval-closure-perl (0.14-1) ... Setting up libdist-checkconflicts-perl (0.11-1) ... Setting up libxcb1:amd64 (1.12-1) ... Setting up python (2.7.13-2) ... Setting up libfontconfig1:amd64 (2.11.0-6.7+b1) ... Setting up libsm6:amd64 (2:1.2.2-1+b3) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u1) ... Setting up parallel (20161222-1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libxcb-render0:amd64 (1.12-1) ... Setting up libtest-differences-perl (0.64-1) ... Setting up libmodule-implementation-perl (0.09-1) ... Setting up libexception-class-perl (1.42-1) ... Setting up libtest-files-perl (0.14-1) ... Setting up libnet-ssleay-perl (1.80-1) ... Setting up libtest-output-perl (1.03-1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up libx11-6:amd64 (2:1.6.4-3+deb9u1) ... Setting up libmodule-runtime-conflicts-perl (0.003-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up libio-socket-ssl-perl (2.044-1) ... Setting up libhtml-tree-perl (5.03-2) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Setting up libfile-listing-perl (6.04-1) ... Setting up libxcb-shm0:amd64 (1.12-1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libhttp-message-perl (6.11-1) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up libxft2:amd64 (2.3.2-1+b2) ... Setting up fontconfig (2.11.0-6.7+b1) ... Regenerating fonts cache... done. Setting up libhttp-negotiate-perl (6.00-2) ... Setting up libtest-most-perl (0.35-1) ... Setting up libpackage-stash-perl (0.37-1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libhttp-cookies-perl (6.01-1) ... Setting up libxss1:amd64 (1:1.2.2-1) ... Setting up ncbi-blast+ (2.6.0-1) ... Setting up libdevel-overloadinfo-perl (0.004-1) ... Setting up libclass-load-perl (0.23-1) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up libpackage-deprecationmanager-perl (0.17-1) ... Setting up libpango-1.0-0:amd64 (1.40.5-1) ... Setting up libclass-load-xs-perl (0.09-2+b1) ... Setting up libcairo2:amd64 (1.14.8-1) ... Setting up libcurl3:amd64 (7.52.1-5+deb9u10) ... Setting up libtk8.6:amd64 (8.6.6-1+b1) ... Setting up libmoose-perl (2.1807-1) ... Setting up libpangoft2-1.0-0:amd64 (1.40.5-1) ... Setting up libpangocairo-1.0-0:amd64 (1.40.5-1) ... Setting up r-base-core (3.3.3-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-littler (0.3.1-1) ... Setting up littler (0.3.1-1) ... Setting up r-cran-gtable (0.2.0-1) ... Setting up r-cran-assertthat (0.1-1) ... Setting up r-cran-rcolorbrewer (1.1-2-1) ... Setting up r-cran-stringi (1.1.2-1) ... Setting up r-cran-pkgkitten (0.1.4-1) ... Setting up r-cran-rcpp (0.12.9-1) ... Setting up r-cran-labeling (0.3-1) ... Setting up r-cran-colorspace (1.3-2-1) ... Setting up r-cran-mass (7.3-45-1) ... Setting up r-cran-plyr (1.8.4-1) ... Setting up r-cran-digest (0.6.11-1) ... Setting up r-cran-magrittr (1.5-3) ... Setting up r-cran-dichromat (2.0.0-3) ... Setting up r-cran-lazyeval (0.2.0-1) ... Setting up r-cran-stringr (1.1.0-1) ... Setting up r-cran-munsell (0.4.3-1) ... Setting up r-cran-reshape2 (1.4.2-1) ... Setting up r-cran-scales (0.4.1-1) ... Setting up r-cran-tibble (1.2-1) ... Setting up r-cran-ggplot2 (2.2.1-2) ... Setting up libwww-perl (6.15-1) ... Setting up liblwp-protocol-https-perl (6.06-2) ... Setting up libxml-parser-perl (2.44-2+b1) ... Setting up libgraph-readwrite-perl (2.09-1) ... Setting up roary (3.8.0+dfsg-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Processing triggers for ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', '-y', 'install', 'roary'] 0m27.7s INFO: Running scripts post_install 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_install_exceptions'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_install_exceptions'] 0m27.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m28.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m28.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpfk7gzh7f to stretch-backports 0m28.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main deb http://security.debian.org stretch/updates main deb http://deb.debian.org/debian/ stretch-backports main 0m28.5s INFO: Running scripts pre_distupgrade 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_distupgrade_exceptions'] 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_distupgrade_exceptions'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m28.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m28.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', 'update'] 0m29.9s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Get:2 http://security.debian.org stretch/updates InRelease [59.1 kB] Get:3 http://deb.debian.org/debian stretch-backports InRelease [78.5 kB] Hit:4 http://deb.debian.org/debian stretch Release Get:5 http://security.debian.org stretch/updates/main amd64 Packages [782 kB] Get:6 http://security.debian.org stretch/updates/main Translation-en [368 kB] Get:7 http://deb.debian.org/debian stretch-backports/main amd64 Packages [612 kB] Get:8 http://deb.debian.org/debian stretch-backports/main Translation-en [467 kB] Fetched 2367 kB in 0s (4144 kB/s) Reading package lists... 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', 'update'] 0m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', '-yf', 'dist-upgrade'] 0m41.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt ca-certificates debian-archive-keyring dpkg e2fslibs e2fsprogs gzip libapt-pkg5.0 libbsd0 libcairo2 libcomerr2 libcurl3 libexpat1 libfreetype6 libgcrypt20 libglib2.0-0 libgmp10 libgnutls30 libgssapi-krb5-2 libhogweed4 libicu57 libjpeg62-turbo libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblz4-1 liblzma5 libnettle6 libnghttp2-14 libp11-kit0 libpython2.7-minimal libpython2.7-stdlib libsasl2-2 libsasl2-modules-db libsqlite3-0 libss2 libssh2-1 libssl1.0.2 libssl1.1 libsystemd0 libtiff5 libudev1 libx11-6 libx11-data login openssl passwd python2.7 python2.7-minimal tar tzdata xz-utils zlib1g 55 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 34.7 MB of archives. After this operation, 103 kB of additional disk space will be used. Get:1 http://security.debian.org stretch/updates/main amd64 tar amd64 1.29b-1.1+deb9u1 [760 kB] Get:2 http://security.debian.org stretch/updates/main amd64 dpkg amd64 1.18.26 [2117 kB] Get:3 http://security.debian.org stretch/updates/main amd64 e2fslibs amd64 1.43.4-2+deb9u2 [208 kB] Get:4 http://security.debian.org stretch/updates/main amd64 e2fsprogs amd64 1.43.4-2+deb9u2 [948 kB] Get:5 http://security.debian.org stretch/updates/main amd64 gzip amd64 1.6-5+deb9u1 [114 kB] Get:6 http://security.debian.org stretch/updates/main amd64 login amd64 1:4.4-4.1+deb9u1 [790 kB] Get:7 http://security.debian.org stretch/updates/main amd64 debian-archive-keyring all 2017.5+deb9u2 [92.4 kB] Get:8 http://security.debian.org stretch/updates/main amd64 liblz4-1 amd64 0.0~r131-2+deb9u1 [33.2 kB] Get:9 http://security.debian.org stretch/updates/main amd64 liblzma5 amd64 5.2.2-1.2+deb9u1 [234 kB] Get:10 http://security.debian.org stretch/updates/main amd64 zlib1g amd64 1:1.2.8.dfsg-5+deb9u1 [87.8 kB] Get:11 http://security.debian.org stretch/updates/main amd64 libapt-pkg5.0 amd64 1.4.11 [917 kB] Get:12 http://security.debian.org stretch/updates/main amd64 apt amd64 1.4.11 [1232 kB] Get:13 http://security.debian.org stretch/updates/main amd64 libsystemd0 amd64 232-25+deb9u14 [282 kB] Get:14 http://security.debian.org stretch/updates/main amd64 python2.7 amd64 2.7.13-2+deb9u6 [286 kB] Get:15 http://security.debian.org stretch/updates/main amd64 libexpat1 amd64 2.2.0-2+deb9u5 [84.7 kB] Get:16 http://security.debian.org stretch/updates/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u3 [574 kB] Get:17 http://security.debian.org stretch/updates/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u6 [1360 kB] Get:18 http://security.debian.org stretch/updates/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u6 [1898 kB] Get:19 http://security.debian.org stretch/updates/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u6 [1382 kB] Get:20 http://security.debian.org stretch/updates/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u6 [390 kB] Get:21 http://security.debian.org stretch/updates/main amd64 libcomerr2 amd64 1.43.4-2+deb9u2 [63.8 kB] Get:22 http://security.debian.org stretch/updates/main amd64 libss2 amd64 1.43.4-2+deb9u2 [68.0 kB] Get:23 http://security.debian.org stretch/updates/main amd64 passwd amd64 1:4.4-4.1+deb9u1 [997 kB] Get:24 http://security.debian.org stretch/updates/main amd64 libudev1 amd64 232-25+deb9u14 [126 kB] Get:25 http://security.debian.org stretch/updates/main amd64 libgcrypt20 amd64 1.7.6-2+deb9u4 [523 kB] Get:26 http://security.debian.org stretch/updates/main amd64 tzdata all 2021a-0+deb9u4 [281 kB] Get:27 http://security.debian.org stretch/updates/main amd64 libssl1.0.2 amd64 1.0.2u-1~deb9u7 [1305 kB] Get:28 http://security.debian.org stretch/updates/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1+deb9u1 [253 kB] Get:29 http://security.debian.org stretch/updates/main amd64 libhogweed4 amd64 3.3-1+deb9u1 [136 kB] Get:30 http://security.debian.org stretch/updates/main amd64 libnettle6 amd64 3.3-1+deb9u1 [192 kB] Get:31 http://security.debian.org stretch/updates/main amd64 libp11-kit0 amd64 0.23.3-2+deb9u1 [112 kB] Get:32 http://security.debian.org stretch/updates/main amd64 libgnutls30 amd64 3.5.8-5+deb9u6 [897 kB] Get:33 http://security.debian.org stretch/updates/main amd64 libgssapi-krb5-2 amd64 1.15-1+deb9u3 [155 kB] Get:34 http://security.debian.org stretch/updates/main amd64 libkrb5-3 amd64 1.15-1+deb9u3 [312 kB] Get:35 http://security.debian.org stretch/updates/main amd64 libkrb5support0 amd64 1.15-1+deb9u3 [62.3 kB] Get:36 http://security.debian.org stretch/updates/main amd64 libk5crypto3 amd64 1.15-1+deb9u3 [120 kB] Get:37 http://security.debian.org stretch/updates/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u2 [68.5 kB] Get:38 http://security.debian.org stretch/updates/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u2 [105 kB] Get:39 http://security.debian.org stretch/updates/main amd64 libldap-common all 2.4.44+dfsg-5+deb9u9 [86.3 kB] Get:40 http://security.debian.org stretch/updates/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u9 [220 kB] Get:41 http://security.debian.org stretch/updates/main amd64 xz-utils amd64 5.2.2-1.2+deb9u1 [266 kB] Get:42 http://security.debian.org stretch/updates/main amd64 openssl amd64 1.1.0l-1~deb9u6 [749 kB] Get:43 http://security.debian.org stretch/updates/main amd64 ca-certificates all 20200601~deb9u2 [168 kB] Get:44 http://security.debian.org stretch/updates/main amd64 libbsd0 amd64 0.8.3-1+deb9u1 [82.9 kB] Get:45 http://security.debian.org stretch/updates/main amd64 libfreetype6 amd64 2.6.3-3.2+deb9u2 [438 kB] Get:46 http://security.debian.org stretch/updates/main amd64 libx11-data all 2:1.6.4-3+deb9u4 [291 kB] Get:47 http://security.debian.org stretch/updates/main amd64 libx11-6 amd64 2:1.6.4-3+deb9u4 [748 kB] Get:48 http://security.debian.org stretch/updates/main amd64 libcairo2 amd64 1.14.8-1+deb9u1 [771 kB] Get:49 http://security.debian.org stretch/updates/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u2 [79.4 kB] Get:50 http://security.debian.org stretch/updates/main amd64 libssh2-1 amd64 1.7.0-1+deb9u2 [139 kB] Get:51 http://security.debian.org stretch/updates/main amd64 libcurl3 amd64 7.52.1-5+deb9u16 [298 kB] Get:52 http://security.debian.org stretch/updates/main amd64 libglib2.0-0 amd64 2.50.3-2+deb9u3 [2693 kB] Get:53 http://security.debian.org stretch/updates/main amd64 libicu57 amd64 57.1-6+deb9u5 [7700 kB] Get:54 http://security.debian.org stretch/updates/main amd64 libjpeg62-turbo amd64 1:1.5.1-2+deb9u2 [134 kB] Get:55 http://security.debian.org stretch/updates/main amd64 libtiff5 amd64 4.0.8-2+deb9u8 [239 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 34.7 MB in 0s (90.1 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 ... 18766 files and directories currently installed.) Preparing to unpack .../tar_1.29b-1.1+deb9u1_amd64.deb ... Unpacking tar (1.29b-1.1+deb9u1) over (1.29b-1.1) ... Setting up tar (1.29b-1.1+deb9u1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18766 files and directories currently installed.) Preparing to unpack .../gzip_1.6-5+deb9u1_amd64.deb ... Unpacking gzip (1.6-5+deb9u1) over (1.6-5+b1) ... Setting up gzip (1.6-5+deb9u1) ... (Reading database ... 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Unpacking libtiff5:amd64 (4.0.8-2+deb9u8) over (4.0.8-2+deb9u5) ... Setting up libnettle6:amd64 (3.3-1+deb9u1) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u5) ... Setting up libjpeg62-turbo:amd64 (1:1.5.1-2+deb9u2) ... Setting up libnghttp2-14:amd64 (1.18.1-1+deb9u2) ... Processing triggers for mime-support (3.60) ... Setting up libldap-common (2.4.44+dfsg-5+deb9u9) ... Setting up tzdata (2021a-0+deb9u4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Apr 3 10:48:43 UTC 2023. Universal Time is now: Mon Apr 3 10:48:43 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libglib2.0-0:amd64 (2.50.3-2+deb9u3) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Setting up libtiff5:amd64 (4.0.8-2+deb9u8) ... Setting up libicu57:amd64 (57.1-6+deb9u5) ... Setting up libbsd0:amd64 (0.8.3-1+deb9u1) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u3) ... Setting up libfreetype6:amd64 (2.6.3-3.2+deb9u2) ... Setting up libssl1.0.2:amd64 (1.0.2u-1~deb9u7) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) ... Setting up libssh2-1:amd64 (1.7.0-1+deb9u2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u6) ... Setting up xz-utils (5.2.2-1.2+deb9u1) ... Setting up libp11-kit0:amd64 (0.23.3-2+deb9u1) ... Setting up openssl (1.1.0l-1~deb9u6) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u3) ... Setting up libpython2.7-minimal:amd64 (2.7.13-2+deb9u6) ... Setting up ca-certificates (20200601~deb9u2) ... Updating certificates in /etc/ssl/certs... 11 added, 0 removed; done. Setting up libx11-data (2:1.6.4-3+deb9u4) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u6) ... Setting up python2.7-minimal (2.7.13-2+deb9u6) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u3) ... Setting up libx11-6:amd64 (2:1.6.4-3+deb9u4) ... Setting up python2.7 (2.7.13-2+deb9u6) ... Setting up libhogweed4:amd64 (3.3-1+deb9u1) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u3) ... Setting up libcairo2:amd64 (1.14.8-1+deb9u1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u6) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u9) ... Setting up libcurl3:amd64 (7.52.1-5+deb9u16) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Processing triggers for ca-certificates (20200601~deb9u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', '-yf', 'dist-upgrade'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m41.9s DUMP: 46096da5bf28ec6e6c755045e954a64e - 0m41.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m41.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m42.2s DUMP: Package: roary Version: 3.8.0+dfsg-1 Installed-Size: 634 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl, libarray-utils-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_3.8.0+dfsg-1_all.deb Size: 170134 MD5sum: d2b5bd8c3cf60d6fabc08169c52a4d40 SHA256: 062eece678b4556ee0de3961c4789d1b51e2e860d582d72e19aedd6f8beef3db 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m42.2s INFO: apt-cache knows about the following packages: roary 0m42.2s INFO: Running scripts pre_install 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_database-server'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_database-server'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_exceptions'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_exceptions'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_extras'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_extras'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'policy'] 0m42.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 100 http://deb.debian.org/debian stretch-backports/main amd64 Packages release o=Debian Backports,a=stretch-backports,n=stretch-backports,l=Debian Backports,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org stretch/updates/main amd64 Packages release v=9,o=Debian,a=oldoldstable,n=stretch,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'policy'] 0m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'policy', 'roary'] 0m42.4s DUMP: roary: Installed: 3.8.0+dfsg-1 Candidate: 3.8.0+dfsg-1 Version table: 3.12.0+dfsg-2~bpo9+1 100 100 http://deb.debian.org/debian stretch-backports/main amd64 Packages *** 3.8.0+dfsg-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'policy', 'roary'] 0m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', '-y', '-t', 'stretch-backports', 'install', 'roary'] 0m43.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libdigest-md5-file-perl The following NEW packages will be installed: libdigest-md5-file-perl The following packages will be upgraded: roary 1 upgraded, 1 newly installed, 0 to remove and 24 not upgraded. Need to get 187 kB of archives. After this operation, 96.3 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 libdigest-md5-file-perl all 0.08-1 [10.6 kB] Get:2 http://deb.debian.org/debian stretch-backports/main amd64 roary all 3.12.0+dfsg-2~bpo9+1 [176 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 187 kB in 0s (3462 kB/s) Selecting previously unselected package libdigest-md5-file-perl. (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 ... 18777 files and directories currently installed.) Preparing to unpack .../libdigest-md5-file-perl_0.08-1_all.deb ... Unpacking libdigest-md5-file-perl (0.08-1) ... Preparing to unpack .../roary_3.12.0+dfsg-2~bpo9+1_all.deb ... Unpacking roary (3.12.0+dfsg-2~bpo9+1) over (3.8.0+dfsg-1) ... Setting up libdigest-md5-file-perl (0.08-1) ... Setting up roary (3.12.0+dfsg-2~bpo9+1) ... 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', '-y', '-t', 'stretch-backports', 'install', 'roary'] 0m43.2s INFO: Running scripts post_install 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_install_exceptions'] 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_install_exceptions'] 0m43.2s INFO: Running scripts post_distupgrade 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_distupgrade_exceptions'] 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_distupgrade_exceptions'] 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_distupgrade_zz_backports'] 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_distupgrade_zz_backports'] 0m43.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m44.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m44.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m44.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m44.9s INFO: Running scripts pre_install 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_database-server'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_database-server'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_exceptions'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_exceptions'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_extras'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_extras'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_foreign_architecture'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_foreign_architecture'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'policy'] 0m45.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 100 http://deb.debian.org/debian stretch-backports/main amd64 Packages release o=Debian Backports,a=stretch-backports,n=stretch-backports,l=Debian Backports,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org stretch/updates/main amd64 Packages release v=9,o=Debian,a=oldoldstable,n=stretch,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'policy'] 0m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'policy', 'roary'] 0m45.1s DUMP: roary: Installed: 3.12.0+dfsg-2~bpo9+1 Candidate: 3.12.0+dfsg-2~bpo9+1 Version table: *** 3.12.0+dfsg-2~bpo9+1 100 100 http://deb.debian.org/debian stretch-backports/main amd64 Packages 100 /var/lib/dpkg/status 3.8.0+dfsg-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m45.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-cache', 'policy', 'roary'] 0m45.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', '-y', '-t', 'stretch-backports', 'install', 'roary=3.12.0+dfsg-2~bpo9+1'] 0m45.3s DUMP: Reading package lists... Building dependency tree... Reading state information... roary is already the newest version (3.12.0+dfsg-2~bpo9+1). 0 upgraded, 0 newly installed, 0 to remove and 24 not upgraded. 0m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', '-y', '-t', 'stretch-backports', 'install', 'roary=3.12.0+dfsg-2~bpo9+1'] 0m45.3s INFO: Running scripts post_install 0m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_install_exceptions'] 0m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_install_exceptions'] 0m45.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m46.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m47.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', '-ac', '--ignore-obsolete'] 0m48.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', '-ac', '--ignore-obsolete'] 0m48.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m48.9s DUMP: 0.15.6 0m48.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m48.9s INFO: Running adequate version 0.15.6 now. 0m48.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'roary'] 0m49.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'roary'] 0m49.0s INFO: Running scripts pre_remove 0m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m49.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_remove_exceptions'] 0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/pre_remove_exceptions'] 0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m51.7s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.11 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bedtools bedtools 2.26.0+dfsg-3 install ok installed bioperl bioperl 1.7.1-2 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed ca-certificates ca-certificates 20200601~deb9u2 install ok installed cd-hit cd-hit 4.6.6-2 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u2 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.26 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u2 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u2 install ok installed fasttree fasttree 2.1.9-1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed fontconfig fontconfig 2.11.0-6.7+b1 install ok installed fontconfig-config fontconfig-config 2.11.0-6.7 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-1 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+deb9u1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libalgorithm-c3-perl libalgorithm-c3-perl 0.10-1 install ok installed libalgorithm-diff-perl libalgorithm-diff-perl 1.19.03-1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.11 install ok installed libarray-utils-perl libarray-utils-perl 0.5-1 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libbio-perl-perl libbio-perl-perl 1.7.1-2 install ok installed libblas-common libblas-common 3.7.0-2 install ok installed libblas3 libblas3 3.7.0-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbsd0:amd64 libbsd0 0.8.3-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcairo2:amd64 libcairo2 1.14.8-1+deb9u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcapture-tiny-perl libcapture-tiny-perl 0.44-1 install ok installed libclass-c3-perl libclass-c3-perl 0.32-1 install ok installed libclass-data-inheritable-perl libclass-data-inheritable-perl 0.08-2 install ok installed libclass-load-perl libclass-load-perl 0.23-1 install ok installed libclass-load-xs-perl libclass-load-xs-perl 0.09-2+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u2 install ok installed libcurl3:amd64 libcurl3 7.52.1-5+deb9u16 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 0.2.10-4+b1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libdevel-globaldestruction-perl libdevel-globaldestruction-perl 0.14-1 install ok installed libdevel-overloadinfo-perl libdevel-overloadinfo-perl 0.004-1 install ok installed libdevel-stacktrace-perl libdevel-stacktrace-perl 2.0200-1 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 libencode-locale-perl libencode-locale-perl 1.05-1 install ok installed libenv-path-perl libenv-path-perl 0.19-1 install ok installed libeval-closure-perl libeval-closure-perl 0.14-1 install ok installed libexception-class-perl libexception-class-perl 1.42-1 install ok installed libexpat1:amd64 libexpat1 2.2.0-2+deb9u5 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libffi6:amd64 libffi6 3.2.1-6 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-1 install ok installed libfile-grep-perl libfile-grep-perl 0.02-1 install ok installed libfile-listing-perl libfile-listing-perl 6.04-1 install ok installed libfile-slurper-perl libfile-slurper-perl 0.009-1 install ok installed libfile-which-perl libfile-which-perl 1.21-1 install ok installed libfindbin-libs-perl libfindbin-libs-perl 2.150-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.11.0-6.7+b1 install ok installed libfreetype6:amd64 libfreetype6 2.6.3-3.2+deb9u2 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u4 install ok installed libgdbm3:amd64 libgdbm3 1.8.3-14 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.50.3-2+deb9u3 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-1+deb9u1 install ok installed libgnutls30:amd64 libgnutls30 3.5.8-5+deb9u6 install ok installed libgomp1:amd64 libgomp1 6.3.0-18+deb9u1 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed libgraph-perl libgraph-perl 1:0.96-2 install ok installed libgraph-readwrite-perl libgraph-readwrite-perl 2.09-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.10-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.15-1+deb9u3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 1.4.2-1 install ok installed libhogweed4:amd64 libhogweed4 3.3-1+deb9u1 install ok installed libhtml-parser-perl libhtml-parser-perl 3.72-3 install ok installed libhtml-tagset-perl libhtml-tagset-perl 3.20-3 install ok installed libhtml-tree-perl libhtml-tree-perl 5.03-2 install ok installed libhttp-cookies-perl libhttp-cookies-perl 6.01-1 install ok installed libhttp-date-perl libhttp-date-perl 6.02-1 install ok installed libhttp-message-perl libhttp-message-perl 6.11-1 install ok installed libhttp-negotiate-perl libhttp-negotiate-perl 6.00-2 install ok installed libice6:amd64 libice6 2:1.0.9-2 install ok installed libicu57:amd64 libicu57 57.1-6+deb9u5 install ok installed libidn11:amd64 libidn11 1.33-1+deb9u1 install ok installed libidn2-0:amd64 libidn2-0 0.16-1+deb9u1 install ok installed libio-all-perl libio-all-perl 0.86-2 install ok installed libio-html-perl libio-html-perl 1.001-1 install ok installed libio-socket-ssl-perl libio-socket-ssl-perl 2.044-1 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 1:1.5.1-2+deb9u2 install ok installed libk5crypto3:amd64 libk5crypto3 1.15-1+deb9u3 install ok installed libkeyutils1:amd64 libkeyutils1 1.5.9-9 install ok installed libkrb5-3:amd64 libkrb5-3 1.15-1+deb9u3 install ok installed libkrb5support0:amd64 libkrb5support0 1.15-1+deb9u3 install ok installed liblapack3 liblapack3 3.7.0-2 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.44+dfsg-5+deb9u9 install ok installed libldap-common libldap-common 2.4.44+dfsg-5+deb9u9 install ok installed liblog-log4perl-perl liblog-log4perl-perl 1.48-1+deb9u1 install ok installed liblwp-mediatypes-perl liblwp-mediatypes-perl 6.02-1 install ok installed liblwp-protocol-https-perl liblwp-protocol-https-perl 6.06-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+deb9u1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+deb9u1 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 0.014-2 install ok installed libmoose-perl libmoose-perl 2.1807-1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libmro-compat-perl libmro-compat-perl 0.12-1 install ok installed libncurses5:amd64 libncurses5 6.0+20161126-1+deb9u2 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libnet-http-perl libnet-http-perl 6.12-1 install ok installed libnet-ssleay-perl libnet-ssleay-perl 1.80-1 install ok installed libnettle6:amd64 libnettle6 3.3-1+deb9u1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.18.1-1+deb9u2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.3-2+deb9u1 install ok installed libpackage-deprecationmanager-perl libpackage-deprecationmanager-perl 0.17-1 install ok installed libpackage-stash-perl libpackage-stash-perl 0.37-1 install ok installed libpackage-stash-xs-perl libpackage-stash-xs-perl 0.28-3+b1 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.40.5-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.40.5-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.40.5-1 install ok installed libpaper-utils libpaper-utils 1.1.24+nmu5 install ok installed libpaper1:amd64 libpaper1 1.1.24+nmu5 install ok installed libparams-classify-perl libparams-classify-perl 0.013-6+b1 install ok installed libparams-util-perl libparams-util-perl 1.07-3+b1 install ok installed libparse-yapp-perl libparse-yapp-perl 1.05-12 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libperl5.24:amd64 libperl5.24 5.24.1-3+deb9u7 install ok installed libperlio-utf8-strict-perl libperlio-utf8-strict-perl 0.006-1+b2 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.34.0-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.28-1+deb9u1 install ok installed libprocps6:amd64 libprocps6 2:3.3.12-3+deb9u1 install ok installed libpsl5:amd64 libpsl5 0.17.0-3 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.13-2 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.13-2+deb9u6 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.13-2+deb9u6 install ok installed libquadmath0:amd64 libquadmath0 6.3.0-18+deb9u1 install ok installed libreadline7:amd64 libreadline7 7.0-3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-1+b1 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27~101-g0780600+dfsg-3+deb9u2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27~101-g0780600+dfsg-3+deb9u2 install ok installed libscalar-list-utils-perl libscalar-list-utils-perl 1:1.47-1 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsensors4:amd64 libsensors4 1:3.4.0-4 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsm6:amd64 libsm6 2:1.2.2-1+b3 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libspiffy-perl libspiffy-perl 0.41-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.16.2-5+deb9u3 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u2 install ok installed libssh2-1:amd64 libssh2-1 1.7.0-1+deb9u2 install ok installed libssl1.0.2:amd64 libssl1.0.2 1.0.2u-1~deb9u7 install ok installed libssl1.1:amd64 libssl1.1 1.1.0l-1~deb9u6 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsub-exporter-perl libsub-exporter-perl 0.986-1 install ok installed libsub-exporter-progressive-perl libsub-exporter-progressive-perl 0.001013-1 install ok installed libsub-identify-perl libsub-identify-perl 0.12-2+b1 install ok installed libsub-install-perl libsub-install-perl 0.928-1 install ok installed libsub-name-perl libsub-name-perl 0.21-1 install ok installed libsub-uplevel-perl libsub-uplevel-perl 0.2600-1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u14 install ok installed libtasn1-6:amd64 libtasn1-6 4.10-1.1+deb9u1 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.6+dfsg-1+b1 install ok installed libtest-deep-perl libtest-deep-perl 1.126-1 install ok installed libtest-differences-perl libtest-differences-perl 0.64-1 install ok installed libtest-exception-perl libtest-exception-perl 0.43-1 install ok installed libtest-file-perl libtest-file-perl 1.442-1 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 1.03-1 install ok installed libtest-simple-perl libtest-simple-perl 1.302075-1 install ok installed libtest-warn-perl libtest-warn-perl 0.32-1 install ok installed libtext-csv-perl libtext-csv-perl 1.33-2 install ok installed libtext-diff-perl libtext-diff-perl 1.44-1 install ok installed libtext-glob-perl libtext-glob-perl 0.10-1 install ok installed libthai-data libthai-data 0.1.26-1 install ok installed libthai0:amd64 libthai0 0.1.26-1 install ok installed libtiff5:amd64 libtiff5 4.0.8-2+deb9u8 install ok installed libtimedate-perl libtimedate-perl 2.3000-2+deb9u1 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libtk8.6:amd64 libtk8.6 8.6.6-1+b1 install ok installed libtry-tiny-perl libtry-tiny-perl 0.28-1 install ok installed libudev1:amd64 libudev1 232-25+deb9u14 install ok installed libunistring0:amd64 libunistring0 0.9.6+really0.9.3-0.1 install ok installed liburi-perl liburi-perl 1.71-1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed libwww-perl libwww-perl 6.15-1 install ok installed libwww-robotrules-perl libwww-robotrules-perl 6.01-1 install ok installed libx11-6:amd64 libx11-6 2:1.6.4-3+deb9u4 install ok installed libx11-data libx11-data 2:1.6.4-3+deb9u4 install ok installed libxau6:amd64 libxau6 1:1.0.8-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.12-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.12-1 install ok installed libxcb1:amd64 libxcb1 1.12-1 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 2.3.2-1+b2 install ok installed libxml-parser-perl libxml-parser-perl 2.44-2+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 1:1.2.2-1 install ok installed libxt6:amd64 libxt6 1:1.1.5-1 install ok installed littler littler 0.3.1-1 install ok installed login login 1:4.4-4.1+deb9u1 install ok installed lsb-base lsb-base 9.20161125 install ok installed mafft mafft 7.307-1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mcl mcl 1:14-137-1+b1 install ok installed mime-support mime-support 3.60 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncbi-blast+ ncbi-blast+ 2.6.0-1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-0+deb9u1 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed netbase netbase 5.4 install ok installed openssl openssl 1.1.0l-1~deb9u6 install ok installed parallel parallel 20161222-1 install ok installed passwd passwd 1:4.4-4.1+deb9u1 install ok installed perl perl 5.24.1-3+deb9u7 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed perl-modules-5.24 perl-modules-5.24 5.24.1-3+deb9u7 install ok installed perl-openssl-defaults:amd64 perl-openssl-defaults 3 install ok installed prank prank 0.0.150803-2 install ok installed procps procps 2:3.3.12-3+deb9u1 install ok installed python python 2.7.13-2 install ok installed python-minimal python-minimal 2.7.13-2 install ok installed python2.7 python2.7 2.7.13-2+deb9u6 install ok installed python2.7-minimal python2.7-minimal 2.7.13-2+deb9u6 install ok installed r-base-core r-base-core 3.3.3-1 install ok installed r-cran-assertthat r-cran-assertthat 0.1-1 install ok installed r-cran-colorspace r-cran-colorspace 1.3-2-1 install ok installed r-cran-dichromat r-cran-dichromat 2.0.0-3 install ok installed r-cran-digest r-cran-digest 0.6.11-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 2.2.1-2 install ok installed r-cran-gtable r-cran-gtable 0.2.0-1 install ok installed r-cran-labeling r-cran-labeling 0.3-1 install ok installed r-cran-lazyeval r-cran-lazyeval 0.2.0-1 install ok installed r-cran-littler r-cran-littler 0.3.1-1 install ok installed r-cran-magrittr r-cran-magrittr 1.5-3 install ok installed r-cran-mass r-cran-mass 7.3-45-1 install ok installed r-cran-munsell r-cran-munsell 0.4.3-1 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.1.4-1 install ok installed r-cran-plyr r-cran-plyr 1.8.4-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-2-1 install ok installed r-cran-rcpp r-cran-rcpp 0.12.9-1 install ok installed r-cran-reshape2 r-cran-reshape2 1.4.2-1 install ok installed r-cran-scales r-cran-scales 0.4.1-1 install ok installed r-cran-stringi r-cran-stringi 1.1.2-1 install ok installed r-cran-stringr r-cran-stringr 1.1.0-1 install ok installed r-cran-tibble r-cran-tibble 1.2-1 install ok installed readline-common readline-common 7.0-3 install ok installed roary roary 3.12.0+dfsg-2~bpo9+1 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysstat sysstat 11.4.3-2 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1+deb9u1 install ok installed tzdata tzdata 2021a-0+deb9u4 install ok installed ucf ucf 3.0036 install ok installed unzip unzip 6.0-21+deb9u2 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed x11-common x11-common 1:7.7+19 install ok installed xdg-utils xdg-utils 1.1.1-1+deb9u2 install ok installed xz-utils xz-utils 5.2.2-1.2+deb9u1 install ok installed zip zip 3.0-11+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5+deb9u1 0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', 'remove', 'bedtools', 'bioperl', 'ca-certificates', 'cd-hit', 'fasttree', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libarray-utils-perl', 'libbio-perl-perl', 'libblas-common', 'libblas3', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libcurl3:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libffi6:amd64', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdbm3:amd64', 'libgfortran3:amd64', 'libglib2.0-0:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhogweed4:amd64', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu57:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl', 'libmro-compat-perl', 'libncurses5:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnumber-compare-perl', 'libp11-kit0:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparams-util-perl', 'libparse-yapp-perl', 'libperl5.24:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps6:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libscalar-list-utils-perl', 'libsensors4:amd64', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl', 'libsub-uplevel-perl', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-simple-perl', 'libtest-warn-perl', 'libtext-csv-perl', 'libtext-diff-perl', 'libtext-glob-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtimedate-perl', 'libtk8.6:amd64', 'libtry-tiny-perl', 'libunistring0:amd64', 'liburi-perl', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'littler', 'lsb-base', 'mafft', 'mcl', 'mime-support', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.24', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python', 'python-minimal', 'python2.7', 'python2.7-minimal', 'r-base-core', 'r-cran-assertthat', 'r-cran-colorspace', 'r-cran-dichromat', 'r-cran-digest', 'r-cran-ggplot2', 'r-cran-gtable', 'r-cran-labeling', 'r-cran-lazyeval', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-munsell', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-reshape2', 'r-cran-scales', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-tibble', 'readline-common', 'sysstat', 'tzdata', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip', 'roary'] 0m53.9s 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 libbio-perl-perl libblas-common libblas3 libbsd0 libcairo2 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libcurl3 libdata-optlist-perl libdata-stag-perl libdatrie1 libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdigest-md5-file-perl libdist-checkconflicts-perl libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libffi6 libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-slurper-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libgdbm3 libgfortran3 libglib2.0-0 libgmp10 libgnutls30 libgomp1 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhogweed4 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu57 libidn11 libidn2-0 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 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncurses5 libnet-http-perl libnet-ssleay-perl libnettle6 libnghttp2-14 libnumber-compare-perl libp11-kit0 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 libperl5.24 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16 libprocps6 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libscalar-list-utils-perl libsensors4 libsm6 libspiffy-perl libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-uplevel-perl libtasn1-6 libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-simple-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl libunistring0 liburi-perl 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 lsb-base mafft mcl mime-support ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.24 perl-openssl-defaults prank procps python python-minimal python2.7 python2.7-minimal r-base-core r-cran-assertthat r-cran-colorspace r-cran-dichromat r-cran-digest r-cran-ggplot2 r-cran-gtable r-cran-labeling r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-munsell r-cran-pkgkitten r-cran-plyr r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble readline-common roary sysstat tzdata ucf unzip x11-common xdg-utils xz-utils zip 0 upgraded, 0 newly installed, 223 to remove and 0 not upgraded. After this operation, 328 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 ... 18792 files and directories currently installed.) Removing roary (3.12.0+dfsg-2~bpo9+1) ... Removing bedtools (2.26.0+dfsg-3) ... Removing bioperl (1.7.1-2) ... Removing r-cran-ggplot2 (2.2.1-2) ... Removing r-cran-scales (0.4.1-1) ... Removing r-cran-tibble (1.2-1) ... Removing r-cran-reshape2 (1.4.2-1) ... Removing r-cran-stringr (1.1.0-1) ... Removing r-cran-stringi (1.1.2-1) ... Removing libgraph-readwrite-perl (2.09-1) ... Removing libxml-parser-perl (2.44-2+b1) ... Removing cd-hit (4.6.6-2) ... Removing fasttree (2.1.9-1) ... Removing libmoose-perl (2.1807-1) ... Removing libdevel-overloadinfo-perl (0.004-1) ... Removing libmro-compat-perl (0.12-1) ... Removing libclass-c3-perl (0.32-1) ... 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 (0.64-1) ... Removing libtext-diff-perl (1.44-1) ... Removing libalgorithm-diff-perl (1.19.03-1) ... Removing libarray-utils-perl (0.5-1) ... Removing libbio-perl-perl (1.7.1-2) ... Removing littler (0.3.1-1) ... Removing libtest-output-perl (1.03-1) ... Removing libcapture-tiny-perl (0.44-1) ... Removing libexception-class-perl (1.42-1) ... Removing libclass-data-inheritable-perl (0.08-2) ... Removing libclass-load-xs-perl (0.09-2+b1) ... Removing libclass-load-perl (0.23-1) ... Removing libeval-closure-perl (0.14-1) ... Removing libsub-exporter-perl (0.986-1) ... 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 (2.0200-1) ... Removing libdigest-md5-file-perl (0.08-1) ... Removing libmodule-runtime-conflicts-perl (0.003-1) ... Removing libdist-checkconflicts-perl (0.11-1) ... Removing libenv-path-perl (0.19-1) ... Removing ncbi-blast+ (2.6.0-1) ... Removing python (2.7.13-2) ... Removing python2.7 (2.7.13-2+deb9u6) ... Removing libpython-stdlib:amd64 (2.7.13-2) ... Removing libpython2.7-stdlib:amd64 (2.7.13-2+deb9u6) ... Removing libfile-find-rule-perl (0.34-1) ... Removing libfile-grep-perl (0.02-1) ... Removing libfile-slurper-perl (0.009-1) ... Removing libfile-which-perl (1.21-1) ... Removing libfindbin-libs-perl (2.150-1) ... Removing libtest-simple-perl (1.302075-1) ... Removing parallel (20161222-1) ... 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 libxml-writer-perl (0.625-1) ... Removing mafft (7.307-1) ... Removing libgraph-perl (1:0.96-2) ... Removing libio-all-perl (0.86-2) ... Removing libio-string-perl (1.08-3) ... Removing liblog-log4perl-perl (1.48-1+deb9u1) ... Removing libpackage-deprecationmanager-perl (0.17-1) ... Removing libpackage-stash-perl (0.37-1) ... Removing libmodule-implementation-perl (0.09-1) ... Removing libmodule-runtime-perl (0.014-2) ... Removing procps (2:3.3.12-3+deb9u1) ... Removing libncurses5:amd64 (6.0+20161126-1+deb9u2) ... Removing libnumber-compare-perl (0.03-1) ... Removing libpackage-stash-xs-perl (0.28-3+b1) ... Removing libparams-classify-perl (0.013-6+b1) ... Removing libparams-util-perl (1.07-3+b1) ... Removing libparse-yapp-perl (1.05-12) ... Removing libperlio-utf8-strict-perl (0.006-1+b2) ... Removing libprocps6:amd64 (2:3.3.12-3+deb9u1) ... Removing python-minimal (2.7.13-2) ... Removing python2.7-minimal (2.7.13-2+deb9u6) ... Removing libpython2.7-minimal:amd64 (2.7.13-2+deb9u6) ... Removing libspiffy-perl (0.41-1) ... Removing libscalar-list-utils-perl (1:1.47-1) ... Removing sysstat (11.4.3-2) ... Removing libsensors4:amd64 (1:3.4.0-4) ... Removing libsqlite3-0:amd64 (3.16.2-5+deb9u3) ... Removing libsub-exporter-progressive-perl (0.001013-1) ... Removing libsub-identify-perl (0.12-2+b1) ... Removing libsub-install-perl (0.928-1) ... Removing libsub-name-perl (0.21-1) ... Removing libtest-warn-perl (0.32-1) ... Removing libtest-exception-perl (0.43-1) ... Removing libsub-uplevel-perl (0.2600-1) ... Removing libtest-deep-perl (1.126-1) ... Removing libtest-file-perl (1.442-1) ... Removing libtext-csv-perl (1.33-2) ... Removing libtext-glob-perl (0.10-1) ... Removing libtry-tiny-perl (0.28-1) ... Removing mcl (1:14-137-1+b1) ... Removing mime-support (3.60) ... Removing ncbi-data (6.1.20170106+dfsg1-0+deb9u1) ... Removing prank (0.0.150803-2) ... Removing r-cran-assertthat (0.1-1) ... Removing r-cran-munsell (0.4.3-1) ... Removing r-cran-colorspace (1.3-2-1) ... Removing r-cran-dichromat (2.0.0-3) ... Removing r-cran-digest (0.6.11-1) ... Removing r-cran-gtable (0.2.0-1) ... Removing r-cran-labeling (0.3-1) ... Removing r-cran-lazyeval (0.2.0-1) ... Removing r-cran-magrittr (1.5-3) ... Removing r-cran-mass (7.3-45-1) ... Removing r-cran-plyr (1.8.4-1) ... Removing r-cran-rcolorbrewer (1.1-2-1) ... Removing xz-utils (5.2.2-1.2+deb9u1) ... Removing r-cran-rcpp (0.12.9-1) ... Removing r-cran-littler (0.3.1-1) ... Removing r-cran-pkgkitten (0.1.4-1) ... Removing r-base-core (3.3.3-1) ... Removing libpangocairo-1.0-0:amd64 (1.40.5-1) ... Removing libpangoft2-1.0-0:amd64 (1.40.5-1) ... Removing libpango-1.0-0:amd64 (1.40.5-1) ... Removing fontconfig (2.11.0-6.7+b1) ... Removing libcairo2:amd64 (1.14.8-1+deb9u1) ... Removing libtk8.6:amd64 (8.6.6-1+b1) ... Removing libxft2:amd64 (2.3.2-1+b2) ... Removing libfontconfig1:amd64 (2.11.0-6.7+b1) ... Removing fontconfig-config (2.11.0-6.7) ... Removing fonts-dejavu-core (2.37-1) ... Removing liblapack3 (3.7.0-2) ... Removing libblas3 (3.7.0-2) ... Removing libblas-common (3.7.0-2) ... Removing libxt6:amd64 (1:1.1.5-1) ... Removing libxcb-shm0:amd64 (1.12-1) ... Removing libsm6:amd64 (2:1.2.2-1+b3) ... Removing libice6:amd64 (2:1.0.9-2) ... Removing libcurl3:amd64 (7.52.1-5+deb9u16) ... Removing libthai0:amd64 (0.1.26-1) ... Removing libdatrie1:amd64 (0.2.10-4+b1) ... Removing libexpat1:amd64 (2.2.0-2+deb9u5) ... Removing libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u9) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Removing libgnutls30:amd64 (3.5.8-5+deb9u6) ... Removing libp11-kit0:amd64 (0.23.3-2+deb9u1) ... Removing libharfbuzz0b:amd64 (1.4.2-1) ... Removing libglib2.0-0:amd64 (2.50.3-2+deb9u3) ... Removing libffi6:amd64 (3.2.1-6) ... Removing libfreetype6:amd64 (2.6.3-3.2+deb9u2) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libhogweed4:amd64 (3.3-1+deb9u1) ... Removing libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) ... Removing libgomp1:amd64 (6.3.0-18+deb9u1) ... Removing libgraphite2-3:amd64 (1.3.10-1) ... Removing libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... Removing libicu57:amd64 (57.1-6+deb9u5) ... Removing libidn11:amd64 (1.33-1+deb9u1) ... Removing libpsl5:amd64 (0.17.0-3) ... Removing libidn2-0:amd64 (0.16-1+deb9u1) ... Removing libtiff5:amd64 (4.0.8-2+deb9u8) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:1.5.1-2+deb9u2) ... Removing libkrb5-3:amd64 (1.15-1+deb9u3) ... Removing libk5crypto3:amd64 (1.15-1+deb9u3) ... Removing libkrb5support0:amd64 (1.15-1+deb9u3) ... Removing libkeyutils1:amd64 (1.5.9-9) ... Removing libldap-common (2.4.44+dfsg-5+deb9u9) ... Removing libnettle6:amd64 (3.3-1+deb9u1) ... Removing libnghttp2-14:amd64 (1.18.1-1+deb9u2) ... Removing libpaper-utils (1.1.24+nmu5) ... Removing libpaper1:amd64 (1.1.24+nmu5) ... Removing libpixman-1-0:amd64 (0.34.0-1) ... Removing libpng16-16:amd64 (1.6.28-1+deb9u1) ... Removing libquadmath0:amd64 (6.3.0-18+deb9u1) ... Removing libreadline7:amd64 (7.0-3) ... Removing libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Removing libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Removing libssh2-1:amd64 (1.7.0-1+deb9u2) ... Removing libssl1.0.2:amd64 (1.0.2u-1~deb9u7) ... Removing libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Removing libtcl8.6:amd64 (8.6.6+dfsg-1+b1) ... Removing libthai-data (0.1.26-1) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing libxcb-render0:amd64 (1.12-1) ... Removing libxss1:amd64 (1:1.2.2-1) ... Removing libxext6:amd64 (2:1.3.3-1+b2) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing x11-common (1:7.7+19) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing lsb-base (9.20161125) ... Removing readline-common (7.0-3) ... Removing tzdata (2021a-0+deb9u4) ... Removing ucf (3.0036) ... Removing unzip (6.0-21+deb9u2) ... Removing xdg-utils (1.1.1-1+deb9u2) ... Removing zip (3.0-11+b1) ... Removing libx11-6:amd64 (2:1.6.4-3+deb9u4) ... Removing libxcb1:amd64 (1.12-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.8.3-1+deb9u1) ... Removing libx11-data (2:1.6.4-3+deb9u4) ... Removing libxau6:amd64 (1:1.0.8-1) ... Removing libwww-perl (6.15-1) ... Removing libhttp-negotiate-perl (6.00-2) ... Removing libfile-listing-perl (6.04-1) ... Removing libhtml-tree-perl (5.03-2) ... Removing libhtml-parser-perl (3.72-3) ... Removing libhtml-tagset-perl (3.20-3) ... Removing libhttp-cookies-perl (6.01-1) ... Removing liblwp-protocol-https-perl (6.06-2) ... Removing libio-socket-ssl-perl (2.044-1) ... Removing libnet-http-perl (6.12-1) ... Removing libnet-ssleay-perl (1.80-1) ... Removing perl-openssl-defaults:amd64 (3) ... Removing libwww-robotrules-perl (6.01-1) ... Removing netbase (5.4) ... Removing ca-certificates (20200601~deb9u2) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libhttp-message-perl (6.11-1) ... Removing libencode-locale-perl (1.05-1) ... Removing libhttp-date-perl (6.02-1) ... Removing libio-html-perl (1.001-1) ... Removing liblwp-mediatypes-perl (6.02-1) ... Removing openssl (1.1.0l-1~deb9u6) ... Removing libssl1.1:amd64 (1.1.0l-1~deb9u6) ... Removing libtimedate-perl (2.3000-2+deb9u1) ... Removing liburi-perl (1.71-1) ... Removing perl (5.24.1-3+deb9u7) ... Removing libperl5.24:amd64 (5.24.1-3+deb9u7) ... Removing libgdbm3:amd64 (1.8.3-14) ... Removing perl-modules-5.24 (5.24.1-3+deb9u7) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', 'remove', 'bedtools', 'bioperl', 'ca-certificates', 'cd-hit', 'fasttree', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libarray-utils-perl', 'libbio-perl-perl', 'libblas-common', 'libblas3', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libcurl3:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libffi6:amd64', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdbm3:amd64', 'libgfortran3:amd64', 'libglib2.0-0:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhogweed4:amd64', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu57:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl', 'libmro-compat-perl', 'libncurses5:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnumber-compare-perl', 'libp11-kit0:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparams-util-perl', 'libparse-yapp-perl', 'libperl5.24:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps6:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libscalar-list-utils-perl', 'libsensors4:amd64', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl', 'libsub-uplevel-perl', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-simple-perl', 'libtest-warn-perl', 'libtext-csv-perl', 'libtext-diff-perl', 'libtext-glob-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtimedate-perl', 'libtk8.6:amd64', 'libtry-tiny-perl', 'libunistring0:amd64', 'liburi-perl', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'littler', 'lsb-base', 'mafft', 'mcl', 'mime-support', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.24', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python', 'python-minimal', 'python2.7', 'python2.7-minimal', 'r-base-core', 'r-cran-assertthat', 'r-cran-colorspace', 'r-cran-dichromat', 'r-cran-digest', 'r-cran-ggplot2', 'r-cran-gtable', 'r-cran-labeling', 'r-cran-lazyeval', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-munsell', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-reshape2', 'r-cran-scales', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-tibble', 'readline-common', 'sysstat', 'tzdata', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip', 'roary'] 0m53.9s INFO: Running scripts post_remove 0m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_remove_exceptions'] 0m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_remove_exceptions'] 0m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg', '--purge', 'bedtools', 'bioperl', 'ca-certificates', 'cd-hit', 'fasttree', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libarray-utils-perl', 'libbio-perl-perl', 'libblas-common', 'libblas3', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libcurl3:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libffi6:amd64', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdbm3:amd64', 'libgfortran3:amd64', 'libglib2.0-0:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhogweed4:amd64', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu57:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl', 'libmro-compat-perl', 'libncurses5:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnumber-compare-perl', 'libp11-kit0:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparams-util-perl', 'libparse-yapp-perl', 'libperl5.24:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps6:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libscalar-list-utils-perl', 'libsensors4:amd64', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl', 'libsub-uplevel-perl', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-simple-perl', 'libtest-warn-perl', 'libtext-csv-perl', 'libtext-diff-perl', 'libtext-glob-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtimedate-perl', 'libtk8.6:amd64', 'libtry-tiny-perl', 'libunistring0:amd64', 'liburi-perl', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'littler', 'lsb-base', 'mafft', 'mcl', 'mime-support', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.24', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python', 'python-minimal', 'python2.7', 'python2.7-minimal', 'r-base-core', 'r-cran-assertthat', 'r-cran-colorspace', 'r-cran-dichromat', 'r-cran-digest', 'r-cran-ggplot2', 'r-cran-gtable', 'r-cran-labeling', 'r-cran-lazyeval', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-munsell', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-reshape2', 'r-cran-scales', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-tibble', 'readline-common', 'sysstat', 'tzdata', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip'] 0m54.8s DUMP: dpkg: warning: ignoring request to remove bedtools which isn't installed dpkg: warning: ignoring request to remove bioperl which isn't installed (Reading database ... 4490 files and directories currently installed.) Purging configuration files for ca-certificates (20200601~deb9u2) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove cd-hit which isn't installed dpkg: warning: ignoring request to remove fasttree which isn't installed Purging configuration files for fontconfig (2.11.0-6.7+b1) ... Purging configuration files for fontconfig-config (2.11.0-6.7) ... Purging configuration files for fonts-dejavu-core (2.37-1) ... dpkg: warning: ignoring request to remove libalgorithm-c3-perl which isn't installed dpkg: warning: ignoring request to remove libalgorithm-diff-perl which isn't installed dpkg: warning: ignoring request to remove libarray-utils-perl which isn't installed dpkg: warning: ignoring request to remove libbio-perl-perl which isn't installed dpkg: warning: ignoring request to remove libblas-common which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcapture-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libclass-c3-perl which isn't installed dpkg: warning: ignoring request to remove libclass-data-inheritable-perl which isn't installed dpkg: warning: ignoring request to remove libclass-load-perl which isn't installed dpkg: warning: ignoring request to remove libclass-load-xs-perl which isn't installed dpkg: warning: ignoring request to remove libcurl3 which isn't installed dpkg: warning: ignoring request to remove libdata-optlist-perl which isn't installed dpkg: warning: ignoring request to remove libdata-stag-perl which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdevel-globaldestruction-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-overloadinfo-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-stacktrace-perl which isn't installed dpkg: warning: ignoring request to remove libdigest-md5-file-perl which isn't installed dpkg: warning: ignoring request to remove libdist-checkconflicts-perl which isn't installed dpkg: warning: ignoring request to remove libencode-locale-perl which isn't installed dpkg: warning: ignoring request to remove libenv-path-perl which isn't installed dpkg: warning: ignoring request to remove libeval-closure-perl which isn't installed dpkg: warning: ignoring request to remove libexception-class-perl which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libffi6 which isn't installed dpkg: warning: ignoring request to remove libfile-find-rule-perl which isn't installed dpkg: warning: ignoring request to remove libfile-grep-perl which isn't installed dpkg: warning: ignoring request to remove libfile-listing-perl which isn't installed dpkg: warning: ignoring request to remove libfile-slurper-perl which isn't installed dpkg: warning: ignoring request to remove libfile-which-perl which isn't installed dpkg: warning: ignoring request to remove libfindbin-libs-perl which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libgdbm3 which isn't installed dpkg: warning: ignoring request to remove libgfortran3 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.50.3-2+deb9u3) ... dpkg: warning: ignoring request to remove libgmp10 which isn't installed dpkg: warning: ignoring request to remove libgnutls30 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraph-perl which isn't installed dpkg: warning: ignoring request to remove libgraph-readwrite-perl which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhogweed4 which isn't installed dpkg: warning: ignoring request to remove libhtml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tagset-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tree-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-cookies-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-date-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-message-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-negotiate-perl which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu57 which isn't installed dpkg: warning: ignoring request to remove libidn11 which isn't installed dpkg: warning: ignoring request to remove libidn2-0 which isn't installed dpkg: warning: ignoring request to remove libio-all-perl which isn't installed dpkg: warning: ignoring request to remove libio-html-perl which isn't installed dpkg: warning: ignoring request to remove libio-socket-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libio-string-perl which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.44+dfsg-5+deb9u9) ... dpkg: warning: ignoring request to remove liblog-log4perl-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-mediatypes-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-protocol-https-perl which isn't installed dpkg: warning: ignoring request to remove libmodule-implementation-perl which isn't installed dpkg: warning: ignoring request to remove libmodule-runtime-conflicts-perl which isn't installed dpkg: warning: ignoring request to remove libmodule-runtime-perl which isn't installed dpkg: warning: ignoring request to remove libmoose-perl which isn't installed dpkg: warning: ignoring request to remove libmro-compat-perl which isn't installed dpkg: warning: ignoring request to remove libncurses5 which isn't installed dpkg: warning: ignoring request to remove libnet-http-perl which isn't installed dpkg: warning: ignoring request to remove libnet-ssleay-perl which isn't installed dpkg: warning: ignoring request to remove libnettle6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnumber-compare-perl which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libpackage-deprecationmanager-perl which isn't installed dpkg: warning: ignoring request to remove libpackage-stash-perl which isn't installed dpkg: warning: ignoring request to remove libpackage-stash-xs-perl which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.24+nmu5) ... dpkg: warning: ignoring request to remove libparams-classify-perl which isn't installed dpkg: warning: ignoring request to remove libparams-util-perl which isn't installed dpkg: warning: ignoring request to remove libparse-yapp-perl which isn't installed dpkg: warning: ignoring request to remove libperl5.24 which isn't installed dpkg: warning: ignoring request to remove libperlio-utf8-strict-perl which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libprocps6 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython-stdlib which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.13-2+deb9u6) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline7 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libscalar-list-utils-perl which isn't installed Purging configuration files for libsensors4:amd64 (1:3.4.0-4) ... dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libspiffy-perl which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed Purging configuration files for libssl1.0.2:amd64 (1.0.2u-1~deb9u7) ... Purging configuration files for libssl1.1:amd64 (1.1.0l-1~deb9u6) ... dpkg: warning: ignoring request to remove libsub-exporter-perl which isn't installed dpkg: warning: ignoring request to remove libsub-exporter-progressive-perl which isn't installed dpkg: warning: ignoring request to remove libsub-identify-perl which isn't installed dpkg: warning: ignoring request to remove libsub-install-perl which isn't installed dpkg: warning: ignoring request to remove libsub-name-perl which isn't installed dpkg: warning: ignoring request to remove libsub-uplevel-perl which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtest-deep-perl which isn't installed dpkg: warning: ignoring request to remove libtest-differences-perl which isn't installed dpkg: warning: ignoring request to remove libtest-exception-perl which isn't installed dpkg: warning: ignoring request to remove libtest-file-perl which isn't installed dpkg: warning: ignoring request to remove libtest-files-perl which isn't installed dpkg: warning: ignoring request to remove libtest-most-perl which isn't installed dpkg: warning: ignoring request to remove libtest-output-perl which isn't installed dpkg: warning: ignoring request to remove libtest-simple-perl which isn't installed dpkg: warning: ignoring request to remove libtest-warn-perl which isn't installed dpkg: warning: ignoring request to remove libtext-csv-perl which isn't installed dpkg: warning: ignoring request to remove libtext-diff-perl which isn't installed dpkg: warning: ignoring request to remove libtext-glob-perl which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtimedate-perl which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libunistring0 which isn't installed dpkg: warning: ignoring request to remove liburi-perl which isn't installed dpkg: warning: ignoring request to remove libwww-perl which isn't installed dpkg: warning: ignoring request to remove libwww-robotrules-perl which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed Purging configuration files for libxau6:amd64 (1:1.0.8-1) ... dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libxml-writer-perl which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed Purging configuration files for libxss1:amd64 (1:1.2.2-1) ... dpkg: warning: ignoring request to remove libxt6 which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed dpkg: warning: ignoring request to remove lsb-base which isn't installed dpkg: warning: ignoring request to remove mafft which isn't installed dpkg: warning: ignoring request to remove mcl which isn't installed Purging configuration files for mime-support (3.60) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-0+deb9u1) ... Purging configuration files for netbase (5.4) ... Purging configuration files for openssl (1.1.0l-1~deb9u6) ... Purging configuration files for parallel (20161222-1) ... Purging configuration files for perl (5.24.1-3+deb9u7) ... dpkg: warning: ignoring request to remove perl-modules-5.24 which isn't installed dpkg: warning: ignoring request to remove perl-openssl-defaults which isn't installed dpkg: warning: ignoring request to remove prank which isn't installed Purging configuration files for procps (2:3.3.12-3+deb9u1) ... Purging configuration files for python (2.7.13-2) ... dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed Purging configuration files for python2.7-minimal (2.7.13-2+deb9u6) ... Purging configuration files for r-base-core (3.3.3-1) ... dpkg: warning: ignoring request to remove r-cran-assertthat which isn't installed dpkg: warning: ignoring request to remove r-cran-colorspace which isn't installed dpkg: warning: ignoring request to remove r-cran-dichromat which isn't installed dpkg: warning: ignoring request to remove r-cran-digest which isn't installed dpkg: warning: ignoring request to remove r-cran-ggplot2 which isn't installed dpkg: warning: ignoring request to remove r-cran-gtable which isn't installed dpkg: warning: ignoring request to remove r-cran-labeling which isn't installed dpkg: warning: ignoring request to remove r-cran-lazyeval which isn't installed dpkg: warning: ignoring request to remove r-cran-littler which isn't installed dpkg: warning: ignoring request to remove r-cran-magrittr which isn't installed dpkg: warning: ignoring request to remove r-cran-mass which isn't installed dpkg: warning: ignoring request to remove r-cran-munsell which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgkitten which isn't installed dpkg: warning: ignoring request to remove r-cran-plyr 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-rcpp which isn't installed dpkg: warning: ignoring request to remove r-cran-reshape2 which isn't installed dpkg: warning: ignoring request to remove r-cran-scales which isn't installed dpkg: warning: ignoring request to remove r-cran-stringi 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-tibble which isn't installed Purging configuration files for readline-common (7.0-3) ... Purging configuration files for sysstat (11.4.3-2) ... Purging configuration files for tzdata (2021a-0+deb9u4) ... Purging configuration files for ucf (3.0036) ... Purging configuration files for unzip (6.0-21+deb9u2) ... Purging configuration files for x11-common (1:7.7+19) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove xz-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 0m54.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg', '--purge', 'bedtools', 'bioperl', 'ca-certificates', 'cd-hit', 'fasttree', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libarray-utils-perl', 'libbio-perl-perl', 'libblas-common', 'libblas3', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libcurl3:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libffi6:amd64', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdbm3:amd64', 'libgfortran3:amd64', 'libglib2.0-0:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhogweed4:amd64', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu57:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl', 'libmro-compat-perl', 'libncurses5:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnumber-compare-perl', 'libp11-kit0:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparams-util-perl', 'libparse-yapp-perl', 'libperl5.24:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps6:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libscalar-list-utils-perl', 'libsensors4:amd64', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl', 'libsub-uplevel-perl', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-simple-perl', 'libtest-warn-perl', 'libtext-csv-perl', 'libtext-diff-perl', 'libtext-glob-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtimedate-perl', 'libtk8.6:amd64', 'libtry-tiny-perl', 'libunistring0:amd64', 'liburi-perl', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'littler', 'lsb-base', 'mafft', 'mcl', 'mime-support', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.24', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python', 'python-minimal', 'python2.7', 'python2.7-minimal', 'r-base-core', 'r-cran-assertthat', 'r-cran-colorspace', 'r-cran-dichromat', 'r-cran-digest', 'r-cran-ggplot2', 'r-cran-gtable', 'r-cran-labeling', 'r-cran-lazyeval', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-munsell', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-reshape2', 'r-cran-scales', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-tibble', 'readline-common', 'sysstat', 'tzdata', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip'] 0m54.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg', '--purge', 'roary'] 0m54.8s DUMP: dpkg: warning: ignoring request to remove roary which isn't installed 0m54.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg', '--purge', 'roary'] 0m54.8s INFO: Running scripts post_purge 0m54.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_purge_exceptions'] 0m54.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_purge_exceptions'] 0m54.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg', '--purge', '--pending'] 0m54.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg', '--purge', '--pending'] 0m54.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg', '--remove', '--pending'] 0m54.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg', '--remove', '--pending'] 0m54.9s INFO: Running scripts post_test 0m54.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_test_exceptions'] 0m54.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'tmp/scripts/post_test_exceptions'] 0m54.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m55.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg-divert', '--list'] 0m55.2s 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 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'dpkg-divert', '--list'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', 'clean'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f', 'apt-get', 'clean'] 0m55.2s DEBUG: Recording chroot state 0m55.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/shm'] 0m55.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/shm'] 0m55.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/console'] 0m55.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/console'] 0m55.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/ptmx'] 0m55.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/ptmx'] 0m55.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/pts'] 0m55.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/dev/pts'] 0m55.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/proc'] 0m55.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f/proc'] 0m55.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m56.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfk7gzh7f'] 0m56.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpfk7gzh7f 0m56.0s INFO: PASS: Upgrading between Debian distributions. 0m56.0s INFO: PASS: All tests. 0m56.0s INFO: piuparts run ends. ret=0 End: 2023-04-03 10:49:03 GMT