Start: 2023-08-04 06:47:26 GMT [buster] Package: circlator Version: 1.5.5-3 Installed-Size: 10301 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 3.12.1), python3-openpyxl, python3-pymummer, python3-pysam, python3:any, prodigal, bwa (>= 0.7.12), mummer, samtools, spades Suggests: canu Description: circularize genome assemblies Homepage: http://sanger-pathogens.github.io/circlator/ Description-md5: cf235cf3121c5ca347cea31d93662299 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, role::program, science::calculation, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/c/circlator/circlator_1.5.5-3_amd64.deb Size: 4325732 MD5sum: 48715c036e9a0f5940dfbc9ffe82ffad SHA256: cf494b1310d5175edef88c3a7dbfe54640eca73a072c6440d1220ad189db652f [buster-next] Package: circlator Version: 1.5.5-3 Installed-Size: 10301 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 3.12.1), python3-openpyxl, python3-pymummer, python3-pysam, python3:any, prodigal, bwa (>= 0.7.12), mummer, samtools, spades Suggests: canu Description: circularize genome assemblies Homepage: http://sanger-pathogens.github.io/circlator/ Description-md5: cf235cf3121c5ca347cea31d93662299 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, role::program, science::calculation, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/c/circlator/circlator_1.5.5-3_amd64.deb Size: 4325732 MD5sum: 48715c036e9a0f5940dfbc9ffe82ffad SHA256: cf494b1310d5175edef88c3a7dbfe54640eca73a072c6440d1220ad189db652f Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz -d buster -d buster-next -B /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat --apt circlator=1.5.5-3 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 1.1.8~202306121314~1.1.7-9-g57dfbde6 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz -d buster -d buster-next -B /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat --apt circlator=1.5.5-3 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-23-amd64 #1 SMP Debian 5.10.179-3 (2023-07-27) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpqqfvdwxw 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpqqfvdwxw 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m2.1s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/proc'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/proc'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/pts'] 0m2.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/pts'] 0m2.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/ptmx'] 0m2.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/ptmx'] 0m2.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/console'] 0m2.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/console'] 0m2.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/shm'] 0m2.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/shm'] 0m2.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m2.2s DEBUG: Created policy-rc.d and chmodded it. 0m2.2s DEBUG: Created resolv.conf. 0m2.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpqqfvdwxw/tmp/scripts/ 0m2.2s INFO: Running scripts post_chroot_unpack 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', 'update'] 0m3.1s DUMP: Hit:1 http://deb.debian.org/debian buster InRelease Reading package lists... 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', 'update'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', '-yf', 'dist-upgrade'] 0m3.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', '-yf', 'dist-upgrade'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.9s DUMP: f6fc0f2636004ef589309651dfd778f4 - 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.9s INFO: Running scripts post_setup 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_setup_dummy_users'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_setup_dummy_users'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_setup_forbid_home'] 0m5.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_setup_forbid_home'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_setup_minimize'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_setup_minimize'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_setup_zz_backports'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_setup_zz_backports'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.0s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 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 bsdutils bsdutils 1:2.33.1-0.1 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 diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 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 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 libblkid1:amd64 libblkid1 2.33.1-0.1 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 libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 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 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 libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 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 libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 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 libmount1:amd64 libmount1 2.33.1-0.1 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 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 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 libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libss2:amd64 libss2 1.44.5-1+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 libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 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 mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.33.1-0.1 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-base perl-base 5.28.1-6+deb10u1 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tzdata tzdata 2021a-0+deb10u6 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat 0m5.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m5.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m5.5s INFO: Running scripts is_testable 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/is_testable_uninstallable'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/is_testable_uninstallable'] 0m5.5s INFO: Running scripts pre_test 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_test_exceptions'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_test_exceptions'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_test_root_password'] 0m5.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_test_root_password'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'show', '--no-all-versions', 'circlator'] 0m5.8s DUMP: Package: circlator Version: 1.5.5-3 Installed-Size: 10301 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 3.12.1), python3-openpyxl, python3-pymummer, python3-pysam, python3:any, prodigal, bwa (>= 0.7.12), mummer, samtools, spades Suggests: canu Description-en: circularize genome assemblies Circlator is a tool to automate assembly circularization for bacterial and small eukaryotic genomes and produce accurate linear representations of circular sequences. Description-md5: cf235cf3121c5ca347cea31d93662299 Homepage: http://sanger-pathogens.github.io/circlator/ Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, role::program, science::calculation, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/c/circlator/circlator_1.5.5-3_amd64.deb Size: 4325732 MD5sum: 48715c036e9a0f5940dfbc9ffe82ffad SHA256: cf494b1310d5175edef88c3a7dbfe54640eca73a072c6440d1220ad189db652f 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'show', '--no-all-versions', 'circlator'] 0m5.8s INFO: apt-cache knows about the following packages: circlator 0m5.8s INFO: Running scripts pre_install 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_database-server'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_database-server'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_exceptions'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_exceptions'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_extras'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_extras'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'policy'] 0m5.9s 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=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'policy'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'policy', 'circlator'] 0m6.0s DUMP: circlator: Installed: (none) Candidate: 1.5.5-3 Version table: 1.5.5-3 500 500 http://deb.debian.org/debian buster/main amd64 Packages 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'policy', 'circlator'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', '-y', 'install', 'circlator'] 0m24.1s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bamtools bwa fastaq gawk libbamtools2.5.1 libcurl3-gnutls libdeflate0 libexpat1 libgdbm-compat4 libgdbm6 libgomp1 libgssapi-krb5-2 libhat-trie0 libhts2 libicu63 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmpdec2 libmpfr6 libncurses6 libnghttp2-14 libnlopt0 libperl5.28 libprocps7 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 libssw0 libxml2 libxslt1.1 libyaml-0-2 lsb-base mime-support mummer perl perl-modules-5.28 procps prodigal python python-joblib python-minimal python-yaml python2 python2-minimal python2.7 python2.7-minimal python3 python3-et-xmlfile python3-jdcal python3-lxml python3-minimal python3-openpyxl python3-pkg-resources python3-pymummer python3-pysam python3.7 python3.7-minimal readline-common samtools spades Suggested packages: canu gawk-doc gdbm-l10n krb5-doc krb5-user sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libb-debug-perl liblocale-codes-perl python-doc python-tk python2-doc python2.7-doc binutils binfmt-support python3-doc python3-tk python3-venv python3-lxml-dbg python-lxml-doc python3-setuptools python3.7-venv python3.7-doc readline-doc Recommended packages: ca-certificates krb5-locales libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils netbase psmisc python-numpy python-pytest python-simplejson python-lz4 python-psutil python3-bs4 python3-html5lib python3-pytest python3-pil cwltool The following NEW packages will be installed: bamtools bwa circlator fastaq gawk libbamtools2.5.1 libcurl3-gnutls libdeflate0 libexpat1 libgdbm-compat4 libgdbm6 libgomp1 libgssapi-krb5-2 libhat-trie0 libhts2 libicu63 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmpdec2 libmpfr6 libncurses6 libnghttp2-14 libnlopt0 libperl5.28 libprocps7 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 libssw0 libxml2 libxslt1.1 libyaml-0-2 lsb-base mime-support mummer perl perl-modules-5.28 procps prodigal python python-joblib python-minimal python-yaml python2 python2-minimal python2.7 python2.7-minimal python3 python3-et-xmlfile python3-jdcal python3-lxml python3-minimal python3-openpyxl python3-pkg-resources python3-pymummer python3-pysam python3.7 python3.7-minimal readline-common samtools spades 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. Need to get 47.3 MB of archives. After this operation, 205 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 perl-modules-5.28 all 5.28.1-6+deb10u1 [2873 kB] Get:2 http://deb.debian.org/debian buster/main amd64 libgdbm6 amd64 1.18.1-4 [64.7 kB] Get:3 http://deb.debian.org/debian buster/main amd64 libgdbm-compat4 amd64 1.18.1-4 [44.1 kB] Get:4 http://deb.debian.org/debian buster/main amd64 libperl5.28 amd64 5.28.1-6+deb10u1 [3894 kB] Get:5 http://deb.debian.org/debian buster/main amd64 perl amd64 5.28.1-6+deb10u1 [204 kB] Get:6 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get:7 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get:8 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get:9 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get:10 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u3 [1551 kB] Get:11 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:12 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get:13 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:14 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:15 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get:17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get:18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:22 http://deb.debian.org/debian buster/main amd64 libmpfr6 amd64 4.0.2-1 [775 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:24 http://deb.debian.org/debian buster/main amd64 gawk amd64 1:4.2.1+dfsg-1 [660 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get:26 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get:27 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get:28 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get:30 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get:32 http://deb.debian.org/debian buster/main amd64 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2.9.4+dfsg1-7+deb10u4 [689 kB] Get:64 http://deb.debian.org/debian buster/main amd64 libxslt1.1 amd64 1.1.32-2.2~deb10u1 [237 kB] Get:65 http://deb.debian.org/debian buster/main amd64 python3-lxml amd64 4.3.2-1+deb10u4 [1163 kB] Get:66 http://deb.debian.org/debian buster/main amd64 python3-openpyxl all 2.4.9-1 [220 kB] Get:67 http://deb.debian.org/debian buster/main amd64 mummer amd64 3.23+dfsg-4 [809 kB] Get:68 http://deb.debian.org/debian buster/main amd64 python3-pymummer all 0.10.3-2 [9268 B] Get:69 http://deb.debian.org/debian buster/main amd64 python3-pysam amd64 0.15.2+ds-2 [1661 kB] Get:70 http://deb.debian.org/debian buster/main amd64 prodigal amd64 1:2.6.3-4 [695 kB] Get:71 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB] Get:72 http://deb.debian.org/debian buster/main amd64 libhat-trie0 amd64 0.1.2-2 [11.8 kB] Get:73 http://deb.debian.org/debian buster/main amd64 libnlopt0 amd64 2.4.2+dfsg-8+b1 [165 kB] Get:74 http://deb.debian.org/debian buster/main amd64 libssw0 amd64 1.1-2 [16.5 kB] Get:75 http://deb.debian.org/debian buster/main amd64 python-joblib all 0.13.0-2 [190 kB] Get:76 http://deb.debian.org/debian buster/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get:77 http://deb.debian.org/debian buster/main amd64 python-yaml amd64 3.13-2 [127 kB] Get:78 http://deb.debian.org/debian buster/main amd64 spades amd64 3.13.0+dfsg2-2 [4755 kB] Get:79 http://deb.debian.org/debian buster/main amd64 circlator amd64 1.5.5-3 [4326 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.3 MB in 2s (30.9 MB/s) Selecting previously unselected package perl-modules-5.28. (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 ... 6462 files and directories currently installed.) Preparing to unpack .../00-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 .../01-libgdbm6_1.18.1-4_amd64.deb ... Unpacking libgdbm6:amd64 (1.18.1-4) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 9245 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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Setting up libmpfr6:amd64 (4.0.2-1) ... Setting up readline-common (7.0-5) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package gawk. (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 ... 9312 files and directories currently installed.) Preparing to unpack .../gawk_1%3a4.2.1+dfsg-1_amd64.deb ... Unpacking gawk (1:4.2.1+dfsg-1) ... Selecting previously unselected package libpython3.7-minimal:amd64. 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Unpacking libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package python3.7. Preparing to unpack .../python3.7_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7 (3.7.3-2+deb10u3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../libpython3-stdlib_3.7.3-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (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 ... 10133 files and directories currently installed.) Preparing to unpack .../00-python3_3.7.3-1_amd64.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../01-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libprocps7:amd64. Preparing to unpack .../02-libprocps7_2%3a3.3.15-2_amd64.deb ... 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Setting up gawk (1:4.2.1+dfsg-1) ... Setting up prodigal (1:2.6.3-4) ... Setting up libyaml-0-2:amd64 (0.2.1-1) ... Setting up bwa (0.7.17-3) ... Setting up libprocps7:amd64 (2:3.3.15-2) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up libnlopt0:amd64 (2.4.2+dfsg-8+b1) ... Setting up libgomp1:amd64 (8.3.0-6) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u7) ... Setting up libicu63:amd64 (63.1-6+deb10u3) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u4) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up libhat-trie0:amd64 (0.1.2-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u4) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u4) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libssw0:amd64 (1.1-2) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u4) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libgdbm6:amd64 (1.18.1-4) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Setting up python2 (2.7.16-1) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... 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 bamtools (2.5.1+dfsg-3) ... Setting up libxslt1.1:amd64 (1.1.32-2.2~deb10u1) ... Setting up python (2.7.16-1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up perl (5.28.1-6+deb10u1) ... Setting up python-joblib (0.13.0-2) ... Setting up python3-lxml:amd64 (4.3.2-1+deb10u4) ... Setting up mummer (3.23+dfsg-4) ... Setting up python3-et-xmlfile (1.0.1-2) ... Setting up python-yaml (3.13-2) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up python3-jdcal (1.0-1.2) ... Setting up samtools (1.9-4) ... Setting up python3-openpyxl (2.4.9-1) ... Setting up spades (3.13.0+dfsg2-2) ... Setting up python3-pysam (0.15.2+ds-2) ... Setting up fastaq (3.17.0-2) ... Setting up python3-pymummer (0.10.3-2) ... Setting up circlator (1.5.5-3) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', '-y', 'install', 'circlator'] 0m24.1s INFO: Running scripts post_install 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_install_exceptions'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_install_exceptions'] 0m24.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m25.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m25.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpqqfvdwxw to buster-next 0m25.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main deb http://security.debian.org buster/updates main deb http://deb.debian.org/debian/ buster-updates main deb http://deb.debian.org/debian/ buster-proposed-updates main 0m25.0s INFO: Running scripts pre_distupgrade 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', 'update'] 0m27.2s DUMP: Hit:1 http://deb.debian.org/debian buster InRelease Get:2 http://deb.debian.org/debian buster-updates InRelease [56.6 kB] Get:3 http://deb.debian.org/debian buster-proposed-updates InRelease [59.2 kB] Get:4 http://security.debian.org buster/updates InRelease [34.8 kB] Get:5 http://deb.debian.org/debian buster-updates/main amd64 Packages [8788 B] Get:6 http://deb.debian.org/debian buster-updates/main Translation-en [6915 B] Get:7 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages [728 B] Get:8 http://deb.debian.org/debian buster-proposed-updates/main Translation-en [859 B] Get:9 http://security.debian.org buster/updates/main amd64 Packages [547 kB] Get:10 http://security.debian.org buster/updates/main Translation-en [295 kB] Fetched 1010 kB in 1s (985 kB/s) Reading package lists... 0m27.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', 'update'] 0m27.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', '-yf', 'dist-upgrade'] 0m37.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: debian-archive-keyring libbz2-1.0 libc-bin libc6 libcurl3-gnutls libexpat1 libgnutls30 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libncurses6 libncursesw6 libpython2.7-minimal libpython2.7-stdlib libpython3.7-minimal libpython3.7-stdlib libsqlite3-0 libssl1.1 libsystemd0 libtasn1-6 libtinfo6 libudev1 libxml2 libxslt1.1 ncurses-base ncurses-bin python-joblib python2.7 python2.7-minimal python3.7 python3.7-minimal tzdata zlib1g 34 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 19.9 MB of archives. After this operation, 20.5 kB of additional disk space will be used. Get:1 http://security.debian.org buster/updates/main amd64 ncurses-bin amd64 6.1+20181013-2+deb10u3 [407 kB] Get:2 http://security.debian.org buster/updates/main amd64 libc6 amd64 2.28-10+deb10u2 [2869 kB] Get:3 http://security.debian.org buster/updates/main amd64 libc-bin amd64 2.28-10+deb10u2 [793 kB] Get:4 http://security.debian.org buster/updates/main amd64 ncurses-base all 6.1+20181013-2+deb10u3 [259 kB] Get:5 http://security.debian.org buster/updates/main amd64 libsystemd0 amd64 241-7~deb10u10 [332 kB] Get:6 http://security.debian.org buster/updates/main amd64 python2.7 amd64 2.7.16-2+deb10u2 [306 kB] Get:7 http://security.debian.org buster/updates/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u5 [1551 kB] Get:8 http://security.debian.org buster/updates/main amd64 libbz2-1.0 amd64 1.0.6-9.2~deb10u2 [45.4 kB] Get:9 http://security.debian.org buster/updates/main amd64 libexpat1 amd64 2.2.6-2+deb10u6 [108 kB] Get:10 http://security.debian.org buster/updates/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u3 [102 kB] Get:11 http://security.debian.org buster/updates/main amd64 libtinfo6 amd64 6.1+20181013-2+deb10u3 [326 kB] Get:12 http://security.debian.org buster/updates/main amd64 libncursesw6 amd64 6.1+20181013-2+deb10u3 [132 kB] Get:13 http://security.debian.org buster/updates/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u2 [641 kB] Get:14 http://security.debian.org buster/updates/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u2 [1911 kB] Get:15 http://security.debian.org buster/updates/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u2 [1367 kB] Get:16 http://security.debian.org buster/updates/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u2 [396 kB] Get:17 http://security.debian.org buster/updates/main amd64 python3.7 amd64 3.7.3-2+deb10u5 [330 kB] Get:18 http://security.debian.org buster/updates/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u5 [1734 kB] Get:19 http://security.debian.org buster/updates/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u5 [1728 kB] Get:20 http://security.debian.org buster/updates/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u5 [589 kB] Get:21 http://security.debian.org buster/updates/main amd64 zlib1g amd64 1:1.2.11.dfsg-1+deb10u2 [90.9 kB] Get:22 http://security.debian.org buster/updates/main amd64 debian-archive-keyring all 2019.1+deb10u2 [110 kB] Get:23 http://security.debian.org buster/updates/main amd64 libudev1 amd64 241-7~deb10u10 [151 kB] Get:24 http://security.debian.org buster/updates/main amd64 libtasn1-6 amd64 4.13-3+deb10u1 [52.0 kB] Get:25 http://security.debian.org buster/updates/main amd64 libgnutls30 amd64 3.6.7-4+deb10u10 [1126 kB] Get:26 http://security.debian.org buster/updates/main amd64 tzdata all 2021a-0+deb10u11 [267 kB] Get:27 http://security.debian.org buster/updates/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u5 [159 kB] Get:28 http://security.debian.org buster/updates/main amd64 libkrb5-3 amd64 1.17-3+deb10u5 [369 kB] Get:29 http://security.debian.org buster/updates/main amd64 libkrb5support0 amd64 1.17-3+deb10u5 [66.0 kB] Get:30 http://security.debian.org buster/updates/main amd64 libk5crypto3 amd64 1.17-3+deb10u5 [122 kB] Get:31 http://security.debian.org buster/updates/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u6 [690 kB] Get:32 http://security.debian.org buster/updates/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u6 [333 kB] Get:33 http://security.debian.org buster/updates/main amd64 libxslt1.1 amd64 1.1.32-2.2~deb10u2 [236 kB] Get:34 http://security.debian.org buster/updates/main amd64 python-joblib all 0.13.0-2+deb10u2 [191 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.9 MB in 0s (67.0 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11715 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.1+20181013-2+deb10u3_amd64.deb ... Unpacking ncurses-bin (6.1+20181013-2+deb10u3) over (6.1+20181013-2+deb10u2) ... Setting up ncurses-bin (6.1+20181013-2+deb10u3) ... (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 ... 11715 files and directories currently installed.) Preparing to unpack .../libc6_2.28-10+deb10u2_amd64.deb ... Unpacking libc6:amd64 (2.28-10+deb10u2) over (2.28-10+deb10u1) ... Setting up libc6:amd64 (2.28-10+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 ... 11715 files and directories currently installed.) Preparing to unpack .../libc-bin_2.28-10+deb10u2_amd64.deb ... Unpacking libc-bin (2.28-10+deb10u2) over (2.28-10+deb10u1) ... Setting up libc-bin (2.28-10+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 ... 11715 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.1+20181013-2+deb10u3_all.deb ... Unpacking ncurses-base (6.1+20181013-2+deb10u3) over (6.1+20181013-2+deb10u2) ... Setting up ncurses-base (6.1+20181013-2+deb10u3) ... (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 ... 11715 files and directories currently installed.) Preparing to unpack .../libsystemd0_241-7~deb10u10_amd64.deb ... Unpacking libsystemd0:amd64 (241-7~deb10u10) over (241-7~deb10u8) ... Setting up libsystemd0:amd64 (241-7~deb10u10) ... (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 ... 11715 files and directories currently installed.) Preparing to unpack .../python2.7_2.7.16-2+deb10u2_amd64.deb ... Unpacking python2.7 (2.7.16-2+deb10u2) over (2.7.16-2+deb10u1) ... Preparing to unpack .../libssl1.1_1.1.1n-0+deb10u5_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1n-0+deb10u5) over (1.1.1n-0+deb10u3) ... Preparing to unpack .../libbz2-1.0_1.0.6-9.2~deb10u2_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.6-9.2~deb10u2) over (1.0.6-9.2~deb10u1) ... Setting up libbz2-1.0:amd64 (1.0.6-9.2~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 ... 11715 files and directories currently installed.) Preparing to unpack .../libexpat1_2.2.6-2+deb10u6_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u6) over (2.2.6-2+deb10u4) ... Preparing to unpack .../libncurses6_6.1+20181013-2+deb10u3_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u3) over (6.1+20181013-2+deb10u2) ... Preparing to unpack .../libtinfo6_6.1+20181013-2+deb10u3_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20181013-2+deb10u3) over (6.1+20181013-2+deb10u2) ... Setting up libtinfo6:amd64 (6.1+20181013-2+deb10u3) ... (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 ... 11715 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.1+20181013-2+deb10u3_amd64.deb ... Unpacking libncursesw6:amd64 (6.1+20181013-2+deb10u3) over (6.1+20181013-2+deb10u2) ... Setting up libncursesw6:amd64 (6.1+20181013-2+deb10u3) ... (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 ... 11715 files and directories currently installed.) Preparing to unpack .../0-libsqlite3-0_3.27.2-3+deb10u2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.27.2-3+deb10u2) over (3.27.2-3+deb10u1) ... Preparing to unpack .../1-libpython2.7-stdlib_2.7.16-2+deb10u2_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.16-2+deb10u2) over (2.7.16-2+deb10u1) ... Preparing to unpack .../2-python2.7-minimal_2.7.16-2+deb10u2_amd64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u2) over (2.7.16-2+deb10u1) ... Preparing to unpack .../3-libpython2.7-minimal_2.7.16-2+deb10u2_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.16-2+deb10u2) over (2.7.16-2+deb10u1) ... Preparing to unpack .../4-python3.7_3.7.3-2+deb10u5_amd64.deb ... Unpacking python3.7 (3.7.3-2+deb10u5) over (3.7.3-2+deb10u3) ... Preparing to unpack .../5-libpython3.7-stdlib_3.7.3-2+deb10u5_amd64.deb ... Unpacking libpython3.7-stdlib:amd64 (3.7.3-2+deb10u5) over (3.7.3-2+deb10u3) ... Preparing to unpack .../6-python3.7-minimal_3.7.3-2+deb10u5_amd64.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u5) over (3.7.3-2+deb10u3) ... Preparing to unpack .../7-libpython3.7-minimal_3.7.3-2+deb10u5_amd64.deb ... Unpacking libpython3.7-minimal:amd64 (3.7.3-2+deb10u5) over (3.7.3-2+deb10u3) ... Preparing to unpack .../8-zlib1g_1%3a1.2.11.dfsg-1+deb10u2_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.11.dfsg-1+deb10u2) over (1:1.2.11.dfsg-1+deb10u1) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-1+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 ... 11715 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2019.1+deb10u2_all.deb ... Unpacking debian-archive-keyring (2019.1+deb10u2) over (2019.1+deb10u1) ... Setting up debian-archive-keyring (2019.1+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 ... 11721 files and directories currently installed.) Preparing to unpack .../libudev1_241-7~deb10u10_amd64.deb ... Unpacking libudev1:amd64 (241-7~deb10u10) over (241-7~deb10u8) ... Setting up libudev1:amd64 (241-7~deb10u10) ... (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 ... 11721 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.13-3+deb10u1_amd64.deb ... Unpacking libtasn1-6:amd64 (4.13-3+deb10u1) over (4.13-3) ... Setting up libtasn1-6:amd64 (4.13-3+deb10u1) ... (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 ... 11721 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.7-4+deb10u10_amd64.deb ... Unpacking libgnutls30:amd64 (3.6.7-4+deb10u10) over (3.6.7-4+deb10u8) ... Setting up libgnutls30:amd64 (3.6.7-4+deb10u10) ... (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 ... 11721 files and directories currently installed.) Preparing to unpack .../0-tzdata_2021a-0+deb10u11_all.deb ... Unpacking tzdata (2021a-0+deb10u11) over (2021a-0+deb10u6) ... Preparing to unpack .../1-libgssapi-krb5-2_1.17-3+deb10u5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u5) over (1.17-3+deb10u4) ... Preparing to unpack .../2-libkrb5-3_1.17-3+deb10u5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u5) over (1.17-3+deb10u4) ... Preparing to unpack .../3-libkrb5support0_1.17-3+deb10u5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u5) over (1.17-3+deb10u4) ... Preparing to unpack .../4-libk5crypto3_1.17-3+deb10u5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-3+deb10u5) over (1.17-3+deb10u4) ... Preparing to unpack .../5-libxml2_2.9.4+dfsg1-7+deb10u6_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u6) over (2.9.4+dfsg1-7+deb10u4) ... Preparing to unpack .../6-libcurl3-gnutls_7.64.0-4+deb10u6_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.64.0-4+deb10u6) over (7.64.0-4+deb10u2) ... Preparing to unpack .../7-libxslt1.1_1.1.32-2.2~deb10u2_amd64.deb ... Unpacking libxslt1.1:amd64 (1.1.32-2.2~deb10u2) over (1.1.32-2.2~deb10u1) ... Preparing to unpack .../8-python-joblib_0.13.0-2+deb10u2_all.deb ... Unpacking python-joblib (0.13.0-2+deb10u2) over (0.13.0-2) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u6) ... Setting up libssl1.1:amd64 (1.1.1n-0+deb10u5) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u2) ... Setting up libpython3.7-minimal:amd64 (3.7.3-2+deb10u5) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u5) ... Setting up tzdata (2021a-0+deb10u11) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Aug 4 06:48:00 UTC 2023. Universal Time is now: Fri Aug 4 06:48:00 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython2.7-minimal:amd64 (2.7.16-2+deb10u2) ... Setting up python2.7-minimal (2.7.16-2+deb10u2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u3) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u5) ... Setting up python-joblib (0.13.0-2+deb10u2) ... Setting up python3.7-minimal (3.7.3-2+deb10u5) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u5) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u6) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u5) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u2) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u5) ... Setting up libxslt1.1:amd64 (1.1.32-2.2~deb10u2) ... Setting up python3.7 (3.7.3-2+deb10u5) ... Setting up python2.7 (2.7.16-2+deb10u2) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u6) ... Processing triggers for libc-bin (2.28-10+deb10u2) ... Processing triggers for mime-support (3.62) ... 0m37.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', '-yf', 'dist-upgrade'] 0m37.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m37.8s DUMP: 66dcb6548b288e247b72cc241eccfddf - 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'show', '--no-all-versions', 'circlator'] 0m38.1s DUMP: Package: circlator Version: 1.5.5-3 Installed-Size: 10301 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 3.12.1), python3-openpyxl, python3-pymummer, python3-pysam, python3:any, prodigal, bwa (>= 0.7.12), mummer, samtools, spades Suggests: canu Description-en: circularize genome assemblies Circlator is a tool to automate assembly circularization for bacterial and small eukaryotic genomes and produce accurate linear representations of circular sequences. Description-md5: cf235cf3121c5ca347cea31d93662299 Homepage: http://sanger-pathogens.github.io/circlator/ Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, role::program, science::calculation, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/c/circlator/circlator_1.5.5-3_amd64.deb Size: 4325732 MD5sum: 48715c036e9a0f5940dfbc9ffe82ffad SHA256: cf494b1310d5175edef88c3a7dbfe54640eca73a072c6440d1220ad189db652f 0m38.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'show', '--no-all-versions', 'circlator'] 0m38.1s INFO: apt-cache knows about the following packages: circlator 0m38.1s INFO: Running scripts pre_install 0m38.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_database-server'] 0m38.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_database-server'] 0m38.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_exceptions'] 0m38.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_exceptions'] 0m38.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_extras'] 0m38.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_extras'] 0m38.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_foreign_architecture'] 0m38.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_foreign_architecture'] 0m38.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m38.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m38.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'policy'] 0m38.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages release v=10-updates,o=Debian,a=oldoldstable-proposed-updates,n=buster-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian buster-updates/main amd64 Packages release o=Debian,a=oldoldstable-updates,n=buster-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org buster/updates/main amd64 Packages release v=10,o=Debian,a=oldoldstable,n=buster,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m38.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'policy'] 0m38.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'policy', 'circlator'] 0m38.2s DUMP: circlator: Installed: 1.5.5-3 Candidate: 1.5.5-3 Version table: *** 1.5.5-3 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m38.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'policy', 'circlator'] 0m38.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', '-y', 'install', 'circlator'] 0m38.7s DUMP: Reading package lists... Building dependency tree... Reading state information... circlator is already the newest version (1.5.5-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m38.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', '-y', 'install', 'circlator'] 0m38.7s INFO: Running scripts post_install 0m38.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_install_exceptions'] 0m38.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_install_exceptions'] 0m38.7s INFO: Running scripts post_distupgrade 0m38.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m38.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m38.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_distupgrade_exceptions'] 0m38.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_distupgrade_exceptions'] 0m38.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m38.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m38.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m38.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m38.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_distupgrade_zz_backports'] 0m38.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_distupgrade_zz_backports'] 0m38.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m39.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m39.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m40.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m40.4s INFO: Running scripts pre_install 0m40.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_database-server'] 0m40.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_database-server'] 0m40.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_exceptions'] 0m40.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_exceptions'] 0m40.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_extras'] 0m40.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_extras'] 0m40.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_foreign_architecture'] 0m40.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_foreign_architecture'] 0m40.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m40.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m40.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'policy'] 0m40.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages release v=10-updates,o=Debian,a=oldoldstable-proposed-updates,n=buster-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian buster-updates/main amd64 Packages release o=Debian,a=oldoldstable-updates,n=buster-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org buster/updates/main amd64 Packages release v=10,o=Debian,a=oldoldstable,n=buster,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'policy'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'policy', 'circlator'] 0m40.5s DUMP: circlator: Installed: 1.5.5-3 Candidate: 1.5.5-3 Version table: *** 1.5.5-3 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-cache', 'policy', 'circlator'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', '-y', 'install', 'circlator=1.5.5-3'] 0m41.0s DUMP: Reading package lists... Building dependency tree... Reading state information... circlator is already the newest version (1.5.5-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m41.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', '-y', 'install', 'circlator=1.5.5-3'] 0m41.0s INFO: Running scripts post_install 0m41.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_install_exceptions'] 0m41.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_install_exceptions'] 0m41.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m41.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m42.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', '-ac', '--ignore-obsolete'] 0m44.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', '-ac', '--ignore-obsolete'] 0m44.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m44.8s DUMP: 0.15.6 0m44.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m44.8s INFO: Running adequate version 0.15.6 now. 0m44.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'circlator'] 0m44.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'circlator'] 0m44.9s INFO: Running scripts pre_remove 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m47.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m47.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_remove_exceptions'] 0m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/pre_remove_exceptions'] 0m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m47.3s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed bamtools bamtools 2.5.1+dfsg-3 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 bsdutils bsdutils 1:2.33.1-0.1 install ok installed bwa bwa 0.7.17-3 install ok installed circlator circlator 1.5.5-3 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+deb10u2 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 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 gawk gawk 1:4.2.1+dfsg-1 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 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 libbamtools2.5.1:amd64 libbamtools2.5.1 2.5.1+dfsg-3 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u2 install ok installed libc-bin libc-bin 2.28-10+deb10u2 install ok installed libc6:amd64 libc6 2.28-10+deb10u2 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.64.0-4+deb10u6 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+deb10u6 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 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 libgdbm6:amd64 libgdbm6 1.18.1-4 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u10 install ok installed libgomp1:amd64 libgomp1 8.3.0-6 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.17-3+deb10u5 install ok installed libhat-trie0:amd64 libhat-trie0 0.1.2-2 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libhts2:amd64 libhts2 1.9-12~deb10u1 install ok installed libicu63:amd64 libicu63 63.1-6+deb10u3 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed libjsoncpp1:amd64 libjsoncpp1 1.7.4-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.17-3+deb10u5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.17-3+deb10u5 install ok installed libkrb5support0:amd64 libkrb5support0 1.17-3+deb10u5 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 libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libmpdec2:amd64 libmpdec2 2.4.2-2 install ok installed libmpfr6:amd64 libmpfr6 4.0.2-1 install ok installed libncurses6:amd64 libncurses6 6.1+20181013-2+deb10u3 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u3 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 libnlopt0:amd64 libnlopt0 2.4.2+dfsg-8+b1 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 libperl5.28:amd64 libperl5.28 5.28.1-6+deb10u1 install ok installed libprocps7:amd64 libprocps7 2:3.3.15-2 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+deb10u2 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.16-2+deb10u2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.7.3-1 install ok installed libpython3.7-minimal:amd64 libpython3.7-minimal 3.7.3-2+deb10u5 install ok installed libpython3.7-stdlib:amd64 libpython3.7-stdlib 3.7.3-2+deb10u5 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+deb10u2 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+deb10u5 install ok installed libssw0:amd64 libssw0 1.1-2 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u10 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3+deb10u1 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u3 install ok installed libudev1:amd64 libudev1 241-7~deb10u10 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libxml2:amd64 libxml2 2.9.4+dfsg1-7+deb10u6 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.32-2.2~deb10u2 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.1-1 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 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 mummer mummer 3.23+dfsg-4 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u3 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u3 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-5.28 perl-modules-5.28 5.28.1-6+deb10u1 install ok installed procps procps 2:3.3.15-2 install ok installed prodigal prodigal 1:2.6.3-4 install ok installed python python 2.7.16-1 install ok installed python-joblib python-joblib 0.13.0-2+deb10u2 install ok installed python-minimal python-minimal 2.7.16-1 install ok installed python-yaml python-yaml 3.13-2 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+deb10u2 install ok installed python2.7-minimal python2.7-minimal 2.7.16-2+deb10u2 install ok installed python3 python3 3.7.3-1 install ok installed python3-et-xmlfile python3-et-xmlfile 1.0.1-2 install ok installed python3-jdcal python3-jdcal 1.0-1.2 install ok installed python3-lxml:amd64 python3-lxml 4.3.2-1+deb10u4 install ok installed python3-minimal python3-minimal 3.7.3-1 install ok installed python3-openpyxl python3-openpyxl 2.4.9-1 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-pysam python3-pysam 0.15.2+ds-2 install ok installed python3.7 python3.7 3.7.3-2+deb10u5 install ok installed python3.7-minimal python3.7-minimal 3.7.3-2+deb10u5 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 spades spades 3.13.0+dfsg2-2 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tzdata tzdata 2021a-0+deb10u11 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u2 0m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', 'remove', 'bamtools', 'bwa', 'fastaq', 'gawk', 'libbamtools2.5.1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhat-trie0:amd64', 'libhts2:amd64', 'libicu63:amd64', 'libjsoncpp1:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libperl5.28:amd64', 'libprocps7:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libssw0:amd64', 'libxml2:amd64', 'libxslt1.1:amd64', 'libyaml-0-2:amd64', 'lsb-base', 'mime-support', 'mummer', 'perl', 'perl-modules-5.28', 'procps', 'prodigal', 'python', 'python-joblib', 'python-minimal', 'python-yaml', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-et-xmlfile', 'python3-jdcal', 'python3-lxml:amd64', 'python3-minimal', 'python3-openpyxl', 'python3-pkg-resources', 'python3-pymummer', 'python3-pysam', 'python3.7', 'python3.7-minimal', 'readline-common', 'samtools', 'spades', 'circlator'] 0m50.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bamtools bwa circlator fastaq gawk libbamtools2.5.1 libcurl3-gnutls libdeflate0 libexpat1 libgdbm-compat4 libgdbm6 libgomp1 libgssapi-krb5-2 libhat-trie0 libhts2 libicu63 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmpdec2 libmpfr6 libncurses6 libnghttp2-14 libnlopt0 libperl5.28 libprocps7 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 libssw0 libxml2 libxslt1.1 libyaml-0-2 lsb-base mime-support mummer perl perl-modules-5.28 procps prodigal python python-joblib python-minimal python-yaml python2 python2-minimal python2.7 python2.7-minimal python3 python3-et-xmlfile python3-jdcal python3-lxml python3-minimal python3-openpyxl python3-pkg-resources python3-pymummer python3-pysam python3.7 python3.7-minimal readline-common samtools spades 0 upgraded, 0 newly installed, 79 to remove and 0 not upgraded. After this operation, 205 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 ... 11726 files and directories currently installed.) Removing circlator (1.5.5-3) ... Removing spades (3.13.0+dfsg2-2) ... Removing bamtools (2.5.1+dfsg-3) ... Removing bwa (0.7.17-3) ... Removing python3-pymummer (0.10.3-2) ... Removing fastaq (3.17.0-2) ... 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 libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Removing samtools (1.9-4) ... Removing python3-pysam (0.15.2+ds-2) ... Removing libhts2:amd64 (1.9-12~deb10u1) ... Removing libcurl3-gnutls:amd64 (7.64.0-4+deb10u6) ... Removing libdeflate0:amd64 (1.2-1) ... Removing python3-pkg-resources (40.8.0-1) ... Removing python3-openpyxl (2.4.9-1) ... Removing python3-lxml:amd64 (4.3.2-1+deb10u4) ... Removing python3-et-xmlfile (1.0.1-2) ... Removing python-joblib (0.13.0-2+deb10u2) ... Removing python-yaml (3.13-2) ... Removing python (2.7.16-1) ... 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 libgdbm6:amd64 (1.18.1-4) ... Removing libgomp1:amd64 (8.3.0-6) ... Removing libgssapi-krb5-2:amd64 (1.17-3+deb10u5) ... Removing libhat-trie0:amd64 (0.1.2-2) ... Removing libxslt1.1:amd64 (1.1.32-2.2~deb10u2) ... Removing libxml2:amd64 (2.9.4+dfsg1-7+deb10u6) ... Removing libicu63:amd64 (63.1-6+deb10u3) ... Removing libjsoncpp1:amd64 (1.7.4-3) ... Removing libkrb5-3:amd64 (1.17-3+deb10u5) ... Removing libk5crypto3:amd64 (1.17-3+deb10u5) ... Removing libkrb5support0:amd64 (1.17-3+deb10u5) ... 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 libmpfr6:amd64 (4.0.2-1) ... Removing procps (2:3.3.15-2) ... Removing libncurses6:amd64 (6.1+20181013-2+deb10u3) ... Removing libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Removing libnlopt0:amd64 (2.4.2+dfsg-8+b1) ... Removing libprocps7:amd64 (2:3.3.15-2) ... Removing libpsl5:amd64 (0.20.2-2) ... Removing libpython-stdlib:amd64 (2.7.16-1) ... Removing python2 (2.7.16-1) ... Removing libpython2-stdlib:amd64 (2.7.16-1) ... Removing python-minimal (2.7.16-1) ... 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 libsigsegv2:amd64 (2.12-2) ... Removing libssh2-1:amd64 (1.8.0-2.1) ... Removing libssw0:amd64 (1.1-2) ... Removing libyaml-0-2:amd64 (0.2.1-1) ... Removing lsb-base (10.2019051400) ... Removing perl-modules-5.28 (5.28.1-6+deb10u1) ... Removing prodigal (1:2.6.3-4) ... Removing python2-minimal (2.7.16-1) ... Removing python3-jdcal (1.0-1.2) ... Removing python3 (3.7.3-1) ... Removing python3.7 (3.7.3-2+deb10u5) ... Removing python3-minimal (3.7.3-1) ... Removing python3.7-minimal (3.7.3-2+deb10u5) ... Removing python2.7 (2.7.16-2+deb10u2) ... Removing libpython2.7-stdlib:amd64 (2.7.16-2+deb10u2) ... Removing libexpat1:amd64 (2.2.6-2+deb10u6) ... Removing libpython3-stdlib:amd64 (3.7.3-1) ... Removing libpython3.7-stdlib:amd64 (3.7.3-2+deb10u5) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec2:amd64 (2.4.2-2) ... Removing python2.7-minimal (2.7.16-2+deb10u2) ... Removing libpython2.7-minimal:amd64 (2.7.16-2+deb10u2) ... find: '/usr/lib/python2.7': No such file or directory Removing libpython3.7-minimal:amd64 (3.7.3-2+deb10u5) ... find: '/usr/lib/python3': No such file or directory Removing libreadline7:amd64 (7.0-5) ... Removing libsqlite3-0:amd64 (3.27.2-3+deb10u2) ... Removing libssl1.1:amd64 (1.1.1n-0+deb10u5) ... Removing mime-support (3.62) ... Removing readline-common (7.0-5) ... Processing triggers for libc-bin (2.28-10+deb10u2) ... 0m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', 'remove', 'bamtools', 'bwa', 'fastaq', 'gawk', 'libbamtools2.5.1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhat-trie0:amd64', 'libhts2:amd64', 'libicu63:amd64', 'libjsoncpp1:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libperl5.28:amd64', 'libprocps7:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libssw0:amd64', 'libxml2:amd64', 'libxslt1.1:amd64', 'libyaml-0-2:amd64', 'lsb-base', 'mime-support', 'mummer', 'perl', 'perl-modules-5.28', 'procps', 'prodigal', 'python', 'python-joblib', 'python-minimal', 'python-yaml', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-et-xmlfile', 'python3-jdcal', 'python3-lxml:amd64', 'python3-minimal', 'python3-openpyxl', 'python3-pkg-resources', 'python3-pymummer', 'python3-pysam', 'python3.7', 'python3.7-minimal', 'readline-common', 'samtools', 'spades', 'circlator'] 0m50.1s INFO: Running scripts post_remove 0m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_remove_exceptions'] 0m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_remove_exceptions'] 0m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg', '--purge', 'bamtools', 'bwa', 'fastaq', 'gawk', 'libbamtools2.5.1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhat-trie0:amd64', 'libhts2:amd64', 'libicu63:amd64', 'libjsoncpp1:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libperl5.28:amd64', 'libprocps7:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libssw0:amd64', 'libxml2:amd64', 'libxslt1.1:amd64', 'libyaml-0-2:amd64', 'lsb-base', 'mime-support', 'mummer', 'perl', 'perl-modules-5.28', 'procps', 'prodigal', 'python', 'python-joblib', 'python-minimal', 'python-yaml', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-et-xmlfile', 'python3-jdcal', 'python3-lxml:amd64', 'python3-minimal', 'python3-openpyxl', 'python3-pkg-resources', 'python3-pymummer', 'python3-pysam', 'python3.7', 'python3.7-minimal', 'readline-common', 'samtools', 'spades'] 0m50.4s DUMP: dpkg: warning: ignoring request to remove bamtools which isn't installed dpkg: warning: ignoring request to remove bwa which isn't installed dpkg: warning: ignoring request to remove fastaq which isn't installed (Reading database ... 6489 files and directories currently installed.) Purging configuration files for gawk (1:4.2.1+dfsg-1) ... dpkg: warning: ignoring request to remove libbamtools2.5.1 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 libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.17-3+deb10u5) ... dpkg: warning: ignoring request to remove libhat-trie0 which isn't installed dpkg: warning: ignoring request to remove libhts2 which isn't installed dpkg: warning: ignoring request to remove libicu63 which isn't installed dpkg: warning: ignoring request to remove libjsoncpp1 which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove 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 libmpdec2 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 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 libnlopt0 which isn't installed dpkg: warning: ignoring request to remove libperl5.28 which isn't installed dpkg: warning: ignoring request to remove libprocps7 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+deb10u2) ... 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 libpython3.7-minimal:amd64 (3.7.3-2+deb10u5) ... dpkg: warning: ignoring request to remove libpython3.7-stdlib 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+deb10u5) ... dpkg: warning: ignoring request to remove libssw0 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed dpkg: warning: ignoring request to remove lsb-base 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-5.28 which isn't installed Purging configuration files for procps (2:3.3.15-2) ... dpkg: warning: ignoring request to remove prodigal which isn't installed Purging configuration files for python (2.7.16-1) ... dpkg: warning: ignoring request to remove python-joblib which isn't installed dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python-yaml 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+deb10u2) ... Purging configuration files for python3 (3.7.3-1) ... dpkg: warning: ignoring request to remove python3-et-xmlfile which isn't installed dpkg: warning: ignoring request to remove python3-jdcal which isn't installed dpkg: warning: ignoring request to remove python3-lxml which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-openpyxl 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-pysam which isn't installed dpkg: warning: ignoring request to remove python3.7 which isn't installed Purging configuration files for python3.7-minimal (3.7.3-2+deb10u5) ... 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 spades which isn't installed 0m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg', '--purge', 'bamtools', 'bwa', 'fastaq', 'gawk', 'libbamtools2.5.1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhat-trie0:amd64', 'libhts2:amd64', 'libicu63:amd64', 'libjsoncpp1:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libperl5.28:amd64', 'libprocps7:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libssw0:amd64', 'libxml2:amd64', 'libxslt1.1:amd64', 'libyaml-0-2:amd64', 'lsb-base', 'mime-support', 'mummer', 'perl', 'perl-modules-5.28', 'procps', 'prodigal', 'python', 'python-joblib', 'python-minimal', 'python-yaml', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-et-xmlfile', 'python3-jdcal', 'python3-lxml:amd64', 'python3-minimal', 'python3-openpyxl', 'python3-pkg-resources', 'python3-pymummer', 'python3-pysam', 'python3.7', 'python3.7-minimal', 'readline-common', 'samtools', 'spades'] 0m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg', '--purge', 'circlator'] 0m50.4s DUMP: dpkg: warning: ignoring request to remove circlator which isn't installed 0m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg', '--purge', 'circlator'] 0m50.4s INFO: Running scripts post_purge 0m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_purge_exceptions'] 0m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_purge_exceptions'] 0m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg', '--purge', '--pending'] 0m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg', '--purge', '--pending'] 0m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg', '--remove', '--pending'] 0m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg', '--remove', '--pending'] 0m50.4s INFO: Running scripts post_test 0m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_test_exceptions'] 0m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'tmp/scripts/post_test_exceptions'] 0m50.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m50.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m50.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg-divert', '--list'] 0m50.9s 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 0m50.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'dpkg-divert', '--list'] 0m50.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', 'clean'] 0m51.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw', 'apt-get', 'clean'] 0m51.0s DEBUG: Recording chroot state 0m52.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/shm'] 0m52.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/shm'] 0m52.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/console'] 0m52.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/console'] 0m52.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/ptmx'] 0m52.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/ptmx'] 0m52.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/pts'] 0m52.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/dev/pts'] 0m52.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/proc'] 0m52.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw/proc'] 0m52.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m52.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpqqfvdwxw'] 0m52.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpqqfvdwxw 0m52.5s INFO: PASS: Upgrading between Debian distributions. 0m52.5s INFO: PASS: All tests. 0m52.5s INFO: piuparts run ends. ret=0 End: 2023-08-04 06:48:18 GMT