Start: 2024-04-17 06:08:33 GMT [bullseye] Package: spades Source: spades (3.13.1+dfsg-2) Version: 3.13.1+dfsg-2+b2 Installed-Size: 22622 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libgcc-s1 (>= 4.0), libgomp1 (>= 6), libhat-trie0, libnlopt0 (>= 2.6.1), libssw0 (>= 1.1), libstdc++6 (>= 9), zlib1g (>= 1:1.2.3.3), python3:any, python3, python3-distutils, python3-joblib, python3-yaml, bwa, bamtools, samtools Description: genome assembler for single-cell and isolates data sets Homepage: http://cab.spbu.ru/software/spades/ Description-md5: a8af60ccfdd2e159193efb52065bef14 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, implemented-in::python, interface::commandline, role::program, scope::utility, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/s/spades/spades_3.13.1+dfsg-2+b2_amd64.deb Size: 4776668 MD5sum: 0e411aff85668712cf73bc1e8a6582eb SHA256: 42f46a112e36e5bd303321f695883125eab5e7b9a01a4623b71545f18e698151 [bullseye-next] Package: spades Source: spades (3.13.1+dfsg-2) Version: 3.13.1+dfsg-2+b2 Installed-Size: 22622 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libgcc-s1 (>= 4.0), libgomp1 (>= 6), libhat-trie0, libnlopt0 (>= 2.6.1), libssw0 (>= 1.1), libstdc++6 (>= 9), zlib1g (>= 1:1.2.3.3), python3:any, python3, python3-distutils, python3-joblib, python3-yaml, bwa, bamtools, samtools Description: genome assembler for single-cell and isolates data sets Homepage: http://cab.spbu.ru/software/spades/ Description-md5: a8af60ccfdd2e159193efb52065bef14 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, implemented-in::python, interface::commandline, role::program, scope::utility, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/s/spades/spades_3.13.1+dfsg-2+b2_amd64.deb Size: 4776668 MD5sum: 0e411aff85668712cf73bc1e8a6582eb SHA256: 42f46a112e36e5bd303321f695883125eab5e7b9a01a4623b71545f18e698151 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-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt spades=3.13.1+dfsg-2+b2 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 1.4.1~202403190841~1.4-4-g85045c69 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-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt spades=3.13.1+dfsg-2+b2 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpnwlkmltw 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpnwlkmltw 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpnwlkmltw/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', 'update'] 0m1.5s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', 'update'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', '-yf', 'dist-upgrade'] 0m2.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', '-yf', 'dist-upgrade'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.2s DUMP: 29fcf27583012b383113cec2bf757015 - 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.2s INFO: Running scripts post_setup 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.6s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.6s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat 0m3.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m4.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m4.0s INFO: Running scripts is_testable 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s INFO: Running scripts pre_test 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_test_root_password'] 0m4.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_test_root_password'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'show', '--no-all-versions', 'spades'] 0m4.4s DUMP: Package: spades Source: spades (3.13.1+dfsg-2) Version: 3.13.1+dfsg-2+b2 Installed-Size: 22622 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libgcc-s1 (>= 4.0), libgomp1 (>= 6), libhat-trie0, libnlopt0 (>= 2.6.1), libssw0 (>= 1.1), libstdc++6 (>= 9), zlib1g (>= 1:1.2.3.3), python3:any, python3, python3-distutils, python3-joblib, python3-yaml, bwa, bamtools, samtools Description-en: genome assembler for single-cell and isolates data sets The SPAdes ?? St. Petersburg genome assembler is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio and Sanger reads. You can also provide additional contigs that will be used as long reads. Description-md5: a8af60ccfdd2e159193efb52065bef14 Homepage: http://cab.spbu.ru/software/spades/ Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, implemented-in::python, interface::commandline, role::program, scope::utility, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/s/spades/spades_3.13.1+dfsg-2+b2_amd64.deb Size: 4776668 MD5sum: 0e411aff85668712cf73bc1e8a6582eb SHA256: 42f46a112e36e5bd303321f695883125eab5e7b9a01a4623b71545f18e698151 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'show', '--no-all-versions', 'spades'] 0m4.4s INFO: apt-cache knows about the following packages: spades 0m4.4s INFO: Running scripts pre_install 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'policy'] 0m4.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'policy'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'policy', 'spades'] 0m4.5s DUMP: spades: Installed: (none) Candidate: 3.13.1+dfsg-2+b2 Version table: 3.13.1+dfsg-2+b2 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'policy', 'spades'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', '-y', 'install', 'spades'] 0m13.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bamtools bwa libbamtools2.5.1 libbrotli1 libcurl3-gnutls libdeflate0 libexpat1 libgomp1 libhat-trie0 libhts3 libjsoncpp24 libldap-2.4-2 libmpdec3 libncurses6 libncursesw6 libnghttp2-14 libnlopt0 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssw0 libyaml-0-2 media-types procps python3 python3-distutils python3-joblib python3-lib2to3 python3-minimal python3-pkg-resources python3-yaml python3.9 python3.9-minimal readline-common samtools Suggested packages: python3-doc python3-tk python3-venv python3-setuptools python3.9-venv python3.9-doc binutils binfmt-support readline-doc cwltool Recommended packages: perl ca-certificates libldap-common libgpm2 publicsuffix libsasl2-modules psmisc python3-numpy python3-pytest python3-simplejson python3-psutil The following NEW packages will be installed: bamtools bwa libbamtools2.5.1 libbrotli1 libcurl3-gnutls libdeflate0 libexpat1 libgomp1 libhat-trie0 libhts3 libjsoncpp24 libldap-2.4-2 libmpdec3 libncurses6 libncursesw6 libnghttp2-14 libnlopt0 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssw0 libyaml-0-2 media-types procps python3 python3-distutils python3-joblib python3-lib2to3 python3-minimal python3-pkg-resources python3-yaml python3.9 python3.9-minimal readline-common samtools spades 0 upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 15.9 MB of archives. After this operation, 59.8 MB of additional disk space will be used. 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Setting up libsqlite3-0:amd64 (3.34.1-3) ... Setting up libnghttp2-14:amd64 (1.43.0-1+deb11u1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up libnlopt0:amd64 (2.7.0-4+b2) ... Setting up libgomp1:amd64 (10.2.1-6) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libhat-trie0:amd64 (0.1.2-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libbamtools2.5.1:amd64 (2.5.1+dfsg-9) ... Setting up libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libjsoncpp24:amd64 (1.9.4-4) ... Setting up bamtools (2.5.1+dfsg-9) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up libssw0:amd64 (1.1-13) ... Setting up readline-common (8.1-1) ... Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u11) ... Setting up procps (2:3.3.17-5) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libhts3:amd64 (1.11-4) ... Setting up samtools (1.11-1) ... Setting up python3.9 (3.9.2-1) ... Setting up python3 (3.9.2-3) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up python3-joblib (0.17.0-4+deb11u1) ... Setting up python3-yaml (5.3.1-5) ... Setting up spades (3.13.1+dfsg-2+b2) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', '-y', 'install', 'spades'] 0m13.7s INFO: Running scripts post_install 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_install_exceptions'] 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_install_exceptions'] 0m13.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m14.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m14.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpnwlkmltw to bullseye-next 0m14.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main deb http://security.debian.org bullseye-security main deb http://deb.debian.org/debian/ bullseye-updates main deb http://deb.debian.org/debian/ bullseye-proposed-updates main 0m14.3s INFO: Running scripts pre_distupgrade 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', 'update'] 0m16.0s DUMP: Get:1 http://security.debian.org bullseye-security InRelease [48.4 kB] Hit:2 http://deb.debian.org/debian bullseye InRelease Get:3 http://deb.debian.org/debian bullseye-updates InRelease [44.1 kB] Get:4 http://deb.debian.org/debian bullseye-proposed-updates InRelease [54.0 kB] Get:5 http://security.debian.org bullseye-security/main amd64 Packages [271 kB] Get:6 http://security.debian.org bullseye-security/main Translation-en [175 kB] Get:7 http://deb.debian.org/debian bullseye-updates/main amd64 Packages [18.8 kB] Get:8 http://deb.debian.org/debian bullseye-updates/main Translation-en [10.9 kB] Get:9 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages [42.8 kB] Get:10 http://deb.debian.org/debian bullseye-proposed-updates/main Translation-en [26.3 kB] Fetched 691 kB in 1s (737 kB/s) Reading package lists... 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', 'update'] 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', '-yf', 'dist-upgrade'] 0m18.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils libblkid1 libgnutls30 libmount1 libsmartcols1 libuuid1 mount util-linux 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3464 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://security.debian.org bullseye-security/main amd64 bsdutils amd64 1:2.36.1-8+deb11u2 [149 kB] Get:2 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 libgnutls30 amd64 3.7.1-5+deb11u5 [1340 kB] Get:3 http://security.debian.org bullseye-security/main amd64 util-linux amd64 2.36.1-8+deb11u2 [1142 kB] Get:4 http://security.debian.org bullseye-security/main amd64 mount amd64 2.36.1-8+deb11u2 [186 kB] Get:5 http://security.debian.org bullseye-security/main amd64 libblkid1 amd64 2.36.1-8+deb11u2 [194 kB] Get:6 http://security.debian.org bullseye-security/main amd64 libmount1 amd64 2.36.1-8+deb11u2 [212 kB] Get:7 http://security.debian.org bullseye-security/main amd64 libsmartcols1 amd64 2.36.1-8+deb11u2 [158 kB] Get:8 http://security.debian.org bullseye-security/main amd64 libuuid1 amd64 2.36.1-8+deb11u2 [83.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3464 kB in 0s (18.1 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8300 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.36.1-8+deb11u2_amd64.deb ... Unpacking bsdutils (1:2.36.1-8+deb11u2) over (1:2.36.1-8+deb11u1) ... Setting up bsdutils (1:2.36.1-8+deb11u2) ... (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 ... 8300 files and directories currently installed.) Preparing to unpack .../util-linux_2.36.1-8+deb11u2_amd64.deb ... Unpacking util-linux (2.36.1-8+deb11u2) over (2.36.1-8+deb11u1) ... Setting up util-linux (2.36.1-8+deb11u2) ... (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 ... 8300 files and directories currently installed.) Preparing to unpack .../mount_2.36.1-8+deb11u2_amd64.deb ... Unpacking mount (2.36.1-8+deb11u2) over (2.36.1-8+deb11u1) ... Preparing to unpack .../libblkid1_2.36.1-8+deb11u2_amd64.deb ... Unpacking libblkid1:amd64 (2.36.1-8+deb11u2) over (2.36.1-8+deb11u1) ... Setting up libblkid1:amd64 (2.36.1-8+deb11u2) ... (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 ... 8300 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.1-5+deb11u5_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.1-5+deb11u5) over (3.7.1-5+deb11u4) ... Setting up libgnutls30:amd64 (3.7.1-5+deb11u5) ... (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 ... 8300 files and directories currently installed.) Preparing to unpack .../libmount1_2.36.1-8+deb11u2_amd64.deb ... Unpacking libmount1:amd64 (2.36.1-8+deb11u2) over (2.36.1-8+deb11u1) ... Setting up libmount1:amd64 (2.36.1-8+deb11u2) ... (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 ... 8300 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.36.1-8+deb11u2_amd64.deb ... Unpacking libsmartcols1:amd64 (2.36.1-8+deb11u2) over (2.36.1-8+deb11u1) ... Setting up libsmartcols1:amd64 (2.36.1-8+deb11u2) ... (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 ... 8300 files and directories currently installed.) Preparing to unpack .../libuuid1_2.36.1-8+deb11u2_amd64.deb ... Unpacking libuuid1:amd64 (2.36.1-8+deb11u2) over (2.36.1-8+deb11u1) ... Setting up libuuid1:amd64 (2.36.1-8+deb11u2) ... Setting up mount (2.36.1-8+deb11u2) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', '-yf', 'dist-upgrade'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.7s DUMP: af4f82d0fe4b7c46e349f25a667927ec - 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'show', '--no-all-versions', 'spades'] 0m19.0s DUMP: Package: spades Source: spades (3.13.1+dfsg-2) Version: 3.13.1+dfsg-2+b2 Installed-Size: 22622 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libgcc-s1 (>= 4.0), libgomp1 (>= 6), libhat-trie0, libnlopt0 (>= 2.6.1), libssw0 (>= 1.1), libstdc++6 (>= 9), zlib1g (>= 1:1.2.3.3), python3:any, python3, python3-distutils, python3-joblib, python3-yaml, bwa, bamtools, samtools Description-en: genome assembler for single-cell and isolates data sets The SPAdes ?? St. Petersburg genome assembler is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio and Sanger reads. You can also provide additional contigs that will be used as long reads. Description-md5: a8af60ccfdd2e159193efb52065bef14 Homepage: http://cab.spbu.ru/software/spades/ Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, implemented-in::python, interface::commandline, role::program, scope::utility, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/s/spades/spades_3.13.1+dfsg-2+b2_amd64.deb Size: 4776668 MD5sum: 0e411aff85668712cf73bc1e8a6582eb SHA256: 42f46a112e36e5bd303321f695883125eab5e7b9a01a4623b71545f18e698151 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'show', '--no-all-versions', 'spades'] 0m19.0s INFO: apt-cache knows about the following packages: spades 0m19.0s INFO: Running scripts pre_install 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_database-server'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_database-server'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_exceptions'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_exceptions'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_extras'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_extras'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'policy'] 0m19.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'policy'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'policy', 'spades'] 0m19.1s DUMP: spades: Installed: 3.13.1+dfsg-2+b2 Candidate: 3.13.1+dfsg-2+b2 Version table: *** 3.13.1+dfsg-2+b2 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'policy', 'spades'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', '-y', 'install', 'spades'] 0m19.5s DUMP: Reading package lists... Building dependency tree... Reading state information... spades is already the newest version (3.13.1+dfsg-2+b2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', '-y', 'install', 'spades'] 0m19.5s INFO: Running scripts post_install 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_install_exceptions'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_install_exceptions'] 0m19.5s INFO: Running scripts post_distupgrade 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m20.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m20.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m20.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m20.3s INFO: Running scripts pre_install 0m20.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_database-server'] 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_database-server'] 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_exceptions'] 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_exceptions'] 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_extras'] 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_extras'] 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'policy'] 0m20.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'policy'] 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'policy', 'spades'] 0m20.5s DUMP: spades: Installed: 3.13.1+dfsg-2+b2 Candidate: 3.13.1+dfsg-2+b2 Version table: *** 3.13.1+dfsg-2+b2 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-cache', 'policy', 'spades'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', '-y', 'install', 'spades=3.13.1+dfsg-2+b2'] 0m21.0s DUMP: Reading package lists... Building dependency tree... Reading state information... spades is already the newest version (3.13.1+dfsg-2+b2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', '-y', 'install', 'spades=3.13.1+dfsg-2+b2'] 0m21.0s INFO: Running scripts post_install 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_install_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_install_exceptions'] 0m21.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m21.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m21.6s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m21.7s INFO: /bin converted to /usr/bin by /usr merge 0m21.7s INFO: /lib converted to /usr/lib by /usr merge 0m21.7s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m21.7s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m21.7s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m21.7s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m21.7s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m21.7s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m21.7s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m21.7s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m21.7s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m21.7s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m21.7s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m21.7s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m21.7s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m21.7s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m21.7s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m21.7s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m21.7s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m21.7s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m21.7s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m21.7s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m21.7s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m21.7s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m21.7s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m21.7s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m21.7s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m21.7s INFO: /sbin converted to /usr/sbin by /usr merge 0m22.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', '-ac', '--ignore-obsolete'] 0m23.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', '-ac', '--ignore-obsolete'] 0m23.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m23.2s DUMP: 0.15.6 0m23.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m23.2s INFO: Running adequate version 0.15.6 now. 0m23.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'spades'] 0m23.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'spades'] 0m23.3s INFO: Running scripts pre_remove 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m25.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m25.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_remove_exceptions'] 0m25.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/pre_remove_exceptions'] 0m25.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m26.0s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed bamtools bamtools 2.5.1+dfsg-9 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u2 install ok installed bwa bwa 0.7.17-6+b1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libbamtools2.5.1:amd64 libbamtools2.5.1 2.5.1+dfsg-9 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u2 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.74.0-1.3+deb11u11 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libdeflate0:amd64 libdeflate0 1.7-1 install ok installed libexpat1:amd64 libexpat1 2.2.10-2+deb11u5 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u5 install ok installed libgomp1:amd64 libgomp1 10.2.1-6 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhat-trie0:amd64 libhat-trie0 0.1.2-2 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libhts3:amd64 libhts3 1.11-4 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libjsoncpp24:amd64 libjsoncpp24 1.9.4-4 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u2 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-1 install ok installed libncurses6:amd64 libncurses6 6.2+20201114-2+deb11u2 install ok installed libncursesw6:amd64 libncursesw6 6.2+20201114-2+deb11u2 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.43.0-1+deb11u1 install ok installed libnlopt0:amd64 libnlopt0 2.7.0-4+b2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libprocps8:amd64 libprocps8 2:3.3.17-5 install ok installed libpsl5:amd64 libpsl5 0.21.0-1.2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.9.2-3 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed libreadline8:amd64 libreadline8 8.1-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-2.1+deb11u1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-2.1+deb11u1 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u2 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.34.1-3 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssh2-1:amd64 libssh2-1 1.9.0-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libssw0:amd64 libssw0 1.1-13 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u2 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.2-1 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed media-types media-types 4.0.0 install ok installed mount mount 2.36.1-8+deb11u2 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed procps procps 2:3.3.17-5 install ok installed python3 python3 3.9.2-3 install ok installed python3-distutils python3-distutils 3.9.2-1 install ok installed python3-joblib python3-joblib 0.17.0-4+deb11u1 install ok installed python3-lib2to3 python3-lib2to3 3.9.2-1 install ok installed python3-minimal python3-minimal 3.9.2-3 install ok installed python3-pkg-resources python3-pkg-resources 52.0.0-4 install ok installed python3-yaml python3-yaml 5.3.1-5 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed readline-common readline-common 8.1-1 install ok installed samtools samtools 1.11-1 install ok installed sed sed 4.7-1 install ok installed spades spades 3.13.1+dfsg-2+b2 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', 'remove', 'bamtools', 'bwa', 'libbamtools2.5.1:amd64', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgomp1:amd64', 'libhat-trie0:amd64', 'libhts3:amd64', 'libjsoncpp24:amd64', 'libldap-2.4-2:amd64', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssw0:amd64', 'libyaml-0-2:amd64', 'media-types', 'procps', 'python3', 'python3-distutils', 'python3-joblib', 'python3-lib2to3', 'python3-minimal', 'python3-pkg-resources', 'python3-yaml', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'spades'] 0m27.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bamtools bwa libbamtools2.5.1 libbrotli1 libcurl3-gnutls libdeflate0 libexpat1 libgomp1 libhat-trie0 libhts3 libjsoncpp24 libldap-2.4-2 libmpdec3 libncurses6 libncursesw6 libnghttp2-14 libnlopt0 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssw0 libyaml-0-2 media-types procps python3 python3-distutils python3-joblib python3-lib2to3 python3-minimal python3-pkg-resources python3-yaml python3.9 python3.9-minimal readline-common samtools spades 0 upgraded, 0 newly installed, 44 to remove and 0 not upgraded. After this operation, 59.8 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 ... 8300 files and directories currently installed.) Removing spades (3.13.1+dfsg-2+b2) ... Removing bamtools (2.5.1+dfsg-9) ... Removing bwa (0.7.17-6+b1) ... Removing libbamtools2.5.1:amd64 (2.5.1+dfsg-9) ... Removing samtools (1.11-1) ... Removing libhts3:amd64 (1.11-4) ... Removing libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u11) ... Removing libbrotli1:amd64 (1.0.9-2+b2) ... Removing libdeflate0:amd64 (1.7-1) ... Removing python3-yaml (5.3.1-5) ... Removing python3-distutils (3.9.2-1) ... Removing python3-joblib (0.17.0-4+deb11u1) ... Removing python3-pkg-resources (52.0.0-4) ... Removing libgomp1:amd64 (10.2.1-6) ... Removing libhat-trie0:amd64 (0.1.2-2) ... Removing libjsoncpp24:amd64 (1.9.4-4) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing procps (2:3.3.17-5) ... Removing libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Removing libnghttp2-14:amd64 (1.43.0-1+deb11u1) ... Removing libnlopt0:amd64 (2.7.0-4+b2) ... Removing libprocps8:amd64 (2:3.3.17-5) ... Removing libpsl5:amd64 (0.21.0-1.2) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing libssh2-1:amd64 (1.9.0-2) ... Removing libssw0:amd64 (1.1-13) ... Removing libyaml-0-2:amd64 (0.2.2-1) ... Removing python3-lib2to3 (3.9.2-1) ... Removing python3 (3.9.2-3) ... Removing python3-minimal (3.9.2-3) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing libexpat1:amd64 (2.2.10-2+deb11u5) ... Removing libpython3-stdlib:amd64 (3.9.2-3) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec3:amd64 (2.5.1-1) ... Removing libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.1-1) ... Removing libsqlite3-0:amd64 (3.34.1-3) ... Removing media-types (4.0.0) ... Removing readline-common (8.1-1) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', 'remove', 'bamtools', 'bwa', 'libbamtools2.5.1:amd64', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgomp1:amd64', 'libhat-trie0:amd64', 'libhts3:amd64', 'libjsoncpp24:amd64', 'libldap-2.4-2:amd64', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssw0:amd64', 'libyaml-0-2:amd64', 'media-types', 'procps', 'python3', 'python3-distutils', 'python3-joblib', 'python3-lib2to3', 'python3-minimal', 'python3-pkg-resources', 'python3-yaml', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'spades'] 0m27.9s INFO: Running scripts post_remove 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_remove_exceptions'] 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_remove_exceptions'] 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg', '--purge', 'bamtools', 'bwa', 'libbamtools2.5.1:amd64', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgomp1:amd64', 'libhat-trie0:amd64', 'libhts3:amd64', 'libjsoncpp24:amd64', 'libldap-2.4-2:amd64', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssw0:amd64', 'libyaml-0-2:amd64', 'media-types', 'procps', 'python3', 'python3-distutils', 'python3-joblib', 'python3-lib2to3', 'python3-minimal', 'python3-pkg-resources', 'python3-yaml', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools'] 0m28.0s 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 libbamtools2.5.1 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 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 libgomp1 which isn't installed dpkg: warning: ignoring request to remove libhat-trie0 which isn't installed dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libjsoncpp24 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 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 libprocps8 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed (Reading database ... 6681 files and directories currently installed.) Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libreadline8 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 libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libssw0 which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed Purging configuration files for media-types (4.0.0) ... Purging configuration files for procps (2:3.3.17-5) ... Purging configuration files for python3 (3.9.2-3) ... dpkg: warning: ignoring request to remove python3-distutils which isn't installed dpkg: warning: ignoring request to remove python3-joblib which isn't installed dpkg: warning: ignoring request to remove python3-lib2to3 which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-yaml which isn't installed dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for readline-common (8.1-1) ... dpkg: warning: ignoring request to remove samtools which isn't installed 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg', '--purge', 'bamtools', 'bwa', 'libbamtools2.5.1:amd64', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgomp1:amd64', 'libhat-trie0:amd64', 'libhts3:amd64', 'libjsoncpp24:amd64', 'libldap-2.4-2:amd64', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssw0:amd64', 'libyaml-0-2:amd64', 'media-types', 'procps', 'python3', 'python3-distutils', 'python3-joblib', 'python3-lib2to3', 'python3-minimal', 'python3-pkg-resources', 'python3-yaml', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools'] 0m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg', '--purge', 'spades'] 0m28.0s DUMP: dpkg: warning: ignoring request to remove spades which isn't installed 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg', '--purge', 'spades'] 0m28.0s INFO: Running scripts post_purge 0m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_purge_exceptions'] 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_purge_exceptions'] 0m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg', '--purge', '--pending'] 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg', '--purge', '--pending'] 0m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg', '--remove', '--pending'] 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg', '--remove', '--pending'] 0m28.0s INFO: Running scripts post_test 0m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_test_exceptions'] 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'tmp/scripts/post_test_exceptions'] 0m28.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m28.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg-divert', '--list'] 0m28.4s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged 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 local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'dpkg-divert', '--list'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', 'clean'] 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw', 'apt-get', 'clean'] 0m28.4s DEBUG: Recording chroot state 0m29.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/shm'] 0m29.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/shm'] 0m29.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/console'] 0m29.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/console'] 0m29.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/ptmx'] 0m29.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/ptmx'] 0m29.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/pts'] 0m29.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/dev/pts'] 0m29.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/proc'] 0m29.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw/proc'] 0m29.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m29.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnwlkmltw'] 0m29.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpnwlkmltw 0m29.7s INFO: PASS: Upgrading between Debian distributions. 0m29.7s INFO: PASS: All tests. 0m29.7s INFO: piuparts run ends. ret=0 End: 2024-04-17 06:09:03 GMT