Start: 2022-12-17 01:39:00 GMT [stretch] Package: ariba Version: 2.6.1+ds-1 Installed-Size: 687 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 3.12.0), python3 (<< 3.6), python3 (>= 3.5~), python3-dendropy (>= 4.1.0), python3-pymummer (>= 0.10.1), python3-pysam (>= 0.9.1), python3:any (>= 3.3.2-2~), libc6 (>= 2.14), libfml0, libgcc1 (>= 1:3.0), libminimap0, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), bowtie2 (>= 2.1.0), cd-hit, mash, mummer Description: Antibiotic Resistance Identification By Assembly Homepage: https://github.com/sanger-pathogens/ariba Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.6.1+ds-1_amd64.deb Size: 103872 MD5sum: 98a107d16d9c27d6a675dfa48bb0bb42 SHA256: 45b8f68dfa8b2984b7f7f72b88d62c12df265b882621a55d5f752dd39d7a0c12 [buster] Package: ariba Version: 2.13.3+ds-1 Installed-Size: 17444 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 3.12.0), python3 (<< 3.8), python3 (>= 3.7~), python3-biopython, python3-bs4, python3-dendropy, python3-matplotlib, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3:any, libc6 (>= 2.14), libfml0 (>= 0.1-4~), libgcc1 (>= 1:3.0), libminimap0, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), bowtie2 (>= 2.1.0), cd-hit, mash, mummer, python3-tk Description: Antibiotic Resistance Identification By Assembly Homepage: https://github.com/sanger-pathogens/ariba Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.13.3+ds-1_amd64.deb Size: 1678912 MD5sum: 77517ce195de03a32365f34e5629bb30 SHA256: a971e793eca324e1333e4cf1c89abd795839a5b7869c10d31a2dca27675f074e Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --upgrade-before-dist-upgrade --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --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 buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster/reference-chroot-metadata.dat --apt ariba=2.13.3+ds-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 --upgrade-before-dist-upgrade --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --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 buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster/reference-chroot-metadata.dat --apt ariba=2.13.3+ds-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-19-amd64 #1 SMP Debian 5.10.149-2 (2022-10-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpgqw_8g1w 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpgqw_8g1w 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/proc'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/proc'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/pts'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/pts'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/ptmx'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/ptmx'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/console'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/console'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/shm'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/shm'] 0m1.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.4s DEBUG: Created policy-rc.d and chmodded it. 0m1.4s DEBUG: Created resolv.conf. 0m1.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpgqw_8g1w/tmp/scripts/ 0m1.4s INFO: Running scripts post_chroot_unpack 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', 'update'] 0m2.2s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', 'update'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s INFO: Running scripts post_setup 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_setup_zz_backports'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_setup_zz_backports'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.7s 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 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.7s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster/reference-chroot-metadata.dat 0m3.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m4.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m4.0s INFO: Running scripts is_testable 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/is_testable_uninstallable'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/is_testable_uninstallable'] 0m4.0s INFO: Running scripts pre_test 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_test_root_password'] 0m4.1s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_test_root_password'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 0m4.2s DUMP: Package: ariba Version: 2.6.1+ds-1 Installed-Size: 687 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 3.12.0), python3 (<< 3.6), python3 (>= 3.5~), python3-dendropy (>= 4.1.0), python3-pymummer (>= 0.10.1), python3-pysam (>= 0.9.1), python3:any (>= 3.3.2-2~), libc6 (>= 2.14), libfml0, libgcc1 (>= 1:3.0), libminimap0, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), bowtie2 (>= 2.1.0), cd-hit, mash, mummer Description-en: Antibiotic Resistance Identification By Assembly ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. The input is a FASTA file of reference genes and paired sequencing reads. ARIBA reports which of the reference genes were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference genes. Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Homepage: https://github.com/sanger-pathogens/ariba Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.6.1+ds-1_amd64.deb Size: 103872 MD5sum: 98a107d16d9c27d6a675dfa48bb0bb42 SHA256: 45b8f68dfa8b2984b7f7f72b88d62c12df265b882621a55d5f752dd39d7a0c12 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 0m4.2s INFO: apt-cache knows about the following packages: ariba 0m4.2s INFO: Running scripts pre_install 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_database-server'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_database-server'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_exceptions'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_exceptions'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_extras'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_extras'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'policy'] 0m4.4s 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: 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'policy'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'policy', 'ariba'] 0m4.4s DUMP: ariba: Installed: (none) Candidate: 2.6.1+ds-1 Version table: 2.6.1+ds-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'policy', 'ariba'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', '-y', 'install', 'ariba'] 0m14.4s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bowtie2 cd-hit dh-python fastaq gawk libatomic1 libcapnp-0.5.3 libcurl3-gnutls libexpat1 libffi6 libfml0 libgdbm3 libgmp10 libgnutls30 libgomp1 libgsl2 libgssapi-krb5-2 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libminimap0 libmpdec2 libmpfr4 libncurses5 libnettle6 libnghttp2-14 libp11-kit0 libperl5.24 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 libtasn1-6 libtbb2 libunistring0 mash mime-support mummer perl perl-modules-5.24 python python-minimal python2.7 python2.7-minimal python3 python3-dendropy python3-minimal python3-pkg-resources python3-pymummer python3-pysam python3.5 python3.5-minimal readline-common samtools Suggested packages: bowtie2-examples libdpkg-perl gawk-doc gnutls-bin gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make python-doc python-tk python2.7-doc binutils binfmt-support python3-doc python3-tk python3-venv python3-setuptools python3.5-venv python3.5-doc readline-doc Recommended packages: ca-certificates krb5-locales libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils netbase rename The following NEW packages will be installed: ariba bowtie2 cd-hit dh-python fastaq gawk libatomic1 libcapnp-0.5.3 libcurl3-gnutls libexpat1 libffi6 libfml0 libgdbm3 libgmp10 libgnutls30 libgomp1 libgsl2 libgssapi-krb5-2 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libminimap0 libmpdec2 libmpfr4 libncurses5 libnettle6 libnghttp2-14 libp11-kit0 libperl5.24 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 libtasn1-6 libtbb2 libunistring0 mash mime-support mummer perl perl-modules-5.24 python python-minimal python2.7 python2.7-minimal python3 python3-dendropy python3-minimal python3-pkg-resources python3-pymummer python3-pysam python3.5 python3.5-minimal readline-common samtools 0 upgraded, 73 newly installed, 0 to remove and 0 not upgraded. Need to get 37.3 MB of archives. After this operation, 193 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 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libmpfr4 amd64 3.1.5-1 [556 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 gawk amd64 1:4.1.4+dfsg-1 [571 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 libpython3.5-minimal amd64 3.5.3-1+deb9u1 [573 kB] Get:24 http://deb.debian.org/debian stretch/main amd64 python3.5-minimal amd64 3.5.3-1+deb9u1 [1691 kB] Get:25 http://deb.debian.org/debian stretch/main amd64 python3-minimal amd64 3.5.3-1 [35.3 kB] Get:26 http://deb.debian.org/debian stretch/main amd64 libmpdec2 amd64 2.4.2-1 [85.2 kB] Get:27 http://deb.debian.org/debian stretch/main amd64 libpython3.5-stdlib amd64 3.5.3-1+deb9u1 [2167 kB] Get:28 http://deb.debian.org/debian stretch/main amd64 python3.5 amd64 3.5.3-1+deb9u1 [229 kB] Get:29 http://deb.debian.org/debian stretch/main amd64 libpython3-stdlib amd64 3.5.3-1 [18.6 kB] Get:30 http://deb.debian.org/debian stretch/main amd64 dh-python all 2.20170125 [86.8 kB] Get:31 http://deb.debian.org/debian stretch/main amd64 python3 amd64 3.5.3-1 [21.6 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b2 [192 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b2 [136 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 libtasn1-6 amd64 4.10-1.1+deb9u1 [50.6 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 libgnutls30 amd64 3.5.8-5+deb9u5 [896 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 libkrb5support0 amd64 1.15-1+deb9u1 [61.9 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 libk5crypto3 amd64 1.15-1+deb9u1 [119 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 libkrb5-3 amd64 1.15-1+deb9u1 [311 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 libgssapi-krb5-2 amd64 1.15-1+deb9u1 [155 kB] Get:43 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [68.4 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [105 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 libldap-common all 2.4.44+dfsg-5+deb9u4 [85.7 kB] Get:46 http://deb.debian.org/debian stretch/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u4 [219 kB] Get:47 http://deb.debian.org/debian stretch/main amd64 python3-pkg-resources all 33.1.1-1 [137 kB] Get:48 http://deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:49 http://deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:50 http://deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:51 http://deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB] Get:52 http://deb.debian.org/debian stretch/main amd64 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Get:63 http://deb.debian.org/debian stretch/main amd64 libfml0 amd64 0.1-2+b1 [68.7 kB] Get:64 http://deb.debian.org/debian stretch/main amd64 libminimap0 amd64 0.2-3+b1 [22.6 kB] Get:65 http://deb.debian.org/debian stretch/main amd64 libatomic1 amd64 6.3.0-18+deb9u1 [8966 B] Get:66 http://deb.debian.org/debian stretch/main amd64 libtbb2 amd64 4.3~20150611-2 [136 kB] Get:67 http://deb.debian.org/debian stretch/main amd64 bowtie2 amd64 2.3.0-2 [1166 kB] Get:68 http://deb.debian.org/debian stretch/main amd64 libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:69 http://deb.debian.org/debian stretch/main amd64 cd-hit amd64 4.6.6-2 [852 kB] Get:70 http://deb.debian.org/debian stretch/main amd64 libcapnp-0.5.3 amd64 0.5.3-2 [584 kB] Get:71 http://deb.debian.org/debian stretch/main amd64 libgsl2 amd64 2.3+dfsg-1 [893 kB] Get:72 http://deb.debian.org/debian stretch/main amd64 mash amd64 1.1.1-2 [126 kB] Get:73 http://deb.debian.org/debian stretch/main amd64 ariba amd64 2.6.1+ds-1 [104 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 37.3 MB in 0s (116 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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Selecting previously unselected package dh-python. Preparing to unpack .../8-dh-python_2.20170125_all.deb ... Unpacking dh-python (2.20170125) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Setting up libpython3.5-minimal:amd64 (3.5.3-1+deb9u1) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u3) ... Setting up python3.5-minimal (3.5.3-1+deb9u1) ... Setting up python3-minimal (3.5.3-1) ... Selecting previously unselected package python3. (Reading database ... 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Unpacking libhogweed4:amd64 (3.3-1+b2) ... Selecting previously unselected package libidn11:amd64. Preparing to unpack .../03-libidn11_1.33-1+deb9u1_amd64.deb ... Unpacking libidn11:amd64 (1.33-1+deb9u1) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../04-libp11-kit0_0.23.3-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.23.3-2) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../05-libtasn1-6_4.10-1.1+deb9u1_amd64.deb ... Unpacking libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Selecting previously unselected package libgnutls30:amd64. Preparing to unpack .../06-libgnutls30_3.5.8-5+deb9u5_amd64.deb ... Unpacking libgnutls30:amd64 (3.5.8-5+deb9u5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.5.9-9_amd64.deb ... Unpacking libkeyutils1:amd64 (1.5.9-9) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../08-libkrb5support0_1.15-1+deb9u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.15-1+deb9u1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../09-libk5crypto3_1.15-1+deb9u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.15-1+deb9u1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../10-libkrb5-3_1.15-1+deb9u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.15-1+deb9u1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../11-libgssapi-krb5-2_1.15-1+deb9u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../12-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3+deb9u1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../13-libsasl2-2_2.1.27~101-g0780600+dfsg-3+deb9u1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../14-libldap-common_2.4.44+dfsg-5+deb9u4_all.deb ... Unpacking libldap-common (2.4.44+dfsg-5+deb9u4) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../15-libldap-2.4-2_2.4.44+dfsg-5+deb9u4_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../16-python3-pkg-resources_33.1.1-1_all.deb ... Unpacking python3-pkg-resources (33.1.1-1) ... Selecting previously unselected package libunistring0:amd64. Preparing to unpack .../17-libunistring0_0.9.6+really0.9.3-0.1_amd64.deb ... Unpacking libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../18-libidn2-0_0.16-1+deb9u1_amd64.deb ... Unpacking libidn2-0:amd64 (0.16-1+deb9u1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../19-libnghttp2-14_1.18.1-1+deb9u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../20-libpsl5_0.17.0-3_amd64.deb ... Unpacking libpsl5:amd64 (0.17.0-3) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../21-librtmp1_2.4+20151223.gitfa8646d.1-1+b1_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../22-libssh2-1_1.7.0-1+deb9u1_amd64.deb ... Unpacking libssh2-1:amd64 (1.7.0-1+deb9u1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../23-libcurl3-gnutls_7.52.1-5+deb9u10_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Selecting previously unselected package libhts1:amd64. Preparing to unpack .../24-libhts1_1.3.2-2_amd64.deb ... Unpacking libhts1:amd64 (1.3.2-2) ... Selecting previously unselected package libncurses5:amd64. Preparing to unpack .../25-libncurses5_6.0+20161126-1+deb9u2_amd64.deb ... Unpacking libncurses5:amd64 (6.0+20161126-1+deb9u2) ... Selecting previously unselected package samtools. Preparing to unpack .../26-samtools_1.3.1-3_amd64.deb ... Unpacking samtools (1.3.1-3) ... Selecting previously unselected package fastaq. Preparing to unpack .../27-fastaq_3.14.0-1_all.deb ... Unpacking fastaq (3.14.0-1) ... Selecting previously unselected package python3-dendropy. Preparing to unpack .../28-python3-dendropy_4.2.0+dfsg-1_all.deb ... Unpacking python3-dendropy (4.2.0+dfsg-1) ... Selecting previously unselected package mummer. Preparing to unpack .../29-mummer_3.23+dfsg-2_amd64.deb ... Unpacking mummer (3.23+dfsg-2) ... Selecting previously unselected package python3-pymummer. Preparing to unpack .../30-python3-pymummer_0.10.1-1_all.deb ... Unpacking python3-pymummer (0.10.1-1) ... Selecting previously unselected package python3-pysam. Preparing to unpack .../31-python3-pysam_0.10.0+ds-2_amd64.deb ... Unpacking python3-pysam (0.10.0+ds-2) ... Selecting previously unselected package libfml0. Preparing to unpack .../32-libfml0_0.1-2+b1_amd64.deb ... Unpacking libfml0 (0.1-2+b1) ... Selecting previously unselected package libminimap0. Preparing to unpack .../33-libminimap0_0.2-3+b1_amd64.deb ... Unpacking libminimap0 (0.2-3+b1) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../34-libatomic1_6.3.0-18+deb9u1_amd64.deb ... Unpacking libatomic1:amd64 (6.3.0-18+deb9u1) ... Selecting previously unselected package libtbb2:amd64. Preparing to unpack .../35-libtbb2_4.3~20150611-2_amd64.deb ... Unpacking libtbb2:amd64 (4.3~20150611-2) ... Selecting previously unselected package bowtie2. Preparing to unpack .../36-bowtie2_2.3.0-2_amd64.deb ... Unpacking bowtie2 (2.3.0-2) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../37-libgomp1_6.3.0-18+deb9u1_amd64.deb ... Unpacking libgomp1:amd64 (6.3.0-18+deb9u1) ... Selecting previously unselected package cd-hit. Preparing to unpack .../38-cd-hit_4.6.6-2_amd64.deb ... Unpacking cd-hit (4.6.6-2) ... Selecting previously unselected package libcapnp-0.5.3. Preparing to unpack .../39-libcapnp-0.5.3_0.5.3-2_amd64.deb ... Unpacking libcapnp-0.5.3 (0.5.3-2) ... Selecting previously unselected package libgsl2:amd64. Preparing to unpack .../40-libgsl2_2.3+dfsg-1_amd64.deb ... Unpacking libgsl2:amd64 (2.3+dfsg-1) ... Selecting previously unselected package mash. Preparing to unpack .../41-mash_1.1.1-2_amd64.deb ... Unpacking mash (1.1.1-2) ... Selecting previously unselected package ariba. Preparing to unpack .../42-ariba_2.6.1+ds-1_amd64.deb ... Unpacking ariba (2.6.1+ds-1) ... Setting up libncurses5:amd64 (6.0+20161126-1+deb9u2) ... Setting up libgomp1:amd64 (6.3.0-18+deb9u1) ... Setting up libatomic1:amd64 (6.3.0-18+deb9u1) ... 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 libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Setting up mime-support (3.60) ... Setting up libldap-common (2.4.44+dfsg-5+deb9u4) ... Setting up libtbb2:amd64 (4.3~20150611-2) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libcapnp-0.5.3 (0.5.3-2) ... Setting up libgsl2:amd64 (2.3+dfsg-1) ... Setting up gawk (1:4.1.4+dfsg-1) ... Setting up libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up perl (5.24.1-3+deb9u7) ... update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode Setting up libssh2-1:amd64 (1.7.0-1+deb9u1) ... Setting up libminimap0 (0.2-3+b1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up libfml0 (0.1-2+b1) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up libidn11:amd64 (1.33-1+deb9u1) ... Setting up libmpdec2:amd64 (2.4.2-1) ... Setting up cd-hit (4.6.6-2) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up mash (1.1.1-2) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up mummer (3.23+dfsg-2) ... Setting up libpython3.5-stdlib:amd64 (3.5.3-1+deb9u1) ... Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u1) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up python (2.7.13-2) ... Setting up python3.5 (3.5.3-1+deb9u1) ... Setting up libpython3-stdlib:amd64 (3.5.3-1) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up bowtie2 (2.3.0-2) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Setting up libhts1:amd64 (1.3.2-2) ... Setting up samtools (1.3.1-3) ... Setting up python3 (3.5.3-1) ... Setting up python3-pkg-resources (33.1.1-1) ... Setting up fastaq (3.14.0-1) ... Setting up python3-pysam (0.10.0+ds-2) ... Setting up python3-pymummer (0.10.1-1) ... Setting up python3-dendropy (4.2.0+dfsg-1) ... Setting up dh-python (2.20170125) ... Setting up ariba (2.6.1+ds-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', '-y', 'install', 'ariba'] 0m14.4s INFO: Running scripts post_install 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_install_exceptions'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_install_exceptions'] 0m14.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m14.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m14.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpgqw_8g1w to buster 0m14.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m14.9s INFO: Running scripts pre_distupgrade 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', 'update'] 0m17.9s DUMP: Get:1 http://deb.debian.org/debian buster InRelease [122 kB] Get:2 http://deb.debian.org/debian buster/main amd64 Packages [7909 kB] Get:3 http://deb.debian.org/debian buster/main Translation-en [5969 kB] Fetched 14.0 MB in 2s (6091 kB/s) Reading package lists... 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', 'update'] 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', '-y', 'upgrade'] 0m25.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages have been kept back: apt ariba bash dash dpkg e2fslibs e2fsprogs gawk libapt-pkg5.0 libatomic1 libcomerr2 libcurl3-gnutls libgcc1 libgnutls30 libgomp1 libgssapi-krb5-2 libidn2-0 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libncurses5 libncursesw5 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libreadline7 libss2 libstdc++6 libtbb2 libtinfo5 login mash mount ncurses-base ncurses-bin perl perl-base python python-minimal python2.7 python2.7-minimal python3 python3-minimal python3-pysam samtools util-linux The following packages will be upgraded: adduser base-files base-passwd bowtie2 bsdutils cd-hit coreutils debconf debian-archive-keyring debianutils dh-python diffutils fastaq findutils gpgv grep gzip hostname init-system-helpers libacl1 libattr1 libaudit-common libaudit1 libblkid1 libbz2-1.0 libc-bin libc6 libcap-ng0 libdb5.3 libdebconfclient0 libexpat1 libfdisk1 libffi6 libfml0 libgcrypt20 libgmp10 libgpg-error0 libhogweed4 libidn11 libkeyutils1 libldap-common liblz4-1 liblzma5 libminimap0 libmount1 libmpdec2 libnettle6 libnghttp2-14 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre3 librtmp1 libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libsigsegv2 libsmartcols1 libsqlite3-0 libssh2-1 libssl1.1 libsystemd0 libtasn1-6 libudev1 libuuid1 mime-support multiarch-support mummer passwd python3-dendropy python3-pkg-resources python3-pymummer readline-common sed sensible-utils sysvinit-utils tar zlib1g 83 upgraded, 0 newly installed, 0 to remove and 49 not upgraded. Need to get 23.9 MB of archives. After this operation, 61.2 MB disk space will be freed. Get:1 http://deb.debian.org/debian buster/main amd64 base-files amd64 10.3+deb10u13 [69.9 kB] Get:2 http://deb.debian.org/debian buster/main amd64 bsdutils amd64 1:2.33.1-0.1 [121 kB] Get:3 http://deb.debian.org/debian buster/main amd64 libc6 amd64 2.28-10+deb10u1 [2863 kB] Get:4 http://deb.debian.org/debian buster/main amd64 libc-bin amd64 2.28-10+deb10u1 [795 kB] Get:5 http://deb.debian.org/debian buster/main amd64 coreutils amd64 8.30-3 [2708 kB] Get:6 http://deb.debian.org/debian buster/main amd64 debianutils amd64 4.8.6.1 [100 kB] Get:7 http://deb.debian.org/debian buster/main amd64 diffutils amd64 1:3.7-3 [371 kB] Get:8 http://deb.debian.org/debian buster/main amd64 findutils amd64 4.6.0+git+20190209-2 [684 kB] Get:9 http://deb.debian.org/debian buster/main amd64 grep amd64 3.3-1 [373 kB] Get:10 http://deb.debian.org/debian buster/main amd64 gzip amd64 1.9-3+deb10u1 [128 kB] Get:11 http://deb.debian.org/debian buster/main amd64 hostname amd64 3.21 [14.8 kB] Get:12 http://deb.debian.org/debian buster/main amd64 sed amd64 4.7-1 [310 kB] Get:13 http://deb.debian.org/debian buster/main amd64 tar amd64 1.30+dfsg-6 [780 kB] Get:14 http://deb.debian.org/debian buster/main amd64 libdebconfclient0 amd64 0.249 [49.1 kB] Get:15 http://deb.debian.org/debian buster/main amd64 base-passwd amd64 3.5.46 [56.7 kB] Get:16 http://deb.debian.org/debian buster/main amd64 init-system-helpers all 1.56+nmu1 [46.8 kB] Get:17 http://deb.debian.org/debian buster/main amd64 sysvinit-utils amd64 2.93-8 [78.4 kB] Get:18 http://deb.debian.org/debian buster/main amd64 debconf all 1.5.71+deb10u1 [145 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libaudit-common all 1:2.8.4-3 [22.4 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libcap-ng0 amd64 0.7.9-2 [14.3 kB] Get:21 http://deb.debian.org/debian buster/main amd64 libaudit1 amd64 1:2.8.4-3 [57.3 kB] Get:22 http://deb.debian.org/debian buster/main amd64 libpam0g amd64 1.3.1-5 [126 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libpcre3 amd64 2:8.39-12 [341 kB] Get:24 http://deb.debian.org/debian buster/main amd64 libselinux1 amd64 2.8-1+b1 [86.9 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libpam-modules-bin amd64 1.3.1-5 [107 kB] Get:26 http://deb.debian.org/debian buster/main amd64 libpam-modules amd64 1.3.1-5 [309 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libgpg-error0 amd64 1.35-1 [71.1 kB] Get:28 http://deb.debian.org/debian buster/main amd64 libgcrypt20 amd64 1.8.4-5+deb10u1 [556 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libsystemd0 amd64 241-7~deb10u8 [331 kB] Get:30 http://deb.debian.org/debian buster/main amd64 libpam-runtime all 1.3.1-5 [211 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libsepol1 amd64 2.8-1 [263 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libsemanage-common all 2.8-2 [17.7 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libsemanage1 amd64 2.8-2 [96.5 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libbz2-1.0 amd64 1.0.6-9.2~deb10u1 [45.3 kB] Get:35 http://deb.debian.org/debian buster/main amd64 passwd amd64 1:4.5-1.1 [1005 kB] Get:36 http://deb.debian.org/debian buster/main amd64 adduser all 3.118 [240 kB] Get:37 http://deb.debian.org/debian buster/main amd64 debian-archive-keyring all 2019.1+deb10u1 [93.5 kB] Get:38 http://deb.debian.org/debian buster/main amd64 zlib1g amd64 1:1.2.11.dfsg-1+deb10u1 [90.8 kB] Get:39 http://deb.debian.org/debian buster/main amd64 gpgv amd64 2.2.12-1+deb10u2 [584 kB] Get:40 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:41 http://deb.debian.org/debian buster/main amd64 libattr1 amd64 1:2.4.48-4 [21.3 kB] Get:42 http://deb.debian.org/debian buster/main amd64 libacl1 amd64 2.2.53-4 [30.4 kB] Get:43 http://deb.debian.org/debian buster/main amd64 libuuid1 amd64 2.33.1-0.1 [78.3 kB] Get:44 http://deb.debian.org/debian buster/main amd64 libblkid1 amd64 2.33.1-0.1 [195 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.5 [683 kB] Get:46 http://deb.debian.org/debian buster/main amd64 libfdisk1 amd64 2.33.1-0.1 [234 kB] Get:47 http://deb.debian.org/debian buster/main amd64 liblz4-1 amd64 1.8.3-1+deb10u1 [53.3 kB] Get:48 http://deb.debian.org/debian buster/main amd64 liblzma5 amd64 5.2.4-1+deb10u1 [153 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libmount1 amd64 2.33.1-0.1 [207 kB] Get:50 http://deb.debian.org/debian buster/main amd64 libsmartcols1 amd64 2.33.1-0.1 [150 kB] Get:51 http://deb.debian.org/debian buster/main amd64 libudev1 amd64 241-7~deb10u8 [151 kB] Get:52 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:53 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:54 http://deb.debian.org/debian buster/main amd64 bowtie2 amd64 2.3.4.3-1 [1188 kB] Get:55 http://deb.debian.org/debian buster/main amd64 cd-hit amd64 4.6.8-2 [521 kB] Get:56 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] Get:57 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get:58 http://deb.debian.org/debian buster/main amd64 fastaq all 3.17.0-2 [47.8 kB] Get:59 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libffi6 amd64 3.2.1-9 [20.8 kB] Get:61 http://deb.debian.org/debian buster/main amd64 libfml0 amd64 0.1-5 [69.3 kB] Get:62 http://deb.debian.org/debian buster/main amd64 libgmp10 amd64 2:6.1.2+dfsg-4+deb10u1 [251 kB] Get:63 http://deb.debian.org/debian buster/main amd64 libhogweed4 amd64 3.4.1-1+deb10u1 [141 kB] Get:64 http://deb.debian.org/debian buster/main amd64 libnettle6 amd64 3.4.1-1+deb10u1 [215 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libidn11 amd64 1.33-2.2 [116 kB] Get:66 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:67 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u7 [90.1 kB] Get:68 http://deb.debian.org/debian buster/main amd64 libminimap0 amd64 0.2-4 [23.0 kB] Get:69 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:70 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get:71 http://deb.debian.org/debian buster/main amd64 libp11-kit0 amd64 0.23.15-2+deb10u1 [316 kB] Get:72 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:73 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u2 [69.2 kB] Get:74 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u2 [106 kB] Get:75 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:76 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:77 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:78 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u3 [1551 kB] Get:79 http://deb.debian.org/debian buster/main amd64 libtasn1-6 amd64 4.13-3 [51.9 kB] Get:80 http://deb.debian.org/debian buster/main amd64 multiarch-support amd64 2.28-10+deb10u1 [216 kB] Get:81 http://deb.debian.org/debian buster/main amd64 mummer amd64 3.23+dfsg-4 [809 kB] Get:82 http://deb.debian.org/debian buster/main amd64 python3-dendropy all 4.4.0-1 [265 kB] Get:83 http://deb.debian.org/debian buster/main amd64 python3-pymummer all 0.10.3-2 [9268 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 23.9 MB in 0s (102 MB/s) (Reading database ... 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Unpacking libssh2-1:amd64 (1.8.0-2.1) over (1.7.0-1+deb9u1) ... Preparing to unpack .../26-libssl1.1_1.1.1n-0+deb10u3_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1n-0+deb10u3) over (1.1.0l-1~deb9u1) ... Preparing to unpack .../27-libtasn1-6_4.13-3_amd64.deb ... Unpacking libtasn1-6:amd64 (4.13-3) over (4.10-1.1+deb9u1) ... Preparing to unpack .../28-multiarch-support_2.28-10+deb10u1_amd64.deb ... Unpacking multiarch-support (2.28-10+deb10u1) over (2.24-11+deb9u4) ... Preparing to unpack .../29-mummer_3.23+dfsg-4_amd64.deb ... Unpacking mummer (3.23+dfsg-4) over (3.23+dfsg-2) ... Preparing to unpack .../30-python3-dendropy_4.4.0-1_all.deb ... Unpacking python3-dendropy (4.4.0-1) over (4.2.0+dfsg-1) ... Preparing to unpack .../31-python3-pymummer_0.10.3-2_all.deb ... Unpacking python3-pymummer (0.10.3-2) over (0.10.1-1) ... Setting up readline-common (7.0-5) ... Setting up libnettle6:amd64 (3.4.1-1+deb10u1) ... Setting up cd-hit (4.6.8-2) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u4) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up mime-support (3.62) ... Installing new version of config file /etc/mime.types ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u7) ... Setting up multiarch-support (2.28-10+deb10u1) ... Setting up mummer (3.23+dfsg-4) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up fastaq (3.17.0-2) ... Setting up bowtie2 (2.3.4.3-1) ... Setting up libtasn1-6:amd64 (4.13-3) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-4+deb10u1) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libminimap0 (0.2-4) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... Setting up libssl1.1:amd64 (1.1.1n-0+deb10u3) ... Setting up libfml0 (0.1-5) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Setting up libffi6:amd64 (3.2.1-9) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up python3-pymummer (0.10.3-2) ... Setting up python3-dendropy (4.4.0-1) ... Setting up dh-python (3.20190308) ... Setting up libidn11:amd64 (1.33-2.2) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libhogweed4:amd64 (3.4.1-1+deb10u1) ... Setting up libp11-kit0:amd64 (0.23.15-2+deb10u1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... 0m25.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', '-y', 'upgrade'] 0m25.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', '-yf', 'dist-upgrade'] 0m45.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: dh-python libcapnp-0.5.3 libgdbm3 libhts1 libidn11 libmpfr4 libperl5.24 libpython3.5-minimal libpython3.5-stdlib libunistring0 python3-distutils python3-lib2to3 python3.5 python3.5-minimal Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libgsl2 The following NEW packages will be installed: blt fdisk fontconfig-config fonts-lyx gcc-8-base libblas3 libbsd0 libcapnp-0.7.0 libcom-err2 libdeflate0 libext2fs2 libfontconfig1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libgsl23 libgslcblas0 libhts2 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui liblapack3 liblcms2-2 libmpfr6 libmurmurhash1 libncurses6 libncursesw6 libperl5.28 libpng16-16 libpython2-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libseccomp2 libtcl8.6 libtiff5 libtinfo6 libtk8.6 libunistring2 libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libzstd1 lsb-base perl-modules-5.28 python-matplotlib-data python2 python2-minimal python3-biopython python3-bs4 python3-cycler python3-dateutil python3-distutils python3-kiwisolver python3-lib2to3 python3-matplotlib python3-numpy python3-pil python3-pyparsing python3-reportlab python3-reportlab-accel python3-six python3-soupsieve python3-tk python3.7 python3.7-minimal tk8.6-blt2.5 ttf-bitstream-vera tzdata ucf x11-common The following packages will be upgraded: apt ariba bash dash dpkg e2fslibs e2fsprogs gawk libapt-pkg5.0 libatomic1 libcomerr2 libcurl3-gnutls libgcc1 libgnutls30 libgomp1 libgssapi-krb5-2 libidn2-0 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libncurses5 libncursesw5 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libreadline7 libss2 libstdc++6 libtbb2 libtinfo5 login mash mount ncurses-base ncurses-bin perl perl-base python python-minimal python2.7 python2.7-minimal python3 python3-minimal python3-pysam samtools util-linux 49 upgraded, 83 newly installed, 1 to remove and 0 not upgraded. Need to get 65.7 MB of archives. After this operation, 192 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 libtinfo6 amd64 6.1+20181013-2+deb10u2 [325 kB] Get:2 http://deb.debian.org/debian buster/main amd64 bash amd64 5.0-4 [1378 kB] Get:3 http://deb.debian.org/debian buster/main amd64 libzstd1 amd64 1.3.8+dfsg-3+deb10u2 [237 kB] Get:4 http://deb.debian.org/debian buster/main amd64 libunistring2 amd64 0.9.10-1 [381 kB] Get:5 http://deb.debian.org/debian buster/main amd64 libidn2-0 amd64 2.0.5-1+deb10u1 [76.7 kB] Get:6 http://deb.debian.org/debian buster/main amd64 libgnutls30 amd64 3.6.7-4+deb10u8 [1126 kB] Get:7 http://deb.debian.org/debian buster/main amd64 libseccomp2 amd64 2.3.3-4 [41.4 kB] Get:8 http://deb.debian.org/debian buster/main amd64 gcc-8-base amd64 8.3.0-6 [191 kB] Get:9 http://deb.debian.org/debian buster/main amd64 libgcc1 amd64 1:8.3.0-6 [40.6 kB] Get:10 http://deb.debian.org/debian buster/main amd64 libstdc++6 amd64 8.3.0-6 [395 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libapt-pkg5.0 amd64 1.8.2.3 [967 kB] Get:12 http://deb.debian.org/debian buster/main amd64 apt amd64 1.8.2.3 [1418 kB] Get:13 http://deb.debian.org/debian buster/main amd64 dpkg amd64 1.19.8 [2210 kB] Get:14 http://deb.debian.org/debian buster/main amd64 dash amd64 0.5.10.2-5 [112 kB] Get:15 http://deb.debian.org/debian buster/main amd64 libcom-err2 amd64 1.44.5-1+deb10u3 [68.4 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libcomerr2 amd64 1.44.5-1+deb10u3 [64.2 kB] Get:17 http://deb.debian.org/debian buster/main amd64 libext2fs2 amd64 1.44.5-1+deb10u3 [221 kB] Get:18 http://deb.debian.org/debian buster/main amd64 e2fslibs amd64 1.44.5-1+deb10u3 [64.2 kB] Get:19 http://deb.debian.org/debian buster/main amd64 e2fsprogs amd64 1.44.5-1+deb10u3 [576 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libncursesw6 amd64 6.1+20181013-2+deb10u2 [132 kB] Get:21 http://deb.debian.org/debian buster/main amd64 fdisk amd64 2.33.1-0.1 [179 kB] Get:22 http://deb.debian.org/debian buster/main amd64 login amd64 1:4.5-1.1 [751 kB] Get:23 http://deb.debian.org/debian buster/main amd64 util-linux amd64 2.33.1-0.1 [1062 kB] Get:24 http://deb.debian.org/debian buster/main amd64 mount amd64 2.33.1-0.1 [174 kB] Get:25 http://deb.debian.org/debian buster/main amd64 ncurses-bin amd64 6.1+20181013-2+deb10u2 [406 kB] Get:26 http://deb.debian.org/debian buster/main amd64 perl-modules-5.28 all 5.28.1-6+deb10u1 [2873 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libgdbm6 amd64 1.18.1-4 [64.7 kB] Get:28 http://deb.debian.org/debian buster/main amd64 libgdbm-compat4 amd64 1.18.1-4 [44.1 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libperl5.28 amd64 5.28.1-6+deb10u1 [3894 kB] Get:30 http://deb.debian.org/debian buster/main amd64 perl amd64 5.28.1-6+deb10u1 [204 kB] Get:31 http://deb.debian.org/debian buster/main amd64 perl-base amd64 5.28.1-6+deb10u1 [1514 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libncurses5 amd64 6.1+20181013-2+deb10u2 [96.2 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libtinfo5 amd64 6.1+20181013-2+deb10u2 [321 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libncursesw5 amd64 6.1+20181013-2+deb10u2 [118 kB] Get:35 http://deb.debian.org/debian buster/main amd64 ncurses-base all 6.1+20181013-2+deb10u2 [258 kB] Get:36 http://deb.debian.org/debian buster/main amd64 libcapnp-0.7.0 amd64 0.7.0-3 [1025 kB] Get:37 http://deb.debian.org/debian buster/main amd64 mash amd64 2.1+dfsg-2 [149 kB] Get:38 http://deb.debian.org/debian buster/main amd64 libgslcblas0 amd64 2.5+dfsg-6 [101 kB] Get:39 http://deb.debian.org/debian buster/main amd64 libgsl23 amd64 2.5+dfsg-6 [880 kB] Get:40 http://deb.debian.org/debian buster/main amd64 libmurmurhash1 amd64 1.3-2 [5556 B] Get:41 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get:42 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:43 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get:44 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get:46 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get:47 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get:48 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:50 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:51 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:52 http://deb.debian.org/debian buster/main amd64 libmpfr6 amd64 4.0.2-1 [775 kB] Get:53 http://deb.debian.org/debian buster/main amd64 gawk amd64 1:4.2.1+dfsg-1 [660 kB] Get:54 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get:55 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get:56 http://deb.debian.org/debian buster/main amd64 python3-pysam amd64 0.15.2+ds-2 [1661 kB] Get:57 http://deb.debian.org/debian buster/main amd64 ariba amd64 2.13.3+ds-1 [1679 kB] Get:58 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get:59 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u4 [158 kB] Get:61 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u4 [369 kB] Get:62 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u4 [122 kB] Get:63 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u4 [65.9 kB] Get:64 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u7 [224 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:66 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get:67 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get:68 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get:69 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get:70 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get:71 http://deb.debian.org/debian buster/main amd64 libquadmath0 amd64 8.3.0-6 [133 kB] Get:72 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get:73 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get:74 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get:75 http://deb.debian.org/debian buster/main amd64 python3-numpy amd64 1:1.16.2-1 [2119 kB] Get:76 http://deb.debian.org/debian buster/main amd64 python3-reportlab-accel amd64 3.5.13-1+deb10u1 [35.3 kB] Get:77 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get:78 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u3 [380 kB] Get:79 http://deb.debian.org/debian buster/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get:80 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get:81 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get:82 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:83 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get:84 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u4 [271 kB] Get:85 http://deb.debian.org/debian buster/main amd64 libwebpdemux2 amd64 0.6.1-2+deb10u1 [87.6 kB] Get:86 http://deb.debian.org/debian buster/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u1 [97.8 kB] Get:87 http://deb.debian.org/debian buster/main amd64 python3-pil amd64 5.4.1-2+deb10u3 [395 kB] Get:88 http://deb.debian.org/debian buster/main amd64 python3-reportlab all 3.5.13-1+deb10u1 [541 kB] Get:89 http://deb.debian.org/debian buster/main amd64 python3-biopython amd64 1.73+dfsg-1 [1287 kB] Get:90 http://deb.debian.org/debian buster/main amd64 python3-soupsieve all 1.8+dfsg-1 [27.6 kB] Get:91 http://deb.debian.org/debian buster/main amd64 python3-bs4 all 4.7.1-1 [94.1 kB] Get:92 http://deb.debian.org/debian buster/main amd64 python3-six all 1.12.0-1 [15.7 kB] Get:93 http://deb.debian.org/debian buster/main amd64 tzdata all 2021a-0+deb10u6 [265 kB] Get:94 http://deb.debian.org/debian buster/main amd64 python3-dateutil all 2.7.3-3 [64.5 kB] Get:95 http://deb.debian.org/debian buster/main amd64 fonts-lyx all 2.3.2-1 [199 kB] Get:96 http://deb.debian.org/debian buster/main amd64 ttf-bitstream-vera all 1.10-8 [352 kB] Get:97 http://deb.debian.org/debian buster/main amd64 python-matplotlib-data all 3.0.2-2 [4138 kB] Get:98 http://deb.debian.org/debian buster/main amd64 python3-pyparsing all 2.2.0+dfsg1-2 [89.6 kB] Get:99 http://deb.debian.org/debian buster/main amd64 libjs-jquery all 3.3.1~dfsg-3+deb10u1 [332 kB] Get:100 http://deb.debian.org/debian buster/main amd64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get:101 http://deb.debian.org/debian buster/main amd64 python3-cycler all 0.10.0-1 [7556 B] Get:102 http://deb.debian.org/debian buster/main amd64 python3-kiwisolver amd64 1.0.1-2+b1 [65.4 kB] Get:103 http://deb.debian.org/debian buster/main amd64 python3-matplotlib amd64 3.0.2-2 [5353 kB] Get:104 http://deb.debian.org/debian buster/main amd64 libtcl8.6 amd64 8.6.9+dfsg-2 [1005 kB] Get:105 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:106 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get:107 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get:108 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:109 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get:110 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:111 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get:112 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get:113 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get:114 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:115 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:116 http://deb.debian.org/debian buster/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:117 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get:118 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get:119 http://deb.debian.org/debian buster/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:120 http://deb.debian.org/debian buster/main amd64 libtk8.6 amd64 8.6.9-2 [768 kB] Get:121 http://deb.debian.org/debian buster/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4 [587 kB] Get:122 http://deb.debian.org/debian buster/main amd64 blt amd64 2.5.3+dfsg-4 [14.8 kB] Get:123 http://deb.debian.org/debian buster/main amd64 python3-tk amd64 3.7.3-1 [97.4 kB] Get:124 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get:125 http://deb.debian.org/debian buster/main amd64 libss2 amd64 1.44.5-1+deb10u3 [72.9 kB] Get:126 http://deb.debian.org/debian buster/main amd64 libatomic1 amd64 8.3.0-6 [9032 B] Get:127 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB] Get:128 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get:129 http://deb.debian.org/debian buster/main amd64 libtbb2 amd64 2018~U6-4 [147 kB] Get:130 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get:131 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get:132 http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 [443 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 65.7 MB in 0s (109 MB/s) Selecting previously unselected package libtinfo6:amd64. (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 ... 9177 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libtinfo6:amd64 (6.1+20181013-2+deb10u2) ... (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 ... 9187 files and directories currently installed.) Preparing to unpack .../archives/bash_5.0-4_amd64.deb ... Unpacking bash (5.0-4) over (4.4-5) ... Setting up bash (5.0-4) ... Installing new version of config file /etc/bash.bashrc ... Installing new version of config file /etc/skel/.profile ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode Selecting previously unselected package libzstd1:amd64. (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 ... 9188 files and directories currently installed.) Preparing to unpack .../libzstd1_1.3.8+dfsg-3+deb10u2_amd64.deb ... Unpacking libzstd1:amd64 (1.3.8+dfsg-3+deb10u2) ... Setting up libzstd1:amd64 (1.3.8+dfsg-3+deb10u2) ... Selecting previously unselected package libunistring2:amd64. (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 ... 9194 files and directories currently installed.) Preparing to unpack .../libunistring2_0.9.10-1_amd64.deb ... Unpacking libunistring2:amd64 (0.9.10-1) ... Setting up libunistring2:amd64 (0.9.10-1) ... (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 ... 9232 files and directories currently installed.) Preparing to unpack .../gcc-8-base_8.3.0-6_amd64.deb ... Unpacking gcc-8-base:amd64 (8.3.0-6) ... Setting up gcc-8-base:amd64 (8.3.0-6) ... (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 ... 9238 files and directories currently installed.) Preparing to unpack .../archives/apt_1.8.2.3_amd64.deb ... Unpacking apt (1.8.2.3) over (1.4.10) ... Preparing to unpack .../libapt-pkg5.0_1.8.2.3_amd64.deb ... Unpacking libapt-pkg5.0:amd64 (1.8.2.3) over (1.4.10) ... Setting up libapt-pkg5.0:amd64 (1.8.2.3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9266 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.19.8_amd64.deb ... Unpacking dpkg (1.19.8) over (1.18.25) ... Setting up dpkg (1.19.8) ... Installing new version of config file /etc/alternatives/README ... Installing new version of config file /etc/cron.daily/dpkg ... Installing new version of config file /etc/logrotate.d/dpkg ... (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 ... 9264 files and directories currently installed.) Preparing to unpack .../dash_0.5.10.2-5_amd64.deb ... Unpacking dash (0.5.10.2-5) over (0.5.8-2.4) ... Setting up dash (0.5.10.2-5) ... (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 ... 9268 files and directories currently installed.) Preparing to unpack .../e2fslibs_1.44.5-1+deb10u3_amd64.deb ... Unpacking e2fslibs:amd64 (1.44.5-1+deb10u3) over (1.43.4-2+deb9u1) ... Selecting previously unselected package libext2fs2:amd64. Preparing to unpack .../libext2fs2_1.44.5-1+deb10u3_amd64.deb ... Unpacking libext2fs2:amd64 (1.44.5-1+deb10u3) ... Setting up libext2fs2:amd64 (1.44.5-1+deb10u3) ... (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 ... 9254 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncursesw6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libncursesw6:amd64 (6.1+20181013-2+deb10u2) ... (Reading database ... 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Unpacking fdisk (2.33.1-0.1) ... Setting up fdisk (2.33.1-0.1) ... (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 ... 9280 files and directories currently installed.) Preparing to unpack .../login_1%3a4.5-1.1_amd64.deb ... Unpacking login (1:4.5-1.1) over (1:4.4-4.1) ... Setting up login (1:4.5-1.1) ... Installing new version of config file /etc/securetty ... (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 ... 9270 files and directories currently installed.) Preparing to unpack .../0-perl_5.28.1-6+deb10u1_amd64.deb ... Unpacking perl (5.28.1-6+deb10u1) over (5.24.1-3+deb9u7) ... Selecting previously unselected package perl-modules-5.28. Preparing to unpack .../1-perl-modules-5.28_5.28.1-6+deb10u1_all.deb ... Unpacking perl-modules-5.28 (5.28.1-6+deb10u1) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../2-libgdbm6_1.18.1-4_amd64.deb ... Unpacking libgdbm6:amd64 (1.18.1-4) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../3-libgdbm-compat4_1.18.1-4_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.18.1-4) ... Selecting previously unselected package libperl5.28:amd64. Preparing to unpack .../4-libperl5.28_5.28.1-6+deb10u1_amd64.deb ... Unpacking libperl5.28:amd64 (5.28.1-6+deb10u1) ... Preparing to unpack .../5-perl-base_5.28.1-6+deb10u1_amd64.deb ... Unpacking perl-base (5.28.1-6+deb10u1) over (5.24.1-3+deb9u7) ... Setting up perl-base (5.28.1-6+deb10u1) ... (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 ... 11170 files and directories currently installed.) Preparing to unpack .../libncursesw5_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncursesw5:amd64 (6.1+20181013-2+deb10u2) over (6.0+20161126-1+deb9u2) ... Setting up libncursesw5:amd64 (6.1+20181013-2+deb10u2) ... (Reading database ... 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Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt-compat ... Setting up libmurmurhash1 (1.3-2) ... Setting up e2fslibs:amd64 (1.44.5-1+deb10u3) ... Setting up libgslcblas0:amd64 (2.5+dfsg-6) ... Setting up gawk (1:4.2.1+dfsg-1) ... Setting up fonts-lyx (2.3.2-1) ... 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 libdeflate0:amd64 (1.2-1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Setting up libgomp1:amd64 (8.3.0-6) ... Setting up libcapnp-0.7.0:amd64 (0.7.0-3) ... Setting up libncurses5:amd64 (6.1+20181013-2+deb10u2) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u4) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up tzdata (2021a-0+deb10u6) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Dec 17 01:39:39 UTC 2022. Universal Time is now: Sat Dec 17 01:39:39 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Setting up libx11-data (2:1.6.7-1+deb10u2) ... Setting up libgsl23:amd64 (2.5+dfsg-6) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libquadmath0:amd64 (8.3.0-6) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up libatomic1:amd64 (8.3.0-6) ... Setting up mash (2.1+dfsg-2) ... Setting up libtcl8.6:amd64 (8.6.9+dfsg-2) ... Setting up libwebp6:amd64 (0.6.1-2+deb10u1) ... Setting up util-linux (2.33.1-0.1) ... update-alternatives: warning: alternative /usr/bin/pg (part of link group pager) doesn't exist; removing from list of alternatives Setting up ucf (3.0038+nmu1) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u4) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up mount (2.33.1-0.1) ... Setting up libcomerr2:amd64 (1.44.5-1+deb10u3) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u4) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Setting up libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Setting up python-matplotlib-data (3.0.2-2) ... Setting up libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up libgdbm6:amd64 (1.18.1-4) ... Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Setting up libtbb2:amd64 (2018~U6-4) ... Setting up python3 (3.7.3-1) ... Setting up python2 (2.7.16-1) ... Setting up python3-six (1.12.0-1) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up libblas3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up python3-pyparsing (2.2.0+dfsg1-2) ... Setting up libfreetype6:amd64 (2.9.1-3+deb10u3) ... Setting up python3-cycler (0.10.0-1) ... Setting up python3-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Setting up python3-kiwisolver (1.0.1-2+b1) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Setting up libgdbm-compat4:amd64 (1.18.1-4) ... Setting up libperl5.28:amd64 (5.28.1-6+deb10u1) ... Setting up libx11-6:amd64 (2:1.6.7-1+deb10u2) ... Setting up python3-dateutil (2.7.3-3) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python (2.7.16-1) ... Setting up python3-soupsieve (1.8+dfsg-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up liblapack3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3-bs4 (4.7.1-1) ... Setting up python3-pil:amd64 (5.4.1-2+deb10u3) ... Setting up perl (5.28.1-6+deb10u1) ... update-alternatives: warning: alternative /usr/bin/prename (part of link group rename) doesn't exist; removing from list of alternatives update-alternatives: warning: /etc/alternatives/rename is dangling; it will be updated with best choice Removing obsolete conffile /etc/perl/sitecustomize.pl ... Setting up python3-numpy (1:1.16.2-1) ... Setting up python3-reportlab (3.5.13-1+deb10u1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up python3-biopython (1.73+dfsg-1) ... Setting up python3-matplotlib (3.0.2-2) ... Setting up libxft2:amd64 (2.3.2-2) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up libtk8.6:amd64 (8.6.9-2) ... Setting up samtools (1.9-4) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4) ... Setting up python3-pysam (0.15.2+ds-2) ... Setting up blt (2.5.3+dfsg-4) ... Setting up python3-tk:amd64 (3.7.3-1) ... Setting up ariba (2.13.3+ds-1) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... Processing triggers for mime-support (3.62) ... 0m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', '-yf', 'dist-upgrade'] 0m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m46.6s DUMP: f6fc0f2636004ef589309651dfd778f4 - 0m46.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m46.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 0m46.7s DUMP: Package: ariba Version: 2.13.3+ds-1 Installed-Size: 17444 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 3.12.0), python3 (<< 3.8), python3 (>= 3.7~), python3-biopython, python3-bs4, python3-dendropy, python3-matplotlib, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3:any, libc6 (>= 2.14), libfml0 (>= 0.1-4~), libgcc1 (>= 1:3.0), libminimap0, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), bowtie2 (>= 2.1.0), cd-hit, mash, mummer, python3-tk Description-en: Antibiotic Resistance Identification By Assembly ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. The input is a FASTA file of reference genes and paired sequencing reads. ARIBA reports which of the reference genes were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference genes. Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Homepage: https://github.com/sanger-pathogens/ariba Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.13.3+ds-1_amd64.deb Size: 1678912 MD5sum: 77517ce195de03a32365f34e5629bb30 SHA256: a971e793eca324e1333e4cf1c89abd795839a5b7869c10d31a2dca27675f074e 0m46.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 0m46.7s INFO: apt-cache knows about the following packages: ariba 0m46.7s INFO: Running scripts pre_install 0m46.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_database-server'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_database-server'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_exceptions'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_exceptions'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_extras'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_extras'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_foreign_architecture'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_foreign_architecture'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'policy'] 0m46.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m46.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'policy'] 0m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'policy', 'ariba'] 0m46.9s DUMP: ariba: Installed: 2.13.3+ds-1 Candidate: 2.13.3+ds-1 Version table: *** 2.13.3+ds-1 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m46.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'policy', 'ariba'] 0m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', '-y', 'install', 'ariba'] 0m47.2s DUMP: Reading package lists... Building dependency tree... Reading state information... ariba is already the newest version (2.13.3+ds-1). The following packages were automatically installed and are no longer required: dh-python libcapnp-0.5.3 libgdbm3 libhts1 libidn11 libmpfr4 libncurses5 libperl5.24 libpython3.5-minimal libpython3.5-stdlib libunistring0 python3-distutils python3-lib2to3 python3.5 python3.5-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', '-y', 'install', 'ariba'] 0m47.2s INFO: Running scripts post_install 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_install_exceptions'] 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_install_exceptions'] 0m47.2s INFO: Running scripts post_distupgrade 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_distupgrade_exceptions'] 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_distupgrade_exceptions'] 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_distupgrade_zz_backports'] 0m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_distupgrade_zz_backports'] 0m47.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m48.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m48.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m48.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m48.9s INFO: Running scripts pre_install 0m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_database-server'] 0m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_database-server'] 0m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_exceptions'] 0m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_exceptions'] 0m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_extras'] 0m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_extras'] 0m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_foreign_architecture'] 0m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_foreign_architecture'] 0m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'policy'] 0m49.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m49.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'policy'] 0m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'policy', 'ariba'] 0m49.0s DUMP: ariba: Installed: 2.13.3+ds-1 Candidate: 2.13.3+ds-1 Version table: *** 2.13.3+ds-1 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m49.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-cache', 'policy', 'ariba'] 0m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', '-y', 'install', 'ariba=2.13.3+ds-1'] 0m49.3s DUMP: Reading package lists... Building dependency tree... Reading state information... ariba is already the newest version (2.13.3+ds-1). The following packages were automatically installed and are no longer required: dh-python libcapnp-0.5.3 libgdbm3 libhts1 libidn11 libmpfr4 libncurses5 libperl5.24 libpython3.5-minimal libpython3.5-stdlib libunistring0 python3-distutils python3-lib2to3 python3.5 python3.5-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', '-y', 'install', 'ariba=2.13.3+ds-1'] 0m49.3s INFO: Running scripts post_install 0m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_install_exceptions'] 0m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_install_exceptions'] 0m49.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m50.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m51.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', '-ac', '--ignore-obsolete'] 0m52.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', '-ac', '--ignore-obsolete'] 0m52.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m52.6s DUMP: 0.15.6 0m52.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m52.6s INFO: Running adequate version 0.15.6 now. 0m52.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'ariba'] 0m52.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'ariba'] 0m52.7s INFO: Running scripts pre_remove 0m52.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m52.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m52.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m52.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m52.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m54.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m54.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_remove_exceptions'] 0m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/pre_remove_exceptions'] 0m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m55.1s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed ariba ariba 2.13.3+ds-1 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed blt blt 2.5.3+dfsg-4 install ok installed bowtie2 bowtie2 2.3.4.3-1 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed cd-hit cd-hit 4.6.8-2 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u1 install ok installed debianutils debianutils 4.8.6.1 install ok installed dh-python dh-python 3.20190308 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fslibs:amd64 e2fslibs 1.44.5-1+deb10u3 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fastaq fastaq 3.17.0-2 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed fontconfig-config fontconfig-config 2.13.1-2 install ok installed fonts-lyx fonts-lyx 2.3.2-1 install ok installed gawk gawk 1:4.2.1+dfsg-1 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libatomic1:amd64 libatomic1 8.3.0-6 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblas3:amd64 libblas3 3.8.0-2 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbsd0:amd64 libbsd0 0.9.1-2+deb10u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u1 install ok installed libc-bin libc-bin 2.28-10+deb10u1 install ok installed libc6:amd64 libc6 2.28-10+deb10u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcapnp-0.5.3 libcapnp-0.5.3 0.5.3-2 install ok installed libcapnp-0.7.0:amd64 libcapnp-0.7.0 0.7.0-3 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libcomerr2:amd64 libcomerr2 1.44.5-1+deb10u3 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.64.0-4+deb10u2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libdeflate0:amd64 libdeflate0 1.2-1 install ok installed libexpat1:amd64 libexpat1 2.2.6-2+deb10u4 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libfml0 libfml0 0.1-5 install ok installed libfontconfig1:amd64 libfontconfig1 2.13.1-2 install ok installed libfreetype6:amd64 libfreetype6 2.9.1-3+deb10u3 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.18.1-4 install ok installed libgdbm3:amd64 libgdbm3 1.8.3-14 install ok installed libgdbm6:amd64 libgdbm6 1.18.1-4 install ok installed libgfortran5:amd64 libgfortran5 8.3.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u8 install ok installed libgomp1:amd64 libgomp1 8.3.0-6 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libgsl23:amd64 libgsl23 2.5+dfsg-6 install ok installed libgslcblas0:amd64 libgslcblas0 2.5+dfsg-6 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.17-3+deb10u4 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libhts1:amd64 libhts1 1.3.2-2 install ok installed libhts2:amd64 libhts2 1.9-12~deb10u1 install ok installed libidn11:amd64 libidn11 1.33-2.2 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed libimagequant0:amd64 libimagequant0 2.12.2-1.1 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:1.5.2-2+deb10u1 install ok installed libjs-jquery libjs-jquery 3.3.1~dfsg-3+deb10u1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.12.1+dfsg-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.17-3+deb10u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.17-3+deb10u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.17-3+deb10u4 install ok installed liblapack3:amd64 liblapack3 3.8.0-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.9-3 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.47+dfsg-3+deb10u7 install ok installed libldap-common libldap-common 2.4.47+dfsg-3+deb10u7 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libminimap0 libminimap0 0.2-4 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libmpdec2:amd64 libmpdec2 2.4.2-2 install ok installed libmpfr4:amd64 libmpfr4 3.1.5-1 install ok installed libmpfr6:amd64 libmpfr6 4.0.2-1 install ok installed libmurmurhash1 libmurmurhash1 1.3-2 install ok installed libncurses5:amd64 libncurses5 6.1+20181013-2+deb10u2 install ok installed libncurses6:amd64 libncurses6 6.1+20181013-2+deb10u2 install ok installed libncursesw5:amd64 libncursesw5 6.1+20181013-2+deb10u2 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u2 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.36.0-2+deb10u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libperl5.24:amd64 libperl5.24 5.24.1-3+deb9u7 install ok installed libperl5.28:amd64 libperl5.28 5.28.1-6+deb10u1 install ok installed libpng16-16:amd64 libpng16-16 1.6.36-6 install ok installed libpsl5:amd64 libpsl5 0.20.2-2 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.16-1 install ok installed libpython2-stdlib:amd64 libpython2-stdlib 2.7.16-1 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.16-2+deb10u1 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.16-2+deb10u1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.7.3-1 install ok installed libpython3.5-minimal:amd64 libpython3.5-minimal 3.5.3-1+deb9u1 install ok installed libpython3.5-stdlib:amd64 libpython3.5-stdlib 3.5.3-1+deb9u1 install ok installed libpython3.7-minimal:amd64 libpython3.7-minimal 3.7.3-2+deb10u3 install ok installed libpython3.7-stdlib:amd64 libpython3.7-stdlib 3.7.3-2+deb10u3 install ok installed libquadmath0:amd64 libquadmath0 8.3.0-6 install ok installed libreadline7:amd64 libreadline7 7.0-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-1+deb10u2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-1+deb10u2 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsigsegv2:amd64 libsigsegv2 2.12-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.27.2-3+deb10u1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libssh2-1:amd64 libssh2-1 1.8.0-2.1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1n-0+deb10u3 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u8 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtbb2:amd64 libtbb2 2018~U6-4 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.9+dfsg-2 install ok installed libtiff5:amd64 libtiff5 4.1.0+git191117-2~deb10u4 install ok installed libtinfo5:amd64 libtinfo5 6.1+20181013-2+deb10u2 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libtk8.6:amd64 libtk8.6 8.6.9-2 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring0:amd64 libunistring0 0.9.6+really0.9.3-0.1 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2+deb10u1 install ok installed libwebpdemux2:amd64 libwebpdemux2 0.6.1-2+deb10u1 install ok installed libwebpmux3:amd64 libwebpmux3 0.6.1-2+deb10u1 install ok installed libx11-6:amd64 libx11-6 2:1.6.7-1+deb10u2 install ok installed libx11-data libx11-data 2:1.6.7-1+deb10u2 install ok installed libxau6:amd64 libxau6 1:1.0.8-1+b2 install ok installed libxcb1:amd64 libxcb1 1.13.1-2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.3-1+b2 install ok installed libxft2:amd64 libxft2 2.3.2-2 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed lsb-base lsb-base 10.2019051400 install ok installed mash mash 2.1+dfsg-2 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mime-support mime-support 3.62 install ok installed mount mount 2.33.1-0.1 install ok installed multiarch-support multiarch-support 2.28-10+deb10u1 install ok installed mummer mummer 3.23+dfsg-4 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u2 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl perl 5.28.1-6+deb10u1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed perl-modules-5.24 perl-modules-5.24 5.24.1-3+deb9u7 install ok installed perl-modules-5.28 perl-modules-5.28 5.28.1-6+deb10u1 install ok installed python python 2.7.16-1 install ok installed python-matplotlib-data python-matplotlib-data 3.0.2-2 install ok installed python-minimal python-minimal 2.7.16-1 install ok installed python2 python2 2.7.16-1 install ok installed python2-minimal python2-minimal 2.7.16-1 install ok installed python2.7 python2.7 2.7.16-2+deb10u1 install ok installed python2.7-minimal python2.7-minimal 2.7.16-2+deb10u1 install ok installed python3 python3 3.7.3-1 install ok installed python3-biopython python3-biopython 1.73+dfsg-1 install ok installed python3-bs4 python3-bs4 4.7.1-1 install ok installed python3-cycler python3-cycler 0.10.0-1 install ok installed python3-dateutil python3-dateutil 2.7.3-3 install ok installed python3-dendropy python3-dendropy 4.4.0-1 install ok installed python3-distutils python3-distutils 3.7.3-1 install ok installed python3-kiwisolver python3-kiwisolver 1.0.1-2+b1 install ok installed python3-lib2to3 python3-lib2to3 3.7.3-1 install ok installed python3-matplotlib python3-matplotlib 3.0.2-2 install ok installed python3-minimal python3-minimal 3.7.3-1 install ok installed python3-numpy python3-numpy 1:1.16.2-1 install ok installed python3-pil:amd64 python3-pil 5.4.1-2+deb10u3 install ok installed python3-pkg-resources python3-pkg-resources 40.8.0-1 install ok installed python3-pymummer python3-pymummer 0.10.3-2 install ok installed python3-pyparsing python3-pyparsing 2.2.0+dfsg1-2 install ok installed python3-pysam python3-pysam 0.15.2+ds-2 install ok installed python3-reportlab python3-reportlab 3.5.13-1+deb10u1 install ok installed python3-reportlab-accel:amd64 python3-reportlab-accel 3.5.13-1+deb10u1 install ok installed python3-six python3-six 1.12.0-1 install ok installed python3-soupsieve python3-soupsieve 1.8+dfsg-1 install ok installed python3-tk:amd64 python3-tk 3.7.3-1 install ok installed python3.5 python3.5 3.5.3-1+deb9u1 install ok installed python3.5-minimal python3.5-minimal 3.5.3-1+deb9u1 install ok installed python3.7 python3.7 3.7.3-2+deb10u3 install ok installed python3.7-minimal python3.7-minimal 3.7.3-2+deb10u3 install ok installed readline-common readline-common 7.0-5 install ok installed samtools samtools 1.9-4 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.12 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-4 install ok installed ttf-bitstream-vera ttf-bitstream-vera 1.10-8 install ok installed tzdata tzdata 2021a-0+deb10u6 install ok installed ucf ucf 3.0038+nmu1 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed x11-common x11-common 1:7.7+19 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 0m55.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m55.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', 'remove', 'blt', 'bowtie2', 'cd-hit', 'dh-python', 'fastaq', 'fontconfig-config', 'fonts-lyx', 'gawk', 'libatomic1:amd64', 'libblas3:amd64', 'libbsd0:amd64', 'libcapnp-0.5.3', 'libcapnp-0.7.0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfml0', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgsl23:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libminimap0', 'libmpdec2:amd64', 'libmpfr4:amd64', 'libmpfr6:amd64', 'libmurmurhash1', 'libncurses5:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.5-minimal:amd64', 'libpython3.5-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libtiff5:amd64', 'libtk8.6:amd64', 'libunistring0:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'lsb-base', 'mash', 'mime-support', 'mummer', 'perl', 'perl-modules-5.24', 'perl-modules-5.28', 'python', 'python-matplotlib-data', 'python-minimal', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-biopython', 'python3-bs4', 'python3-cycler', 'python3-dateutil', 'python3-dendropy', 'python3-distutils', 'python3-kiwisolver', 'python3-lib2to3', 'python3-matplotlib', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pymummer', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-six', 'python3-soupsieve', 'python3-tk:amd64', 'python3.5', 'python3.5-minimal', 'python3.7', 'python3.7-minimal', 'readline-common', 'samtools', 'tk8.6-blt2.5', 'ttf-bitstream-vera', 'tzdata', 'ucf', 'x11-common', 'ariba'] 0m58.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ariba blt bowtie2 cd-hit dh-python fastaq fontconfig-config fonts-lyx gawk libatomic1 libblas3 libbsd0 libcapnp-0.5.3 libcapnp-0.7.0 libcurl3-gnutls libdeflate0 libexpat1 libfml0 libfontconfig1 libfreetype6 libgdbm-compat4 libgdbm3 libgdbm6 libgfortran5 libgomp1 libgsl23 libgslcblas0 libgssapi-krb5-2 libhts1 libhts2 libidn11 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libminimap0 libmpdec2 libmpfr4 libmpfr6 libmurmurhash1 libncurses5 libncurses6 libnghttp2-14 libperl5.24 libperl5.28 libpng16-16 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 libtbb2 libtcl8.6 libtiff5 libtk8.6 libunistring0 libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 lsb-base mash mime-support mummer perl perl-modules-5.24 perl-modules-5.28 python python-matplotlib-data python-minimal python2 python2-minimal python2.7 python2.7-minimal python3 python3-biopython python3-bs4 python3-cycler python3-dateutil python3-dendropy python3-distutils python3-kiwisolver python3-lib2to3 python3-matplotlib python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pymummer python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-six python3-soupsieve python3-tk python3.5 python3.5-minimal python3.7 python3.7-minimal readline-common samtools tk8.6-blt2.5 ttf-bitstream-vera tzdata ucf x11-common 0 upgraded, 0 newly installed, 138 to remove and 0 not upgraded. After this operation, 307 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 ... 17462 files and directories currently installed.) Removing ariba (2.13.3+ds-1) ... Removing python3-tk:amd64 (3.7.3-1) ... Removing blt (2.5.3+dfsg-4) ... Removing bowtie2 (2.3.4.3-1) ... Removing cd-hit (4.6.8-2) ... Removing dh-python (3.20190308) ... Removing python3-pymummer (0.10.3-2) ... Removing fastaq (3.17.0-2) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-4) ... Removing libtk8.6:amd64 (8.6.9-2) ... Removing libxft2:amd64 (2.3.2-2) ... Removing libfontconfig1:amd64 (2.13.1-2) ... Removing fontconfig-config (2.13.1-2) ... Removing python3-matplotlib (3.0.2-2) ... Removing python-matplotlib-data (3.0.2-2) ... Removing fonts-lyx (2.3.2-1) ... Removing mummer (3.23+dfsg-4) ... Removing gawk (1:4.2.1+dfsg-1) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing libtbb2:amd64 (2018~U6-4) ... Removing libatomic1:amd64 (8.3.0-6) ... Removing python3-biopython (1.73+dfsg-1) ... Removing python3-numpy (1:1.16.2-1) ... Removing liblapack3:amd64 (3.8.0-2) ... Removing libblas3:amd64 (3.8.0-2) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing libcapnp-0.5.3 (0.5.3-2) ... Removing mash (2.1+dfsg-2) ... Removing libcapnp-0.7.0:amd64 (0.7.0-3) ... Removing libhts1:amd64 (1.3.2-2) ... Removing samtools (1.9-4) ... Removing python3.5 (3.5.3-1+deb9u1) ... Removing python3.5-minimal (3.5.3-1+deb9u1) ... Removing python3-distutils (3.7.3-1) ... Removing python3-bs4 (4.7.1-1) ... Removing python3-soupsieve (1.8+dfsg-1) ... Removing libfml0 (0.1-5) ... Removing python3-reportlab (3.5.13-1+deb10u1) ... Removing python3-pil:amd64 (5.4.1-2+deb10u3) ... Removing libfreetype6:amd64 (2.9.1-3+deb10u3) ... Removing perl (5.28.1-6+deb10u1) ... Removing libperl5.28:amd64 (5.28.1-6+deb10u1) ... Removing libgdbm-compat4:amd64 (1.18.1-4) ... Removing libperl5.24:amd64 (5.24.1-3+deb9u7) ... Removing libgdbm3:amd64 (1.8.3-14) ... Removing libgdbm6:amd64 (1.18.1-4) ... Removing libgfortran5:amd64 (8.3.0-6) ... Removing libgomp1:amd64 (8.3.0-6) ... Removing libgsl23:amd64 (2.5+dfsg-6) ... Removing libgslcblas0:amd64 (2.5+dfsg-6) ... Removing libidn11:amd64 (1.33-2.2) ... Removing libimagequant0:amd64 (2.12.2-1.1) ... Removing libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Removing libjs-jquery-ui (1.12.1+dfsg-5) ... Removing libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Removing liblcms2-2:amd64 (2.9-3) ... Removing libminimap0 (0.2-4) ... Removing libpython3.5-stdlib:amd64 (3.5.3-1+deb9u1) ... Removing libmpfr4:amd64 (3.1.5-1) ... Removing libmpfr6:amd64 (4.0.2-1) ... Removing libmurmurhash1 (1.3-2) ... Removing libncurses5:amd64 (6.1+20181013-2+deb10u2) ... Removing libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Removing libpng16-16:amd64 (1.6.36-6) ... Removing python (2.7.16-1) ... Removing libpython-stdlib:amd64 (2.7.16-1) ... Removing python2 (2.7.16-1) ... Removing libpython2-stdlib:amd64 (2.7.16-1) ... Removing python2.7 (2.7.16-2+deb10u1) ... Removing libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Removing python-minimal (2.7.16-1) ... Removing libpython3.5-minimal:amd64 (3.5.3-1+deb9u1) ... Removing libquadmath0:amd64 (8.3.0-6) ... Removing libsigsegv2:amd64 (2.12-2) ... Removing libtcl8.6:amd64 (8.6.9+dfsg-2) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Removing libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Removing libwebp6:amd64 (0.6.1-2+deb10u1) ... Removing libxext6:amd64 (2:1.3.3-1+b2) ... 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 (10.2019051400) ... Removing perl-modules-5.24 (5.24.1-3+deb9u7) ... Removing perl-modules-5.28 (5.28.1-6+deb10u1) ... Removing python2-minimal (2.7.16-1) ... Removing python3-cycler (0.10.0-1) ... Removing python3-dateutil (2.7.3-3) ... Removing python3-dendropy (4.4.0-1) ... Removing python3-kiwisolver (1.0.1-2+b1) ... Removing python3-lib2to3 (3.7.3-1) ... Removing python3-pkg-resources (40.8.0-1) ... Removing python3-pyparsing (2.2.0+dfsg1-2) ... Removing python3-pysam (0.15.2+ds-2) ... Removing python3-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Removing python3-six (1.12.0-1) ... Removing ttf-bitstream-vera (1.10-8) ... Removing tzdata (2021a-0+deb10u6) ... Removing ucf (3.0038+nmu1) ... Removing libx11-6:amd64 (2:1.6.7-1+deb10u2) ... Removing libxcb1:amd64 (1.13.1-2) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.9.1-2+deb10u1) ... Removing libhts2:amd64 (1.9-12~deb10u1) ... Removing libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Removing libdeflate0:amd64 (1.2-1) ... Removing python3 (3.7.3-1) ... Removing python3.7 (3.7.3-2+deb10u3) ... Removing libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Removing libkrb5-3:amd64 (1.17-3+deb10u4) ... Removing libk5crypto3:amd64 (1.17-3+deb10u4) ... Removing libkrb5support0:amd64 (1.17-3+deb10u4) ... Removing libkeyutils1:amd64 (1.6-6) ... Removing libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Removing libldap-common (2.4.47+dfsg-3+deb10u7) ... Removing libpython3-stdlib:amd64 (3.7.3-1) ... Removing libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec2:amd64 (2.4.2-2) ... Removing libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Removing libpsl5:amd64 (0.20.2-2) ... Removing python2.7-minimal (2.7.16-2+deb10u1) ... Removing libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... find: '/usr/lib/python2.7': No such file or directory Removing libreadline7:amd64 (7.0-5) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Removing libssh2-1:amd64 (1.8.0-2.1) ... Removing libx11-data (2:1.6.7-1+deb10u2) ... Removing libxau6:amd64 (1:1.0.8-1+b2) ... Removing mime-support (3.62) ... Removing python3-minimal (3.7.3-1) ... Removing readline-common (7.0-5) ... Removing python3.7-minimal (3.7.3-2+deb10u3) ... Removing libexpat1:amd64 (2.2.6-2+deb10u4) ... Removing libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... find: '/usr/lib/python3': No such file or directory Removing libssl1.1:amd64 (1.1.1n-0+deb10u3) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... 0m58.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', 'remove', 'blt', 'bowtie2', 'cd-hit', 'dh-python', 'fastaq', 'fontconfig-config', 'fonts-lyx', 'gawk', 'libatomic1:amd64', 'libblas3:amd64', 'libbsd0:amd64', 'libcapnp-0.5.3', 'libcapnp-0.7.0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfml0', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgsl23:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libminimap0', 'libmpdec2:amd64', 'libmpfr4:amd64', 'libmpfr6:amd64', 'libmurmurhash1', 'libncurses5:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.5-minimal:amd64', 'libpython3.5-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libtiff5:amd64', 'libtk8.6:amd64', 'libunistring0:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'lsb-base', 'mash', 'mime-support', 'mummer', 'perl', 'perl-modules-5.24', 'perl-modules-5.28', 'python', 'python-matplotlib-data', 'python-minimal', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-biopython', 'python3-bs4', 'python3-cycler', 'python3-dateutil', 'python3-dendropy', 'python3-distutils', 'python3-kiwisolver', 'python3-lib2to3', 'python3-matplotlib', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pymummer', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-six', 'python3-soupsieve', 'python3-tk:amd64', 'python3.5', 'python3.5-minimal', 'python3.7', 'python3.7-minimal', 'readline-common', 'samtools', 'tk8.6-blt2.5', 'ttf-bitstream-vera', 'tzdata', 'ucf', 'x11-common', 'ariba'] 0m58.3s INFO: Running scripts post_remove 0m58.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_remove_exceptions'] 0m58.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_remove_exceptions'] 0m58.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg', '--purge', 'blt', 'bowtie2', 'cd-hit', 'dh-python', 'fastaq', 'fontconfig-config', 'fonts-lyx', 'gawk', 'libatomic1:amd64', 'libblas3:amd64', 'libbsd0:amd64', 'libcapnp-0.5.3', 'libcapnp-0.7.0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfml0', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgsl23:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libminimap0', 'libmpdec2:amd64', 'libmpfr4:amd64', 'libmpfr6:amd64', 'libmurmurhash1', 'libncurses5:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.5-minimal:amd64', 'libpython3.5-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libtiff5:amd64', 'libtk8.6:amd64', 'libunistring0:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'lsb-base', 'mash', 'mime-support', 'mummer', 'perl', 'perl-modules-5.24', 'perl-modules-5.28', 'python', 'python-matplotlib-data', 'python-minimal', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-biopython', 'python3-bs4', 'python3-cycler', 'python3-dateutil', 'python3-dendropy', 'python3-distutils', 'python3-kiwisolver', 'python3-lib2to3', 'python3-matplotlib', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pymummer', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-six', 'python3-soupsieve', 'python3-tk:amd64', 'python3.5', 'python3.5-minimal', 'python3.7', 'python3.7-minimal', 'readline-common', 'samtools', 'tk8.6-blt2.5', 'ttf-bitstream-vera', 'tzdata', 'ucf', 'x11-common'] 0m58.7s DUMP: dpkg: warning: ignoring request to remove blt which isn't installed dpkg: warning: ignoring request to remove bowtie2 which isn't installed dpkg: warning: ignoring request to remove cd-hit which isn't installed dpkg: warning: ignoring request to remove dh-python which isn't installed dpkg: warning: ignoring request to remove fastaq which isn't installed (Reading database ... 4667 files and directories currently installed.) Purging configuration files for fontconfig-config (2.13.1-2) ... dpkg: warning: ignoring request to remove fonts-lyx which isn't installed Purging configuration files for gawk (1:4.2.1+dfsg-1) ... dpkg: warning: ignoring request to remove libatomic1 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 libcapnp-0.5.3 which isn't installed dpkg: warning: ignoring request to remove libcapnp-0.7.0 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfml0 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 libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm3 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgsl23 which isn't installed dpkg: warning: ignoring request to remove libgslcblas0 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... dpkg: warning: ignoring request to remove libhts1 which isn't installed dpkg: warning: ignoring request to remove libhts2 which isn't installed dpkg: warning: ignoring request to remove libidn11 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 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 libjs-jquery which isn't installed Purging configuration files for libjs-jquery-ui (1.12.1+dfsg-5) ... 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 liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.47+dfsg-3+deb10u7) ... dpkg: warning: ignoring request to remove libminimap0 which isn't installed dpkg: warning: ignoring request to remove libmpdec2 which isn't installed dpkg: warning: ignoring request to remove libmpfr4 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libmurmurhash1 which isn't installed dpkg: warning: ignoring request to remove libncurses5 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libperl5.24 which isn't installed dpkg: warning: ignoring request to remove libperl5.28 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 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 dpkg: warning: ignoring request to remove libpython2-stdlib which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.5-minimal:amd64 (3.5.3-1+deb9u1) ... dpkg: warning: ignoring request to remove libpython3.5-stdlib which isn't installed Purging configuration files for libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... dpkg: warning: ignoring request to remove libpython3.7-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 libsigsegv2 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 libssl1.1:amd64 (1.1.1n-0+deb10u3) ... dpkg: warning: ignoring request to remove libtbb2 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libunistring0 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove 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 libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove lsb-base which isn't installed dpkg: warning: ignoring request to remove mash which isn't installed Purging configuration files for mime-support (3.62) ... dpkg: warning: ignoring request to remove mummer which isn't installed Purging configuration files for perl (5.28.1-6+deb10u1) ... dpkg: warning: ignoring request to remove perl-modules-5.24 which isn't installed dpkg: warning: ignoring request to remove perl-modules-5.28 which isn't installed Purging configuration files for python (2.7.16-1) ... Purging configuration files for python-matplotlib-data (3.0.2-2) ... dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python2 which isn't installed dpkg: warning: ignoring request to remove python2-minimal which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed Purging configuration files for python2.7-minimal (2.7.16-2+deb10u1) ... Purging configuration files for python3 (3.7.3-1) ... dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-bs4 which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-dendropy which isn't installed dpkg: warning: ignoring request to remove python3-distutils which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-lib2to3 which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pymummer which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-reportlab-accel which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-soupsieve which isn't installed dpkg: warning: ignoring request to remove python3-tk which isn't installed dpkg: warning: ignoring request to remove python3.5 which isn't installed Purging configuration files for python3.5-minimal (3.5.3-1+deb9u1) ... dpkg: warning: ignoring request to remove python3.7 which isn't installed Purging configuration files for python3.7-minimal (3.7.3-2+deb10u3) ... Purging configuration files for readline-common (7.0-5) ... dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove tk8.6-blt2.5 which isn't installed dpkg: warning: ignoring request to remove ttf-bitstream-vera which isn't installed Purging configuration files for tzdata (2021a-0+deb10u6) ... Purging configuration files for ucf (3.0038+nmu1) ... Purging configuration files for x11-common (1:7.7+19) ... 0m58.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg', '--purge', 'blt', 'bowtie2', 'cd-hit', 'dh-python', 'fastaq', 'fontconfig-config', 'fonts-lyx', 'gawk', 'libatomic1:amd64', 'libblas3:amd64', 'libbsd0:amd64', 'libcapnp-0.5.3', 'libcapnp-0.7.0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfml0', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgsl23:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libminimap0', 'libmpdec2:amd64', 'libmpfr4:amd64', 'libmpfr6:amd64', 'libmurmurhash1', 'libncurses5:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.5-minimal:amd64', 'libpython3.5-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libtiff5:amd64', 'libtk8.6:amd64', 'libunistring0:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'lsb-base', 'mash', 'mime-support', 'mummer', 'perl', 'perl-modules-5.24', 'perl-modules-5.28', 'python', 'python-matplotlib-data', 'python-minimal', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-biopython', 'python3-bs4', 'python3-cycler', 'python3-dateutil', 'python3-dendropy', 'python3-distutils', 'python3-kiwisolver', 'python3-lib2to3', 'python3-matplotlib', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pymummer', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-six', 'python3-soupsieve', 'python3-tk:amd64', 'python3.5', 'python3.5-minimal', 'python3.7', 'python3.7-minimal', 'readline-common', 'samtools', 'tk8.6-blt2.5', 'ttf-bitstream-vera', 'tzdata', 'ucf', 'x11-common'] 0m58.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg', '--purge', 'ariba'] 0m58.7s DUMP: dpkg: warning: ignoring request to remove ariba which isn't installed 0m58.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg', '--purge', 'ariba'] 0m58.7s INFO: Running scripts post_purge 0m58.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_purge_exceptions'] 0m58.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_purge_exceptions'] 0m58.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg', '--purge', '--pending'] 0m58.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg', '--purge', '--pending'] 0m58.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg', '--remove', '--pending'] 0m58.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg', '--remove', '--pending'] 0m58.8s INFO: Running scripts post_test 0m58.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_test_exceptions'] 0m58.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'tmp/scripts/post_test_exceptions'] 0m58.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m59.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m59.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg-divert', '--list'] 0m59.0s 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 0m59.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'dpkg-divert', '--list'] 0m59.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', 'clean'] 0m59.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w', 'apt-get', 'clean'] 0m59.1s DEBUG: Recording chroot state 0m59.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/shm'] 0m59.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/shm'] 0m59.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/console'] 0m59.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/console'] 0m59.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/ptmx'] 0m59.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/ptmx'] 0m59.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/pts'] 0m59.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/dev/pts'] 0m59.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/proc'] 0m59.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w/proc'] 0m59.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m59.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpgqw_8g1w'] 0m59.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpgqw_8g1w 0m59.8s INFO: PASS: Upgrading between Debian distributions. 0m59.8s INFO: PASS: All tests. 0m59.8s INFO: piuparts run ends. ret=0 End: 2022-12-17 01:40:00 GMT