Start: 2023-09-02 05:00:56 GMT Package: optimir Version: 1.2-1 Installed-Size: 7403 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-pysam, python3:any, bowtie2, cutadapt, samtools Recommends: r-cran-gridextra, r-cran-ggplot2 Description: Integrating genetic variations in miRNA alignment Homepage: https://github.com/FlorianThibord/OptimiR Description-md5: 759e6ff9eaeea6644852b82160c2085c Section: science Priority: optional Filename: pool/main/o/optimir/optimir_1.2-1_all.deb Size: 1027180 MD5sum: b6ec3be94a80aa6ebd4e83f826dd2a20 SHA256: 5e496b8ffd436d79108fee140254044e7141fd44aa2776058a08233fd5b3a599 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 --merged-usr -i /usr/lib32/ -i /usr/libx32/ --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt optimir=1.2-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.8~202306121314~1.1.7-9-g57dfbde6 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --merged-usr -i /usr/lib32/ -i /usr/libx32/ --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt optimir=1.2-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-25-amd64 #1 SMP Debian 5.10.191-1 (2023-08-16) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpvjpedjdj 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpvjpedjdj 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m2.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m2.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/proc'] 0m2.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/proc'] 0m2.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/pts'] 0m2.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/pts'] 0m2.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/ptmx'] 0m2.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/ptmx'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/console'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/console'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/shm'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/shm'] 0m2.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m2.3s DEBUG: Created policy-rc.d and chmodded it. 0m2.3s DEBUG: Created resolv.conf. 0m2.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpvjpedjdj/tmp/scripts/ 0m2.3s INFO: Running scripts post_chroot_unpack 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-get', 'update'] 0m7.5s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [210 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9568 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7010 kB] Fetched 16.8 MB in 4s (3740 kB/s) Reading package lists... 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-get', 'update'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-get', '-yf', 'dist-upgrade'] 0m8.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: liblzma5 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 229 kB of archives. After this operation, 26.6 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.4.4-0.1 [229 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 229 kB in 0s (5791 kB/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 ... 5196 files and directories currently installed.) Preparing to unpack .../liblzma5_5.4.4-0.1_amd64.deb ... Unpacking liblzma5:amd64 (5.4.4-0.1) over (5.4.1-0.2) ... Setting up liblzma5:amd64 (5.4.4-0.1) ... Processing triggers for libc-bin (2.37-7) ... 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-get', '-yf', 'dist-upgrade'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.3s DUMP: ba49e40efa379e5d5dc2883739ed97a1 - 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.3s INFO: Running scripts post_setup 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_setup_dummy_users'] 0m10.6s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_setup_dummy_users'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_setup_forbid_home'] 0m10.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_setup_forbid_home'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.6s 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' 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_setup_minimize'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_setup_minimize'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_setup_zz_backports'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_setup_zz_backports'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-get', 'clean'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-get', 'clean'] 0m10.7s DEBUG: Recording chroot state 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m11.5s DUMP: install ok installed apt apt 2.7.3 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b4 install ok installed bsdutils bsdutils 1:2.39.2-1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.11 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.22.0 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-2 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.11-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.3 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.1.1-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.1-1 install ok installed libblkid1:amd64 libblkid1 2.39.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.37-7 install ok installed libc6:amd64 libc6 2.37-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-2 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 13.2.0-2 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.2-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.1-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-2 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.4-0.1 install ok installed libmd0:amd64 libmd0 1.1.0-1 install ok installed libmount1:amd64 libmount1 2.39.2-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.0-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-7 install ok installed libpam-runtime libpam-runtime 1.5.2-7 install ok installed libpam0g:amd64 libpam0g 1.5.2-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.5-1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1 install ok installed libsepol2:amd64 libsepol2 3.5-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.2-1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-2 install ok installed libsystemd0:amd64 libsystemd0 254.1-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.4+20230625-2 install ok installed libudev1:amd64 libudev1 254.1-3 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.39.2-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-1 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20230808-1 install ok installed mount mount 2.39.2-1 install ok installed ncurses-base ncurses-base 6.4+20230625-2 install ok installed ncurses-bin ncurses-bin 6.4+20230625-2 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-8 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.07-1 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-10 install ok installed usr-is-merged usr-is-merged 37 install ok installed util-linux util-linux 2.39.2-1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-3 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg-divert', '--list'] 0m11.5s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg-divert', '--list'] 0m11.5s INFO: Running scripts is_testable 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/is_testable_uninstallable'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/is_testable_uninstallable'] 0m11.6s INFO: apt-cache does not know about any of the requested packages 0m11.6s INFO: Running scripts pre_test 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_test_exceptions'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_test_exceptions'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_test_root_password'] 0m11.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_test_root_password'] 0m11.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj'] 0m12.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj'] 0m12.9s DEBUG: No broken symlinks as far as we can find. 0m12.9s INFO: Running scripts pre_install 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_install_database-server'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_install_database-server'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_install_exceptions'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_install_exceptions'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_install_extras'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_install_extras'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj'] 0m13.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj'] 0m14.3s DEBUG: No broken symlinks as far as we can find. 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-cache', 'policy'] 0m15.5s 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: 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-cache', 'policy'] 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-cache', 'policy', 'optimir'] 0m15.5s DUMP: optimir: Installed: (none) Candidate: 1.2-1 Version table: 1.2-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-cache', 'policy', 'optimir'] 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-get', '-y', 'install', 'optimir=1.2-1'] 1m27.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: bowtie2 cutadapt cython3 fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-noto-core fonts-noto-mono fonts-urw-base35 libblas3 libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libopenjp2-7 libperl5.36 libpixman-1-0 libpng16-16 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl3 libtiff6 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1 mailcap media-types mime-support perl perl-modules-5.36 pigz python3 python3-biopython python3-cairo python3-cutadapt python3-dnaio python3-freetype python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pysam python3-reportlab python3-rlpycairo python3-xopen python3.11 python3.11-minimal readline-common samtools sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core Suggested packages: bowtie2-examples cython-doc fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gdbm-l10n low-memory-monitor 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 muscle3 phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 python3-scipy raxml t-coffee wise gcc gfortran python3-dev python3-pytest python-pil-doc python3-setuptools pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python3.11-venv python3.11-doc binutils binfmt-support readline-doc cwltool sgml-base-doc debhelper Recommended packages: python3-dev gcc ca-certificates libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils r-cran-gridextra r-cran-ggplot2 netbase python-biopython-doc ncbi-blast+ python3-olefile The following NEW packages will be installed: bowtie2 cutadapt cython3 fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-noto-core fonts-noto-mono fonts-urw-base35 libblas3 libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libopenjp2-7 libperl5.36 libpixman-1-0 libpng16-16 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl3 libtiff6 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1 mailcap media-types mime-support optimir perl perl-modules-5.36 pigz python3 python3-biopython python3-cairo python3-cutadapt python3-dnaio python3-freetype python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pysam python3-reportlab python3-rlpycairo python3-xopen python3.11 python3.11-minimal readline-common samtools sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 108 newly installed, 0 to remove and 0 not upgraded. Need to get 75.8 MB of archives. After this operation, 296 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 perl-modules-5.36 all 5.36.0-8 [2816 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libperl5.36 amd64 5.36.0-8 [4199 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl amd64 5.36.0-8 [239 kB] Get:6 http://deb.debian.org/debian sid/main amd64 pigz amd64 2.8-1 [62.7 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.0.10-1 [2014 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.5-3 [815 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.5.0-2 [99.0 kB] Get:10 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.5-3 [2034 kB] Get:11 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.4-5+b1 [26.5 kB] Get:12 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:13 http://deb.debian.org/debian sid/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get:14 http://deb.debian.org/debian sid/main amd64 mime-support all 3.66 [10.9 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20230625-2 [134 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-3 [32.3 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-3 [79.1 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:19 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-3 [333 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-3 [134 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:24 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.42.0-1 [859 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.5-3 [1802 kB] Get:28 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.5-3 [582 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.4-5+b1 [9492 B] Get:30 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.4-5+b1 [26.5 kB] Get:31 http://deb.debian.org/debian sid/main amd64 sgml-base all 1.31 [15.4 kB] Get:32 http://deb.debian.org/debian sid/main amd64 bowtie2 amd64 2.5.0-3+b3 [1434 kB] Get:33 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 68.1.2-1 [241 kB] Get:34 http://deb.debian.org/debian sid/main amd64 python3-xopen all 1.7.0-2 [16.9 kB] Get:35 http://deb.debian.org/debian sid/main amd64 python3-dnaio amd64 0.10.0-1+b1 [58.4 kB] Get:36 http://deb.debian.org/debian sid/main amd64 python3-cutadapt amd64 4.2-1+b1 [222 kB] Get:37 http://deb.debian.org/debian sid/main amd64 cutadapt all 4.2-1 [23.5 kB] Get:38 http://deb.debian.org/debian sid/main amd64 cython3 amd64 0.29.36-1 [1298 kB] Get:39 http://deb.debian.org/debian sid/main amd64 fonts-noto-mono all 20201225-2 [398 kB] Get:40 http://deb.debian.org/debian sid/main amd64 fonts-noto-core all 20201225-2 [12.2 MB] Get:41 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:42 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libpng16-16 amd64 1.6.40-1 [275 kB] Get:46 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[9852 B] Get:102 http://deb.debian.org/debian sid/main amd64 python3-reportlab all 4.0.4-11 [668 kB] Get:103 http://deb.debian.org/debian sid/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:104 http://deb.debian.org/debian sid/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:105 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.81+dfsg-1 [1597 kB] Get:106 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.21.0+ds-1 [3110 kB] Get:107 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.17-1 [628 kB] Get:108 http://deb.debian.org/debian sid/main amd64 optimir all 1.2-1 [1027 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 75.8 MB in 1s (126 MB/s) Selecting previously unselected package perl-modules-5.36. (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 ... 5198 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.36_5.36.0-8_all.deb ... Unpacking perl-modules-5.36 (5.36.0-8) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.23-3_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-3) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.23-3_amd64.deb ... 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Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up fonts-noto-mono (20201225-2) ... Setting up libglib2.0-0:amd64 (2.77.2-1) ... No schema files found: doing nothing. Setting up libtirpc-common (1.3.3+ds-1) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libsqlite3-0:amd64 (3.42.0-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libnghttp2-14:amd64 (1.55.1-1) ... Setting up libdeflate0:amd64 (1.18-1) ... Setting up libgomp1:amd64 (13.2.0-2) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libkrb5support0:amd64 (1.20.1-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-3) ... Setting up libfontenc1:amd64 (1:1.1.4-1) ... Setting up perl-modules-5.36 (5.36.0-8) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.6-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.4+20230625-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.13-3) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16:amd64 (1.6.40-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libncursesw6:amd64 (6.4+20230625-2) ... Setting up libk5crypto3:amd64 (1.20.1-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-3) ... Setting up libgfortran5:amd64 (13.2.0-2) ... Setting up libwebp7:amd64 (1.2.4-0.2) ... Setting up fonts-dejavu-extra (2.37-8) ... Setting up pigz (2.8-1) ... Setting up libtiff6:amd64 (4.5.1+git230720-1) ... Setting up libopenjp2-7:amd64 (2.5.0-2) ... Setting up libssh2-1:amd64 (1.11.0-2) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.20.1-3) ... Setting up libwebpmux3:amd64 (1.2.4-0.2) ... Setting up libbsd0:amd64 (0.11.7-4) ... Setting up readline-common (8.2-1.3) ... Setting up fonts-noto-core (20201225-2) ... Setting up libgdbm6:amd64 (1.23-3) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.2-4) ... Setting up libwebpdemux2:amd64 (1.2.4-0.2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... 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Setting up libpython3-stdlib:amd64 (3.11.4-5+b1) ... Setting up python3.11 (3.11.5-3) ... Setting up python3 (3.11.4-5+b1) ... Setting up python3-freetype (2.4.0-1) ... Setting up bowtie2 (2.5.0-3+b3) ... Setting up python3-pil:amd64 (10.0.0-1) ... Setting up cython3 (0.29.36-1) ... Setting up python3-pkg-resources (68.1.2-1) ... Setting up python3-pysam (0.21.0+ds-1) ... Setting up python3-cairo:amd64 (1.24.0-1.1) ... Setting up python3-xopen (1.7.0-2) ... Setting up python3-rlpycairo (0.3.0-2) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-reportlab (4.0.4-11) ... Setting up python3-dnaio (0.10.0-1+b1) ... Setting up python3-cutadapt (4.2-1+b1) ... Setting up cutadapt (4.2-1) ... Processing triggers for libc-bin (2.37-7) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.81+dfsg-1) ... Setting up optimir (1.2-1) ... /usr/lib/python3/dist-packages/optimir/libs/get_counts.py:453: SyntaxWarning: "is" with a literal. Did you mean "=="? if prefix is '': 1m27.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-get', '-y', 'install', 'optimir=1.2-1'] 1m27.5s INFO: Running scripts post_install 1m27.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_install_exceptions'] 1m27.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_install_exceptions'] 1m27.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj'] 1m28.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj'] 1m31.1s DEBUG: No broken symlinks as far as we can find. 1m31.1s INFO: /bin converted to /usr/bin by /usr merge 1m31.1s INFO: /lib converted to /usr/lib by /usr merge 1m31.1s INFO: /lib/init converted to /usr/lib/init by /usr merge 1m31.1s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 1m31.1s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 1m31.1s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 1m31.1s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 1m31.1s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 1m31.1s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 1m31.1s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 1m31.1s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 1m31.1s INFO: /lib64 converted to /usr/lib64 by /usr merge 1m31.1s INFO: /sbin converted to /usr/sbin by /usr merge 1m32.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', '-ac', '--ignore-obsolete'] 1m34.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', '-ac', '--ignore-obsolete'] 1m34.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m34.0s DUMP: 0.15.6 1m34.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m34.0s INFO: Running adequate version 0.15.6 now. 1m34.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'optimir'] 1m34.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'optimir'] 1m34.1s INFO: Running scripts pre_remove 1m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m37.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m37.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_remove_exceptions'] 1m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/pre_remove_exceptions'] 1m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m38.0s DUMP: install ok installed apt apt 2.7.3 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b4 install ok installed bowtie2 bowtie2 2.5.0-3+b3 install ok installed bsdutils bsdutils 1:2.39.2-1 install ok installed coreutils coreutils 9.1-1 install ok installed cutadapt cutadapt 4.2-1 install ok installed cython3 cython3 0.29.36-1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.11 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.22.0 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig-config fontconfig-config 2.14.2-4 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-extra fonts-dejavu-extra 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-noto-core fonts-noto-core 20201225-2 install ok installed fonts-noto-mono fonts-noto-mono 20201225-2 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-7 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-2 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.11-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.3 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.1.1-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.1-1 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.39.2-1 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b6 install ok installed libbsd0:amd64 libbsd0 0.11.7-4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.37-7 install ok installed libc6:amd64 libc6 2.37-7 install ok installed libcairo2:amd64 libcairo2 1.16.0-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-2 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 8.2.1-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-2 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libdeflate0:amd64 libdeflate0 1.18-1 install ok installed libexpat1:amd64 libexpat1 2.5.0-2 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.14.2-4 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.4-1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3 install ok installed libgcc-s1:amd64 libgcc-s1 13.2.0-2 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.2-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgfortran5:amd64 libgfortran5 13.2.0-2 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.77.2-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.1-4 install ok installed libgomp1:amd64 libgomp1 13.2.0-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-2 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.0.1-1 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libhts3:amd64 libhts3 1.17+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.5.1-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1 install ok installed libimagequant0:amd64 libimagequant0 2.17.0-1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-3 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.4-0.1 install ok installed libmd0:amd64 libmd0 1.1.0-1 install ok installed libmount1:amd64 libmount1 2.39.2-1 install ok installed libncurses6:amd64 libncurses6 6.4+20230625-2 install ok installed libncursesw6:amd64 libncursesw6 6.4+20230625-2 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.55.1-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.0-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-7 install ok installed libpam-runtime libpam-runtime 1.5.2-7 install ok installed libpam0g:amd64 libpam0g 1.5.2-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-8 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.40-1 install ok installed libpsl5:amd64 libpsl5 0.21.2-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.4-5+b1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.5-3 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.5-3 install ok installed libraqm0:amd64 libraqm0 0.10.1-1 install ok installed libreadline8:amd64 libreadline8 8.2-1.3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-3 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-3 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.5-1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1 install ok installed libsepol2:amd64 libsepol2 3.5-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.2-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.42.0-1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssh2-1:amd64 libssh2-1 1.11.0-2 install ok installed libssl3:amd64 libssl3 3.0.10-1 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-2 install ok installed libsystemd0:amd64 libsystemd0 254.1-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-1 install ok installed libtinfo6:amd64 libtinfo6 6.4+20230625-2 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libudev1:amd64 libudev1 254.1-3 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.39.2-1 install ok installed libwebp7:amd64 libwebp7 1.2.4-0.2 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.2.4-0.2 install ok installed libwebpmux3:amd64 libwebpmux3 1.2.4-0.2 install ok installed libx11-6:amd64 libx11-6 2:1.8.6-1 install ok installed libx11-data libx11-data 2:1.8.6-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-1 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mailcap mailcap 3.70+nmu1 install ok installed mawk mawk 1.3.4.20230808-1 install ok installed media-types media-types 10.1.0 install ok installed mime-support mime-support 3.66 install ok installed mount mount 2.39.2-1 install ok installed ncurses-base ncurses-base 6.4+20230625-2 install ok installed ncurses-bin ncurses-bin 6.4+20230625-2 install ok installed optimir optimir 1.2-1 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl perl 5.36.0-8 install ok installed perl-base perl-base 5.36.0-8 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-8 install ok installed pigz pigz 2.8-1 install ok installed python3 python3 3.11.4-5+b1 install ok installed python3-biopython python3-biopython 1.81+dfsg-1 install ok installed python3-cairo:amd64 python3-cairo 1.24.0-1.1 install ok installed python3-cutadapt python3-cutadapt 4.2-1+b1 install ok installed python3-dnaio python3-dnaio 0.10.0-1+b1 install ok installed python3-freetype python3-freetype 2.4.0-1 install ok installed python3-minimal python3-minimal 3.11.4-5+b1 install ok installed python3-numpy python3-numpy 1:1.24.2-1 install ok installed python3-pil:amd64 python3-pil 10.0.0-1 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-1 install ok installed python3-pysam python3-pysam 0.21.0+ds-1 install ok installed python3-reportlab python3-reportlab 4.0.4-11 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-2 install ok installed python3-xopen python3-xopen 1.7.0-2 install ok installed python3.11 python3.11 3.11.5-3 install ok installed python3.11-minimal python3.11-minimal 3.11.5-3 install ok installed readline-common readline-common 8.2-1.3 install ok installed samtools samtools 1.17-1 install ok installed sed sed 4.9-1 install ok installed sgml-base sgml-base 1.31 install ok installed sysvinit-utils sysvinit-utils 3.07-1 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-10 install ok installed usr-is-merged usr-is-merged 37 install ok installed util-linux util-linux 2.39.2-1 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+23 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+6 install ok installed xml-core xml-core 0.18+nmu1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-3 1m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-get', 'remove', 'bowtie2', 'cutadapt', 'cython3', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-noto-core', 'fonts-noto-mono', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1: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', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxrender1:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.36', 'pigz', 'python3', 'python3-biopython', 'python3-cairo:amd64', 'python3-cutadapt', 'python3-dnaio', 'python3-freetype', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-xopen', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'optimir'] 2m29.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bowtie2 cutadapt cython3 fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-noto-core fonts-noto-mono fonts-urw-base35 libblas3 libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libopenjp2-7 libperl5.36 libpixman-1-0 libpng16-16 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl3 libtiff6 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1 mailcap media-types mime-support optimir perl perl-modules-5.36 pigz python3 python3-biopython python3-cairo python3-cutadapt python3-dnaio python3-freetype python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pysam python3-reportlab python3-rlpycairo python3-xopen python3.11 python3.11-minimal readline-common samtools sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 108 to remove and 0 not upgraded. After this operation, 296 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 ... 13068 files and directories currently installed.) Removing optimir (1.2-1) ... Removing bowtie2 (2.5.0-3+b3) ... Removing cutadapt (4.2-1) ... Removing python3-pysam (0.21.0+ds-1) ... Removing cython3 (0.29.36-1) ... Removing python3-biopython (1.81+dfsg-1) ... Removing python3-reportlab (4.0.4-11) ... Removing python3-rlpycairo (0.3.0-2) ... Removing python3-cairo:amd64 (1.24.0-1.1) ... Removing libcairo2:amd64 (1.16.0-7) ... Removing libfontconfig1:amd64 (2.14.2-4) ... Removing fontconfig-config (2.14.2-4) ... Removing fonts-dejavu-extra (2.37-8) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-noto-core (20201225-2) ... Removing fonts-noto-mono (20201225-2) ... Removing fonts-urw-base35 (20200910-7) ... Removing python3-numpy (1:1.24.2-1) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing xfonts-utils (1:7.7+6) ... Removing python3-pil:amd64 (10.0.0-1) ... Removing libraqm0:amd64 (0.10.1-1) ... Removing samtools (1.17-1) ... Removing libhts3:amd64 (1.17+ds-1) ... Removing libcurl3-gnutls:amd64 (8.2.1-2) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing libtiff6:amd64 (4.5.1+git230720-1) ... Removing libdeflate0:amd64 (1.18-1) ... Removing python3-cutadapt (4.2-1+b1) ... Removing python3-dnaio (0.10.0-1+b1) ... Removing python3-xopen (1.7.0-2) ... Removing python3-pkg-resources (68.1.2-1) ... Removing python3-freetype (2.4.0-1) ... Removing python3 (3.11.4-5+b1) ... Removing python3.11 (3.11.5-3) ... Removing python3-minimal (3.11.4-5+b1) ... Removing python3.11-minimal (3.11.5-3) ... Removing libexpat1:amd64 (2.5.0-2) ... Removing libfontenc1:amd64 (1:1.1.4-1) ... Removing libfribidi0:amd64 (1.0.13-3) ... Removing libpython3-stdlib:amd64 (3.11.4-5+b1) ... Removing libpython3.11-stdlib:amd64 (3.11.5-3) ... find: '/usr/lib/python3': No such file or directory Removing mime-support (3.66) ... Removing mailcap (3.70+nmu1) ... Removing perl (5.36.0-8) ... Removing libperl5.36:amd64 (5.36.0-8) ... Removing libgdbm-compat4:amd64 (1.23-3) ... Removing libgdbm6:amd64 (1.23-3) ... Removing libgfortran5:amd64 (13.2.0-2) ... Removing libharfbuzz0b:amd64 (8.0.1-1) ... Removing libglib2.0-0:amd64 (2.77.2-1) ... Removing libimagequant0:amd64 (2.17.0-1) ... Removing libgomp1:amd64 (13.2.0-2) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libnsl2:amd64 (1.3.0-2) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-3) ... Removing libhtscodecs2:amd64 (1.5.1-1) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2) ... Removing libkrb5-3:amd64 (1.20.1-3) ... Removing libk5crypto3:amd64 (1.20.1-3) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-3) ... Removing liblcms2-2:amd64 (2.14-2) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Removing liblerc4:amd64 (4.0.0+ds-2) ... Removing libncurses6:amd64 (6.4+20230625-2) ... Removing libncursesw6:amd64 (6.4+20230625-2) ... Removing libnghttp2-14:amd64 (1.55.1-1) ... Removing libopenjp2-7:amd64 (2.5.0-2) ... Removing libpixman-1-0:amd64 (0.42.2-1) ... Removing libpsl5:amd64 (0.21.2-1) ... Removing libpython3.11-minimal:amd64 (3.11.5-3) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.2-1.3) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-3) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-3) ... Removing libsqlite3-0:amd64 (3.42.0-1) ... Removing libssh2-1:amd64 (1.11.0-2) ... Removing libssl3:amd64 (3.0.10-1) ... Removing libtirpc-common (1.3.3+ds-1) ... Removing libwebpmux3:amd64 (1.2.4-0.2) ... Removing libwebpdemux2:amd64 (1.2.4-0.2) ... Removing libwebp7:amd64 (1.2.4-0.2) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing media-types (10.1.0) ... Removing perl-modules-5.36 (5.36.0-8) ... Removing pigz (2.8-1) ... Removing readline-common (8.2-1.3) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.18+nmu1) ... Removing sgml-base (1.31) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libfreetype6:amd64 (2.13.2+dfsg-1) ... Removing libbrotli1:amd64 (1.0.9-2+b6) ... Removing libx11-6:amd64 (2:1.8.6-1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.7-4) ... Removing libpng16-16:amd64 (1.6.40-1) ... Removing libx11-data (2:1.8.6-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Processing triggers for libc-bin (2.37-7) ... 2m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-get', 'remove', 'bowtie2', 'cutadapt', 'cython3', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-noto-core', 'fonts-noto-mono', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1: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', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxrender1:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.36', 'pigz', 'python3', 'python3-biopython', 'python3-cairo:amd64', 'python3-cutadapt', 'python3-dnaio', 'python3-freetype', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-xopen', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'optimir'] 2m29.8s INFO: Running scripts post_remove 2m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_remove_exceptions'] 2m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_remove_exceptions'] 2m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg', '--purge', 'bowtie2', 'cutadapt', 'cython3', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-noto-core', 'fonts-noto-mono', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1: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', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxrender1:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.36', 'pigz', 'python3', 'python3-biopython', 'python3-cairo:amd64', 'python3-cutadapt', 'python3-dnaio', 'python3-freetype', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-xopen', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 2m30.3s DUMP: dpkg: warning: ignoring request to remove bowtie2 which isn't installed dpkg: warning: ignoring request to remove cutadapt which isn't installed dpkg: warning: ignoring request to remove cython3 which isn't installed (Reading database ... 5258 files and directories currently installed.) Purging configuration files for fontconfig-config (2.14.2-4) ... Purging configuration files for fonts-dejavu-core (2.37-8) ... dpkg: warning: ignoring request to remove fonts-dejavu-extra which isn't installed Purging configuration files for fonts-dejavu-mono (2.37-8) ... Purging configuration files for fonts-noto-core (20201225-2) ... Purging configuration files for fonts-noto-mono (20201225-2) ... Purging configuration files for fonts-urw-base35 (20200910-7) ... 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 libcairo2 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 libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 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 (2.77.2-1) ... 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 (1.20.1-3) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 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 libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 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 libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libperl5.36 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.5-3) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib 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 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 libssl3 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.3+ds-1) ... 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 libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed Purging configuration files for mailcap (3.70+nmu1) ... Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove mime-support which isn't installed Purging configuration files for perl (5.36.0-8) ... dpkg: warning: ignoring request to remove perl-modules-5.36 which isn't installed dpkg: warning: ignoring request to remove pigz which isn't installed Purging configuration files for python3 (3.11.4-5+b1) ... dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-cutadapt which isn't installed dpkg: warning: ignoring request to remove python3-dnaio which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-xopen which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.5-3) ... Purging configuration files for readline-common (8.2-1.3) ... dpkg: warning: ignoring request to remove samtools which isn't installed Purging configuration files for sgml-base (1.31) ... Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+6) ... Purging configuration files for xml-core (0.18+nmu1) ... 2m30.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg', '--purge', 'bowtie2', 'cutadapt', 'cython3', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-noto-core', 'fonts-noto-mono', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1: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', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxrender1:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.36', 'pigz', 'python3', 'python3-biopython', 'python3-cairo:amd64', 'python3-cutadapt', 'python3-dnaio', 'python3-freetype', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-xopen', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 2m30.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg', '--purge', 'optimir'] 2m30.3s DUMP: dpkg: warning: ignoring request to remove optimir which isn't installed 2m30.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg', '--purge', 'optimir'] 2m30.3s INFO: Running scripts post_purge 2m30.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_purge_exceptions'] 2m30.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_purge_exceptions'] 2m30.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg', '--purge', '--pending'] 2m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg', '--purge', '--pending'] 2m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg', '--remove', '--pending'] 2m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg', '--remove', '--pending'] 2m30.4s INFO: Running scripts post_test 2m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_test_exceptions'] 2m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'tmp/scripts/post_test_exceptions'] 2m30.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj'] 2m30.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj'] 2m31.7s DEBUG: No broken symlinks as far as we can find. 2m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg-divert', '--list'] 2m31.7s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 2m31.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'dpkg-divert', '--list'] 2m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-get', 'clean'] 2m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj', 'apt-get', 'clean'] 2m31.8s DEBUG: Recording chroot state 2m32.8s INFO: PASS: Installation and purging test. 2m33.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/shm'] 2m33.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/shm'] 2m33.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/console'] 2m33.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/console'] 2m33.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/ptmx'] 2m33.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/ptmx'] 2m33.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/pts'] 2m33.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/dev/pts'] 2m33.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/proc'] 2m33.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj/proc'] 2m33.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj'] 2m33.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpvjpedjdj'] 2m33.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpvjpedjdj 2m33.7s INFO: PASS: All tests. 2m33.7s INFO: piuparts run ends. ret=0 End: 2023-09-02 05:03:30 GMT