Start: 2022-07-27 01:18:42 GMT [testing] Package: yanagiba Version: 1.0.0-5 Installed-Size: 57 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-nanomath, python3-pandas, python3:any Description: filter low quality Oxford Nanopore reads basecalled with Albacore Homepage: https://github.com/Adamtaranto/Yanagiba Description-md5: af57b968c50c6245e1c69de3c25cfcb8 Section: science Priority: optional Filename: pool/main/y/yanagiba/yanagiba_1.0.0-5_all.deb Size: 25592 MD5sum: 2c43135f5f6a333048dc36a7789f3170 SHA256: 21bcdc37e48753b58d93036efa4989dacd1baa6a2e59f86fac44378dc670506a [sid] Package: yanagiba Version: 1.0.0-5 Installed-Size: 57 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-nanomath, python3-pandas, python3:any Description: filter low quality Oxford Nanopore reads basecalled with Albacore Homepage: https://github.com/Adamtaranto/Yanagiba Description-md5: af57b968c50c6245e1c69de3c25cfcb8 Section: science Priority: optional Filename: pool/main/y/yanagiba/yanagiba_1.0.0-5_all.deb Size: 25592 MD5sum: 2c43135f5f6a333048dc36a7789f3170 SHA256: 21bcdc37e48753b58d93036efa4989dacd1baa6a2e59f86fac44378dc670506a 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 --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt yanagiba=1.0.0-5 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt yanagiba=1.0.0-5 0m0.0s INFO: Running on: Linux piu-slave-conova-01 4.19.0-21-amd64 #1 SMP Debian 4.19.249-2 (2022-06-30) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpfar43dmp 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpfar43dmp 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m1.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/proc'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/proc'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/pts'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/pts'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/ptmx'] 0m1.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/ptmx'] 0m1.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/console'] 0m1.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/console'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/shm'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/shm'] 0m1.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m1.6s DEBUG: Created policy-rc.d and chmodded it. 0m1.6s DEBUG: Created resolv.conf. 0m1.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpfar43dmp/tmp/scripts/ 0m1.6s INFO: Running scripts post_chroot_unpack 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', 'update'] 0m5.5s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [157 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8508 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5791 kB] Fetched 14.5 MB in 3s (5012 kB/s) Reading package lists... 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', 'update'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', '-yf', 'dist-upgrade'] 0m5.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', '-yf', 'dist-upgrade'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.3s DUMP: ce7bb44aa95f0f2322f5a0f3520dd0db - 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.3s INFO: Running scripts post_setup 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_setup_dummy_users'] 0m7.2s DUMP: useradd warning: dummy1000's uid 1000 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1001's uid 1001 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1002's uid 1002 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1003's uid 1003 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1004's uid 1004 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1005's uid 1005 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1006's uid 1006 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1007's uid 1007 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1008's uid 1008 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1009's uid 1009 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1010's uid 1010 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_setup_dummy_users'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_setup_forbid_home'] 0m7.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_setup_forbid_home'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.2s 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' 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_setup_minimize'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_setup_minimize'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_setup_zz_backports'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_setup_zz_backports'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.3s DUMP: install ok installed adduser adduser 3.121 install ok installed apt apt 2.5.1 install ok installed base-files base-files 12.2 install ok installed base-passwd base-passwd 3.5.52 install ok installed bash bash 5.1-6.1 install ok installed bsdutils bsdutils 1:2.38-4 install ok installed coreutils coreutils 8.32-4.1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-8 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.21.9 install ok installed e2fsprogs e2fsprogs 1.46.5-2 install ok installed findutils findutils 4.9.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.1.0-7 install ok installed gpgv gpgv 2.2.35-3 install ok installed grep grep 3.7-1 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.64 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1+b1 install ok installed libblkid1:amd64 libblkid1 2.38-4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5 install ok installed libc-bin libc-bin 2.33-8 install ok installed libc6:amd64 libc6 2.33-8 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.5-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.28-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.263 install ok installed libext2fs2:amd64 libext2fs2 1.46.5-2 install ok installed libffi8:amd64 libffi8 3.4.2-4 install ok installed libgcc-s1:amd64 libgcc-s1 12.1.0-7 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1 install ok installed libgnutls30:amd64 libgnutls30 3.7.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.45-2 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1 install ok installed libmount1:amd64 libmount1 2.38-4 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-13 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-13 install ok installed libpam-runtime libpam-runtime 1.4.0-13 install ok installed libpam0g:amd64 libpam0g 1.4.0-13 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-14 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b1 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b1 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38-4 install ok installed libss2:amd64 libss2 1.46.5-2 install ok installed libstdc++6:amd64 libstdc++6 12.1.0-7 install ok installed libsystemd0:amd64 libsystemd0 251.2-7 install ok installed libtasn1-6:amd64 libtasn1-6 4.18.0-4 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libudev1:amd64 libudev1 251.2-7 install ok installed libunistring2:amd64 libunistring2 1.0-1 install ok installed libuuid1:amd64 libuuid1 2.38-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.11.1+dfsg1-2 install ok installed logsave logsave 1.46.5-2 install ok installed lsb-base lsb-base 11.2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38-4 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed passwd passwd 1:4.11.1+dfsg1-2 install ok installed perl-base perl-base 5.34.0-5 install ok installed sed sed 4.8-1 install ok installed sgml-base sgml-base 1.30 install ok installed sysvinit-utils sysvinit-utils 3.03-1 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022a-1 install ok installed util-linux util-linux 2.38-4 install ok installed util-linux-extra util-linux-extra 2.38-4 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m7.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 0m7.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 0m7.6s INFO: Running scripts is_testable 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/is_testable_uninstallable'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/is_testable_uninstallable'] 0m7.6s INFO: Running scripts pre_test 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_test_exceptions'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_test_exceptions'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_test_root_password'] 0m7.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_test_root_password'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'show', '--no-all-versions', 'yanagiba'] 0m7.9s DUMP: Package: yanagiba Version: 1.0.0-5 Installed-Size: 57 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-nanomath, python3-pandas, python3:any Description-en: filter low quality Oxford Nanopore reads basecalled with Albacore Yanagiba is used to filter short or low quality Oxford Nanopore reads which have been basecalled with Albacore. It takes fastq.gz and an Albacore summary file as input. If no Albacore summary file is provided attempt to calculate mean qscore from directly from fastq file using NanoMath. Note: Calculated quality scores appear to be lower for reads called with Metrichor, you may need to lower your minqual setting in this case. Description-md5: af57b968c50c6245e1c69de3c25cfcb8 Homepage: https://github.com/Adamtaranto/Yanagiba Section: science Priority: optional Filename: pool/main/y/yanagiba/yanagiba_1.0.0-5_all.deb Size: 25592 MD5sum: 2c43135f5f6a333048dc36a7789f3170 SHA256: 21bcdc37e48753b58d93036efa4989dacd1baa6a2e59f86fac44378dc670506a 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'show', '--no-all-versions', 'yanagiba'] 0m7.9s INFO: apt-cache knows about the following packages: yanagiba 0m7.9s INFO: Running scripts pre_install 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_database-server'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_database-server'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_exceptions'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_exceptions'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_extras'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_extras'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'policy'] 0m8.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'policy'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'policy', 'yanagiba'] 0m8.1s DUMP: yanagiba: Installed: (none) Candidate: 1.0.0-5 Version table: 1.0.0-5 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'policy', 'yanagiba'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', '-y', 'install', 'yanagiba'] 0m52.2s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: fonts-urw-base35 libblas3 libbrotli1 libbsd0 libdeflate0 libexpat1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblerc3 libmd0 libmpdec3 libncursesw6 libnsl2 libopenjp2-7 libperl5.34 libpng16-16 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libquadmath0 libraqm0 libreadline8 libsqlite3-0 libssl3 libtiff5 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support perl perl-modules-5.34 python3 python3-biopython python3-dateutil python3-deprecated python3-minimal python3-nanomath python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3-six python3-tz python3-wrapt python3.10 python3.10-minimal readline-common w3c-sgml-lib xml-core Suggested packages: fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gdbm-l10n krb5-doc krb5-user liblcms2-utils sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise gcc gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc python3-statsmodels python-pil-doc python3-setuptools pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python3.10-venv python3.10-doc binutils binfmt-support readline-doc debhelper Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 bzip2 file xz-utils netbase python-biopython-doc ncbi-blast+ python3-scipy python3-matplotlib python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-xlwt python3-bs4 python3-html5lib python3-lxml python3-tables python3-jinja2 python3-numba python3-olefile The following NEW packages will be installed: fonts-urw-base35 libblas3 libbrotli1 libbsd0 libdeflate0 libexpat1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblerc3 libmd0 libmpdec3 libncursesw6 libnsl2 libopenjp2-7 libperl5.34 libpng16-16 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libquadmath0 libraqm0 libreadline8 libsqlite3-0 libssl3 libtiff5 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support perl perl-modules-5.34 python3 python3-biopython python3-dateutil python3-deprecated python3-minimal python3-nanomath python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3-six python3-tz python3-wrapt python3.10 python3.10-minimal readline-common w3c-sgml-lib xml-core yanagiba 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded. Need to get 45.4 MB of archives. After this operation, 192 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.34 all 5.34.0-5 [2850 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-1 [82.9 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-1 [58.6 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libperl5.34 amd64 5.34.0-5 [4177 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.34.0-5 [298 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.4-2 [2034 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libpython3.10-minimal amd64 3.10.5-1 [828 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.4.8-1 [109 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 python3.10-minimal amd64 3.10.5-1 [2093 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.10.5-3 [38.6 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 media-types all 8.0.0 [33.4 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 mime-support all 3.66 [10.9 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.3+20220423-2 [133 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20-1 [65.7 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20-1 [111 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-1 [15.7 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20-1 [363 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20-1 [166 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.2-2 [13.8 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.2-2 [83.9 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.1.2-1.2 [73.9 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.1.2-1.2 [168 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.39.1-1 [836 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libpython3.10-stdlib amd64 3.10.5-1 [1704 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 python3.10 amd64 3.10.5-1 [541 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.10.5-3 [21.7 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.10.5-3 [38.2 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-1 [6367 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.10.1-2 [156 kB] Get:33 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libwebp7 amd64 1.2.2-2+b1 [277 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libtiff5 amd64 4.4.0-3 [312 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.2-2+b1 [98.4 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.2-2+b1 [108 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 59.6.0-1.2 [196 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.21.5-1+b1 [3227 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.11-1 [82.4 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.11-1 [42.3 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.2.0-1+b1 [467 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.11-1 [566 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.79+dfsg-3+b1 [1425 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-3 [17.5 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.1-6 [79.2 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 python3-wrapt amd64 1.13.3-1+b2 [41.6 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 python3-deprecated all 1.2.13-2 [13.7 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.1-1 [34.8 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.3.5+dfsg-5+b1 [3409 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.3.5+dfsg-5 [2654 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 python3-nanomath all 1.2.1+ds-1 [8120 B] Get:78 http://deb.debian.org/debian bookworm/main amd64 yanagiba all 1.0.0-5 [25.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 45.4 MB in 0s (159 MB/s) Selecting previously unselected package perl-modules-5.34. (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 ... 6651 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.34_5.34.0-5_all.deb ... Unpacking perl-modules-5.34 (5.34.0-5) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.23-1_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-1) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.23-1_amd64.deb ... 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Unpacking python3.10-minimal (3.10.5-1) ... Setting up libssl3:amd64 (3.0.4-2) ... Setting up libpython3.10-minimal:amd64 (3.10.5-1) ... Setting up libexpat1:amd64 (2.4.8-1) ... Setting up python3.10-minimal (3.10.5-1) ... Selecting previously unselected package python3-minimal. (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 ... 8947 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.10.5-3_amd64.deb ... Unpacking python3-minimal (3.10.5-3) ... 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Unpacking libwebp7:amd64 (1.2.2-2+b1) ... Selecting previously unselected package libtiff5:amd64. Preparing to unpack .../25-libtiff5_4.4.0-3_amd64.deb ... Unpacking libtiff5:amd64 (4.4.0-3) ... Selecting previously unselected package libwebpdemux2:amd64. Preparing to unpack .../26-libwebpdemux2_1.2.2-2+b1_amd64.deb ... Unpacking libwebpdemux2:amd64 (1.2.2-2+b1) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../27-libwebpmux3_1.2.2-2+b1_amd64.deb ... Unpacking libwebpmux3:amd64 (1.2.2-2+b1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../28-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../29-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../30-libxcb1_1.14-3_amd64.deb ... 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Selecting previously unselected package yanagiba. Preparing to unpack .../48-yanagiba_1.0.0-5_all.deb ... Unpacking yanagiba (1.0.0-5) ... Setting up media-types (8.0.0) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up liblcms2-2:amd64 (2.12~rc1-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libkeyutils1:amd64 (1.6.3-1) ... Setting up libglib2.0-0:amd64 (2.72.3-1) ... No schema files found: doing nothing. Setting up libtirpc-common (1.3.2-2) ... Setting up libbrotli1:amd64 (1.0.9-2+b4) ... Setting up libsqlite3-0:amd64 (3.39.1-1) ... Setting up libdeflate0:amd64 (1.12-1) ... Setting up fonts-urw-base35 (20200910-1) ... Setting up libgomp1:amd64 (12.1.0-7) ... Setting up perl-modules-5.34 (5.34.0-5) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libkrb5support0:amd64 (1.20-1) ... Setting up libblas3:amd64 (3.10.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.2-1) ... Setting up liblerc3:amd64 (3.0+ds-1) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libquadmath0:amd64 (12.1.0-7) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libpng16-16:amd64 (1.6.37-5) ... Setting up libncursesw6:amd64 (6.3+20220423-2) ... Setting up libk5crypto3:amd64 (1.20-1) ... Setting up libgfortran5:amd64 (12.1.0-7) ... Setting up libwebp7:amd64 (1.2.2-2+b1) ... Setting up libmd0:amd64 (1.0.4-2) ... Setting up xml-core (0.18+nmu1) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up libopenjp2-7:amd64 (2.5.0-1) ... Setting up libkrb5-3:amd64 (1.20-1) ... Setting up libtiff5:amd64 (4.4.0-3) ... Setting up libwebpmux3:amd64 (1.2.2-2+b1) ... Setting up libbsd0:amd64 (0.11.6-1) ... Setting up readline-common (8.1.2-1.2) ... Setting up libgdbm6:amd64 (1.23-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.10.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.14-3) ... Setting up libwebpdemux2:amd64 (1.2.2-2+b1) ... Setting up libreadline8:amd64 (8.1.2-1.2) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-3) ... Setting up libgssapi-krb5-2:amd64 (1.20-1) ... Setting up libgdbm-compat4:amd64 (1.23-1) ... Setting up libharfbuzz0b:amd64 (2.7.4-1+b1) ... Setting up libtirpc3:amd64 (1.3.2-2) ... Setting up libperl5.34:amd64 (5.34.0-5) ... Setting up perl (5.34.0-5) ... Setting up libraqm0:amd64 (0.7.0-4) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up mailcap (3.70+nmu1) ... Setting up mime-support (3.66) ... Setting up libpython3.10-stdlib:amd64 (3.10.5-1) ... Setting up libpython3-stdlib:amd64 (3.10.5-3) ... Setting up python3.10 (3.10.5-1) ... Setting up python3 (3.10.5-3) ... Setting up python3-tz (2022.1-1) ... Setting up python3-six (1.16.0-3) ... Setting up python3-pil:amd64 (9.2.0-1+b1) ... Setting up python3-reportlab-accel:amd64 (3.6.11-1) ... Setting up python3-wrapt (1.13.3-1+b2) ... Setting up python3-reportlab (3.6.11-1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up python3-deprecated (1.2.13-2) ... Setting up python3-pkg-resources (59.6.0-1.2) ... Setting up python3-renderpm:amd64 (3.6.11-1) ... Setting up python3-numpy (1:1.21.5-1+b1) ... Setting up python3-pandas-lib:amd64 (1.3.5+dfsg-5+b1) ... Setting up python3-pandas (1.3.5+dfsg-5) ... Setting up python3-nanomath (1.2.1+ds-1) ... Processing triggers for sgml-base (1.30) ... Setting up w3c-sgml-lib (1.3-3) ... Processing triggers for libc-bin (2.33-8) ... Setting up python3-biopython (1.79+dfsg-3+b1) ... Setting up yanagiba (1.0.0-5) ... 0m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', '-y', 'install', 'yanagiba'] 0m52.2s INFO: Running scripts post_install 0m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_install_exceptions'] 0m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_install_exceptions'] 0m52.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 0m52.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 0m52.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpfar43dmp to sid 0m52.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m52.8s INFO: Running scripts pre_distupgrade 0m52.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m52.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m52.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m52.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m52.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m52.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m52.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m52.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m52.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m52.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m52.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', 'update'] 0m56.4s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [192 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9269 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6849 kB] Fetched 16.3 MB in 3s (6387 kB/s) Reading package lists... 0m56.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', 'update'] 0m56.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', '-yf', 'dist-upgrade'] 0m59.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: adduser apt bsdutils libapt-pkg6.0 libblkid1 liblcms2-2 libmount1 libsmartcols1 libsqlite3-0 libssl3 libsystemd0 libudev1 libuuid1 mount util-linux util-linux-extra 16 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 8701 kB of archives. After this operation, 81.9 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.38-5 [151 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.38-5 [164 kB] Get:3 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.38-5 [168 kB] Get:4 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.38-5 [1225 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 251.3-1 [410 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 251.3-1 [183 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.5.2 [1032 kB] Get:8 http://deb.debian.org/debian sid/main amd64 adduser all 3.123 [136 kB] Get:9 http://deb.debian.org/debian sid/main amd64 apt amd64 2.5.2 [1501 kB] Get:10 http://deb.debian.org/debian sid/main amd64 mount amd64 2.38-5 [192 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.38-5 [206 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.38-5 [223 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.38-5 [85.7 kB] Get:14 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.13.1-1 [152 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.39.2-1 [838 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.0.5-1 [2035 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8701 kB in 0s (101 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13783 files and directories currently installed.) Preparing to unpack .../libudev1_251.3-1_amd64.deb ... Unpacking libudev1:amd64 (251.3-1) over (251.2-7) ... Setting up libudev1:amd64 (251.3-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13783 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.5.2_amd64.deb ... Unpacking libapt-pkg6.0:amd64 (2.5.2) over (2.5.1) ... Setting up libapt-pkg6.0:amd64 (2.5.2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13783 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.123_all.deb ... Unpacking adduser (3.123) over (3.121) ... Setting up adduser (3.123) ... Installing new version of config file /etc/deluser.conf ... (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 ... 13749 files and directories currently installed.) Preparing to unpack .../archives/apt_2.5.2_amd64.deb ... Unpacking apt (2.5.2) over (2.5.1) ... Setting up apt (2.5.2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13749 files and directories currently installed.) Preparing to unpack .../mount_2.38-5_amd64.deb ... Unpacking mount (2.38-5) over (2.38-4) ... Preparing to unpack .../libblkid1_2.38-5_amd64.deb ... Unpacking libblkid1:amd64 (2.38-5) over (2.38-4) ... Setting up libblkid1:amd64 (2.38-5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13750 files and directories currently installed.) Preparing to unpack .../libmount1_2.38-5_amd64.deb ... Unpacking libmount1:amd64 (2.38-5) over (2.38-4) ... Setting up libmount1:amd64 (2.38-5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13751 files and directories currently installed.) Preparing to unpack .../libuuid1_2.38-5_amd64.deb ... Unpacking libuuid1:amd64 (2.38-5) over (2.38-4) ... Setting up libuuid1:amd64 (2.38-5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13751 files and directories currently installed.) Preparing to unpack .../liblcms2-2_2.13.1-1_amd64.deb ... Unpacking liblcms2-2:amd64 (2.13.1-1) over (2.12~rc1-2) ... Preparing to unpack .../libsqlite3-0_3.39.2-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.39.2-1) over (3.39.1-1) ... Preparing to unpack .../libssl3_3.0.5-1_amd64.deb ... Unpacking libssl3:amd64 (3.0.5-1) over (3.0.4-2) ... Setting up liblcms2-2:amd64 (2.13.1-1) ... Setting up libsqlite3-0:amd64 (3.39.2-1) ... Setting up libssl3:amd64 (3.0.5-1) ... Setting up mount (2.38-5) ... Processing triggers for libc-bin (2.33-8) ... Processing triggers for mailcap (3.70+nmu1) ... 0m59.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', '-yf', 'dist-upgrade'] 0m59.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m0.0s DUMP: 9b1c89650b7e04c4ce7f9082902446c9 - 1m0.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m0.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'show', '--no-all-versions', 'yanagiba'] 1m0.2s DUMP: Package: yanagiba Version: 1.0.0-5 Installed-Size: 57 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-nanomath, python3-pandas, python3:any Description-en: filter low quality Oxford Nanopore reads basecalled with Albacore Yanagiba is used to filter short or low quality Oxford Nanopore reads which have been basecalled with Albacore. It takes fastq.gz and an Albacore summary file as input. If no Albacore summary file is provided attempt to calculate mean qscore from directly from fastq file using NanoMath. Note: Calculated quality scores appear to be lower for reads called with Metrichor, you may need to lower your minqual setting in this case. Description-md5: af57b968c50c6245e1c69de3c25cfcb8 Homepage: https://github.com/Adamtaranto/Yanagiba Section: science Priority: optional Filename: pool/main/y/yanagiba/yanagiba_1.0.0-5_all.deb Size: 25592 MD5sum: 2c43135f5f6a333048dc36a7789f3170 SHA256: 21bcdc37e48753b58d93036efa4989dacd1baa6a2e59f86fac44378dc670506a 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'show', '--no-all-versions', 'yanagiba'] 1m0.2s INFO: apt-cache knows about the following packages: yanagiba 1m0.2s INFO: Running scripts pre_install 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_database-server'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_database-server'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_exceptions'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_exceptions'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_extras'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_extras'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_foreign_architecture'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_foreign_architecture'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'policy'] 1m0.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'policy'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'policy', 'yanagiba'] 1m0.4s DUMP: yanagiba: Installed: 1.0.0-5 Candidate: 1.0.0-5 Version table: *** 1.0.0-5 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'policy', 'yanagiba'] 1m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', '-y', 'install', 'yanagiba'] 1m0.7s DUMP: Reading package lists... Building dependency tree... Reading state information... yanagiba is already the newest version (1.0.0-5). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', '-y', 'install', 'yanagiba'] 1m0.7s INFO: Running scripts post_install 1m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_install_exceptions'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_install_exceptions'] 1m0.8s INFO: Running scripts post_distupgrade 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_distupgrade_exceptions'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_distupgrade_exceptions'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_distupgrade_zz_backports'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_distupgrade_zz_backports'] 1m0.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 1m1.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 1m1.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 1m2.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 1m2.0s INFO: Running scripts pre_install 1m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_database-server'] 1m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_database-server'] 1m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_exceptions'] 1m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_exceptions'] 1m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_extras'] 1m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_extras'] 1m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_foreign_architecture'] 1m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_foreign_architecture'] 1m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'policy'] 1m2.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'policy'] 1m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'policy', 'yanagiba'] 1m2.1s DUMP: yanagiba: Installed: 1.0.0-5 Candidate: 1.0.0-5 Version table: *** 1.0.0-5 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-cache', 'policy', 'yanagiba'] 1m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', '-y', 'install', 'yanagiba=1.0.0-5'] 1m2.5s DUMP: Reading package lists... Building dependency tree... Reading state information... yanagiba is already the newest version (1.0.0-5). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', '-y', 'install', 'yanagiba=1.0.0-5'] 1m2.5s INFO: Running scripts post_install 1m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_install_exceptions'] 1m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_install_exceptions'] 1m2.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 1m3.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 1m4.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', '-ac', '--ignore-obsolete'] 1m5.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', '-ac', '--ignore-obsolete'] 1m5.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m5.7s DUMP: 0.15.2 1m5.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m5.7s INFO: Running adequate version 0.15.2 now. 1m5.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'yanagiba'] 1m5.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'yanagiba'] 1m5.9s INFO: Running scripts pre_remove 1m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_remove_exceptions'] 1m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/pre_remove_exceptions'] 1m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m7.7s DUMP: install ok installed adduser adduser 3.123 install ok installed apt apt 2.5.2 install ok installed base-files base-files 12.2 install ok installed base-passwd base-passwd 3.5.52 install ok installed bash bash 5.1-6.1 install ok installed bsdutils bsdutils 1:2.38-5 install ok installed coreutils coreutils 8.32-4.1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-8 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.21.9 install ok installed e2fsprogs e2fsprogs 1.46.5-2 install ok installed findutils findutils 4.9.0-3 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-1 install ok installed gcc-12-base:amd64 gcc-12-base 12.1.0-7 install ok installed gpgv gpgv 2.2.35-3 install ok installed grep grep 3.7-1 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.64 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.2 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1+b1 install ok installed libblas3:amd64 libblas3 3.10.1-2 install ok installed libblkid1:amd64 libblkid1 2.38-5 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b4 install ok installed libbsd0:amd64 libbsd0 0.11.6-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5 install ok installed libc-bin libc-bin 2.33-8 install ok installed libc6:amd64 libc6 2.33-8 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.5-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.28-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.263 install ok installed libdeflate0:amd64 libdeflate0 1.12-1 install ok installed libexpat1:amd64 libexpat1 2.4.8-1 install ok installed libext2fs2:amd64 libext2fs2 1.46.5-2 install ok installed libffi8:amd64 libffi8 3.4.2-4 install ok installed libfreetype6:amd64 libfreetype6 2.12.1+dfsg-3 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2.1 install ok installed libgcc-s1:amd64 libgcc-s1 12.1.0-7 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-1 install ok installed libgdbm6:amd64 libgdbm6 1.23-1 install ok installed libgfortran5:amd64 libgfortran5 12.1.0-7 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.72.3-1 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1 install ok installed libgnutls30:amd64 libgnutls30 3.7.6-2 install ok installed libgomp1:amd64 libgomp1 12.1.0-7 install ok installed libgpg-error0:amd64 libgpg-error0 1.45-2 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20-1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 2.7.4-1+b1 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1 install ok installed libimagequant0:amd64 libimagequant0 2.17.0-1 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.2-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20-1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-1 install ok installed libkrb5-3:amd64 libkrb5-3 1.20-1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20-1 install ok installed liblapack3:amd64 liblapack3 3.10.1-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.13.1-1 install ok installed liblerc3:amd64 liblerc3 3.0+ds-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38-5 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-2 install ok installed libncursesw6:amd64 libncursesw6 6.3+20220423-2 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-13 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-13 install ok installed libpam-runtime libpam-runtime 1.4.0-13 install ok installed libpam0g:amd64 libpam0g 1.4.0-13 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-14 install ok installed libperl5.34:amd64 libperl5.34 5.34.0-5 install ok installed libpng16-16:amd64 libpng16-16 1.6.37-5 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.10.5-3 install ok installed libpython3.10-minimal:amd64 libpython3.10-minimal 3.10.5-1 install ok installed libpython3.10-stdlib:amd64 libpython3.10-stdlib 3.10.5-1 install ok installed libquadmath0:amd64 libquadmath0 12.1.0-7 install ok installed libraqm0:amd64 libraqm0 0.7.0-4 install ok installed libreadline8:amd64 libreadline8 8.1.2-1.2 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b1 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b1 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.39.2-1 install ok installed libss2:amd64 libss2 1.46.5-2 install ok installed libssl3:amd64 libssl3 3.0.5-1 install ok installed libstdc++6:amd64 libstdc++6 12.1.0-7 install ok installed libsystemd0:amd64 libsystemd0 251.3-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.18.0-4 install ok installed libtiff5:amd64 libtiff5 4.4.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libtirpc-common libtirpc-common 1.3.2-2 install ok installed libtirpc3:amd64 libtirpc3 1.3.2-2 install ok installed libudev1:amd64 libudev1 251.3-1 install ok installed libunistring2:amd64 libunistring2 1.0-1 install ok installed libuuid1:amd64 libuuid1 2.38-5 install ok installed libwebp7:amd64 libwebp7 1.2.2-2+b1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.2.2-2+b1 install ok installed libwebpmux3:amd64 libwebpmux3 1.2.2-2+b1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb1:amd64 libxcb1 1.14-3 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.11.1+dfsg1-2 install ok installed logsave logsave 1.46.5-2 install ok installed lsb-base lsb-base 11.2 install ok installed mailcap mailcap 3.70+nmu1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed media-types media-types 8.0.0 install ok installed mime-support mime-support 3.66 install ok installed mount mount 2.38-5 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed passwd passwd 1:4.11.1+dfsg1-2 install ok installed perl perl 5.34.0-5 install ok installed perl-base perl-base 5.34.0-5 install ok installed perl-modules-5.34 perl-modules-5.34 5.34.0-5 install ok installed python3 python3 3.10.5-3 install ok installed python3-biopython python3-biopython 1.79+dfsg-3+b1 install ok installed python3-dateutil python3-dateutil 2.8.1-6 install ok installed python3-deprecated python3-deprecated 1.2.13-2 install ok installed python3-minimal python3-minimal 3.10.5-3 install ok installed python3-nanomath python3-nanomath 1.2.1+ds-1 install ok installed python3-numpy python3-numpy 1:1.21.5-1+b1 install ok installed python3-pandas python3-pandas 1.3.5+dfsg-5 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 1.3.5+dfsg-5+b1 install ok installed python3-pil:amd64 python3-pil 9.2.0-1+b1 install ok installed python3-pkg-resources python3-pkg-resources 59.6.0-1.2 install ok installed python3-renderpm:amd64 python3-renderpm 3.6.11-1 install ok installed python3-reportlab python3-reportlab 3.6.11-1 install ok installed python3-reportlab-accel:amd64 python3-reportlab-accel 3.6.11-1 install ok installed python3-six python3-six 1.16.0-3 install ok installed python3-tz python3-tz 2022.1-1 install ok installed python3-wrapt python3-wrapt 1.13.3-1+b2 install ok installed python3.10 python3.10 3.10.5-1 install ok installed python3.10-minimal python3.10-minimal 3.10.5-1 install ok installed readline-common readline-common 8.1.2-1.2 install ok installed sed sed 4.8-1 install ok installed sgml-base sgml-base 1.30 install ok installed sysvinit-utils sysvinit-utils 3.03-1 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022a-1 install ok installed util-linux util-linux 2.38-5 install ok installed util-linux-extra util-linux-extra 2.38-5 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed xml-core xml-core 0.18+nmu1 install ok installed yanagiba yanagiba 1.0.0-5 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4 1m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', 'remove', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc3:amd64', 'libmd0:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.34:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtiff5:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.34', 'python3', 'python3-biopython', 'python3-dateutil', 'python3-deprecated', 'python3-minimal', 'python3-nanomath', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-six', 'python3-tz', 'python3-wrapt', 'python3.10', 'python3.10-minimal', 'readline-common', 'w3c-sgml-lib', 'xml-core', 'yanagiba'] 1m37.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: fonts-urw-base35 libblas3 libbrotli1 libbsd0 libdeflate0 libexpat1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblerc3 libmd0 libmpdec3 libncursesw6 libnsl2 libopenjp2-7 libperl5.34 libpng16-16 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libquadmath0 libraqm0 libreadline8 libsqlite3-0 libssl3 libtiff5 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support perl perl-modules-5.34 python3 python3-biopython python3-dateutil python3-deprecated python3-minimal python3-nanomath python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3-six python3-tz python3-wrapt python3.10 python3.10-minimal readline-common w3c-sgml-lib xml-core yanagiba 0 upgraded, 0 newly installed, 78 to remove and 0 not upgraded. After this operation, 192 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 ... 13751 files and directories currently installed.) Removing yanagiba (1.0.0-5) ... Removing python3-biopython (1.79+dfsg-3+b1) ... Removing python3-renderpm:amd64 (3.6.11-1) ... Removing fonts-urw-base35 (20200910-1) ... Removing python3-nanomath (1.2.1+ds-1) ... Removing python3-pandas (1.3.5+dfsg-5) ... Removing python3-pandas-lib:amd64 (1.3.5+dfsg-5+b1) ... Removing python3-numpy (1:1.21.5-1+b1) ... Removing liblapack3:amd64 (3.10.1-2) ... Removing libblas3:amd64 (3.10.1-2) ... Removing python3-reportlab (3.6.11-1) ... Removing python3-pil:amd64 (9.2.0-1+b1) ... Removing libraqm0:amd64 (0.7.0-4) ... Removing libharfbuzz0b:amd64 (2.7.4-1+b1) ... Removing libfreetype6:amd64 (2.12.1+dfsg-3) ... Removing libbrotli1:amd64 (1.0.9-2+b4) ... Removing libxcb1:amd64 (1.14-3) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.6-1) ... Removing libtiff5:amd64 (4.4.0-3) ... Removing libdeflate0:amd64 (1.12-1) ... Removing python3-deprecated (1.2.13-2) ... Removing python3-wrapt (1.13.3-1+b2) ... Removing python3-dateutil (2.8.1-6) ... Removing python3-six (1.16.0-3) ... Removing python3-reportlab-accel:amd64 (3.6.11-1) ... Removing python3-pkg-resources (59.6.0-1.2) ... Removing libfribidi0:amd64 (1.0.8-2.1) ... Removing mime-support (3.66) ... Removing mailcap (3.70+nmu1) ... Removing perl (5.34.0-5) ... Removing libperl5.34:amd64 (5.34.0-5) ... Removing libgdbm-compat4:amd64 (1.23-1) ... Removing libgdbm6:amd64 (1.23-1) ... Removing libgfortran5:amd64 (12.1.0-7) ... Removing libglib2.0-0:amd64 (2.72.3-1) ... Removing libimagequant0:amd64 (2.17.0-1) ... Removing libgomp1:amd64 (12.1.0-7) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.2-1) ... Removing liblcms2-2:amd64 (2.13.1-1) ... Removing liblerc3:amd64 (3.0+ds-1) ... Removing libmd0:amd64 (1.0.4-2) ... Removing libopenjp2-7:amd64 (2.5.0-1) ... Removing libpng16-16:amd64 (1.6.37-5) ... Removing libquadmath0:amd64 (12.1.0-7) ... Removing libwebpmux3:amd64 (1.2.2-2+b1) ... Removing libwebpdemux2:amd64 (1.2.2-2+b1) ... Removing libwebp7:amd64 (1.2.2-2+b1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing perl-modules-5.34 (5.34.0-5) ... Removing python3-tz (2022.1-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.18+nmu1) ... Removing python3 (3.10.5-3) ... Removing python3.10 (3.10.5-1) ... Removing python3-minimal (3.10.5-3) ... Removing python3.10-minimal (3.10.5-1) ... Removing libexpat1:amd64 (2.4.8-1) ... Removing libpython3-stdlib:amd64 (3.10.5-3) ... Removing libpython3.10-stdlib:amd64 (3.10.5-1) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-2) ... Removing libtirpc3:amd64 (1.3.2-2) ... Removing libgssapi-krb5-2:amd64 (1.20-1) ... Removing libkrb5-3:amd64 (1.20-1) ... Removing libk5crypto3:amd64 (1.20-1) ... Removing libkeyutils1:amd64 (1.6.3-1) ... Removing libkrb5support0:amd64 (1.20-1) ... Removing libmpdec3:amd64 (2.5.1-2) ... Removing libncursesw6:amd64 (6.3+20220423-2) ... Removing libpython3.10-minimal:amd64 (3.10.5-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.1.2-1.2) ... Removing libsqlite3-0:amd64 (3.39.2-1) ... Removing libssl3:amd64 (3.0.5-1) ... Removing libtirpc-common (1.3.2-2) ... Removing media-types (8.0.0) ... Removing readline-common (8.1.2-1.2) ... Processing triggers for sgml-base (1.30) ... Processing triggers for libc-bin (2.33-8) ... 1m37.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', 'remove', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc3:amd64', 'libmd0:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.34:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtiff5:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.34', 'python3', 'python3-biopython', 'python3-dateutil', 'python3-deprecated', 'python3-minimal', 'python3-nanomath', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-six', 'python3-tz', 'python3-wrapt', 'python3.10', 'python3.10-minimal', 'readline-common', 'w3c-sgml-lib', 'xml-core', 'yanagiba'] 1m37.5s INFO: Running scripts post_remove 1m37.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_remove_exceptions'] 1m37.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_remove_exceptions'] 1m37.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg', '--purge', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc3:amd64', 'libmd0:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.34:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtiff5:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.34', 'python3', 'python3-biopython', 'python3-dateutil', 'python3-deprecated', 'python3-minimal', 'python3-nanomath', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-six', 'python3-tz', 'python3-wrapt', 'python3.10', 'python3.10-minimal', 'readline-common', 'w3c-sgml-lib', 'xml-core'] 1m37.7s DUMP: (Reading database ... 6630 files and directories currently installed.) Purging configuration files for fonts-urw-base35 (20200910-1) ... dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 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 libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 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 libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.72.3-1) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20-1) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove liblerc3 which isn't installed dpkg: warning: ignoring request to remove libmd0 which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libperl5.34 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.10-minimal:amd64 (3.10.5-1) ... dpkg: warning: ignoring request to remove libpython3.10-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssl3 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed Purging configuration files for libtirpc-common (1.3.2-2) ... dpkg: warning: ignoring request to remove libtirpc3 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed Purging configuration files for mailcap (3.70+nmu1) ... Purging configuration files for media-types (8.0.0) ... dpkg: warning: ignoring request to remove mime-support which isn't installed Purging configuration files for perl (5.34.0-5) ... dpkg: warning: ignoring request to remove perl-modules-5.34 which isn't installed Purging configuration files for python3 (3.10.5-3) ... dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-deprecated which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-nanomath which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pandas which isn't installed dpkg: warning: ignoring request to remove python3-pandas-lib which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-renderpm which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-reportlab-accel which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-wrapt which isn't installed dpkg: warning: ignoring request to remove python3.10 which isn't installed Purging configuration files for python3.10-minimal (3.10.5-1) ... Purging configuration files for readline-common (8.1.2-1.2) ... Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for xml-core (0.18+nmu1) ... dpkg: warning: while removing xml-core, directory '/etc/sgml' not empty so not removed Processing triggers for sgml-base (1.30) ... 1m37.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg', '--purge', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc3:amd64', 'libmd0:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.34:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtiff5:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.34', 'python3', 'python3-biopython', 'python3-dateutil', 'python3-deprecated', 'python3-minimal', 'python3-nanomath', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-six', 'python3-tz', 'python3-wrapt', 'python3.10', 'python3.10-minimal', 'readline-common', 'w3c-sgml-lib', 'xml-core'] 1m37.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg', '--purge', 'yanagiba'] 1m37.7s DUMP: dpkg: warning: ignoring request to remove yanagiba which isn't installed 1m37.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg', '--purge', 'yanagiba'] 1m37.7s INFO: Running scripts post_purge 1m37.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_purge_exceptions'] 1m37.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_purge_exceptions'] 1m37.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg', '--purge', '--pending'] 1m37.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg', '--purge', '--pending'] 1m37.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg', '--remove', '--pending'] 1m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg', '--remove', '--pending'] 1m37.8s INFO: Running scripts post_test 1m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_test_exceptions'] 1m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'tmp/scripts/post_test_exceptions'] 1m37.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 1m38.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 1m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg-divert', '--list'] 1m38.3s 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 1m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'dpkg-divert', '--list'] 1m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', 'clean'] 1m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfar43dmp', 'apt-get', 'clean'] 1m38.3s DEBUG: Recording chroot state 1m38.7s INFO: Warning: Package purging left files on system: /var/lib/sgml-base/supercatalog.old not owned 1m39.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/shm'] 1m39.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/shm'] 1m39.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/console'] 1m39.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/console'] 1m39.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/ptmx'] 1m39.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/ptmx'] 1m39.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/pts'] 1m39.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/dev/pts'] 1m39.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/proc'] 1m39.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfar43dmp/proc'] 1m39.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 1m39.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfar43dmp'] 1m39.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpfar43dmp 1m39.4s INFO: PASS: Upgrading between Debian distributions. 1m39.4s INFO: PASS: All tests. 1m39.4s INFO: piuparts run ends. ret=0 End: 2022-07-27 01:20:21 GMT