Start: 2020-12-06 22:16:13 GMT Package: optimir Version: 1.0-3 Installed-Size: 7404 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_1.0-3_all.deb Size: 1028064 MD5sum: 4ff00e8c13b9c17e3be3b6c1413490bc SHA256: b6550b1083ea4758e73d1d2aec38b609e59d159ff7f9b414524f4f6303a21c94 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --install-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid_amd64.tar.gz -d sid --no-upgrade-test --apt optimir=1.0-3 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.2~202004292038~1.1.1-19-g418151e2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --install-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid_amd64.tar.gz -d sid --no-upgrade-test --apt optimir=1.0-3 0m0.0s INFO: Running on: Linux piu-slave-conova-01 4.19.0-13-amd64 #1 SMP Debian 4.19.160-2 (2020-11-28) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpiub296s1 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpiub296s1 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpiub296s1', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid_amd64.tar.gz'] 0m1.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpiub296s1', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid_amd64.tar.gz'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpiub296s1/proc'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpiub296s1/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/tmpiub296s1/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/tmpiub296s1/dev/pts'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/ptmx'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/ptmx'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/console'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/console'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/shm'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/shm'] 0m1.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m1.5s DEBUG: Created policy-rc.d and chmodded it. 0m1.5s DEBUG: Created resolv.conf. 0m1.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpiub296s1/tmp/scripts/ 0m1.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts-leftovers to /srv/piuparts.debian.org/tmp/tmpiub296s1/tmp/scripts/ 0m1.5s INFO: Running scripts post_chroot_unpack 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', 'update'] 0m5.5s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [153 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [8541 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6425 kB] Fetched 15.1 MB in 3s (5094 kB/s) Reading package lists... 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', 'update'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', '-yf', 'dist-upgrade'] 0m5.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', '-yf', 'dist-upgrade'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.6s DUMP: c2c6d701d80bbca8f0e270d8929b5737 - 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.6s INFO: Running scripts post_setup 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_dummy_users'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_dummy_users'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_fake-essential'] 0m9.4s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... init-system-helpers is already the newest version (1.59). The following additional packages will be installed: sensible-utils ucf Suggested packages: dbconfig-mysql | dbconfig-pgsql | dbconfig-sqlite3 | dbconfig-no-thanks The following NEW packages will be installed: dbconfig-common sensible-utils ucf 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 698 kB of archives. After this operation, 1858 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:2 http://deb.debian.org/debian sid/main amd64 ucf all 3.0043 [74.0 kB] Get:3 http://deb.debian.org/debian sid/main amd64 dbconfig-common all 2.0.17 [608 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 698 kB in 0s (7548 kB/s) Selecting previously unselected package sensible-utils. (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 ... 6604 files and directories currently installed.) Preparing to unpack .../sensible-utils_0.0.12+nmu1_all.deb ... Unpacking sensible-utils (0.0.12+nmu1) ... Selecting previously unselected package ucf. Preparing to unpack .../archives/ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package dbconfig-common. Preparing to unpack .../dbconfig-common_2.0.17_all.deb ... Unpacking dbconfig-common (2.0.17) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up ucf (3.0043) ... Setting up dbconfig-common (2.0.17) ... Creating config file /etc/dbconfig-common/config with new version 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_fake-essential'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_forbid_home'] 0m9.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_forbid_home'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.5s 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' 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_minimize'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_minimize'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_zz_backports'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_setup_zz_backports'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', 'clean'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', 'clean'] 0m9.5s DEBUG: Recording chroot state 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.9s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.1.12 install ok installed base-files base-files 11 install ok installed base-passwd base-passwd 3.5.48 install ok installed bash bash 5.1~rc3-1 install ok installed bsdutils bsdutils 1:2.36.1-2 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-2 install ok installed dbconfig-common dbconfig-common 2.0.17 install ok installed debconf debconf 1.5.74 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.20.5 install ok installed e2fsprogs e2fsprogs 1.45.6-1 install ok installed findutils findutils 4.7.0+git20201010-2 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.0-23 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-19 install ok installed gpgv gpgv 2.2.20-1 install ok installed grep grep 3.6-1 install ok installed gzip gzip 1.10-2 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.59 install ok installed libacl1:amd64 libacl1 2.2.53-8 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.1.12 install ok installed libattr1:amd64 libattr1 1:2.4.48-5 install ok installed libaudit-common libaudit-common 1:2.8.5-3.1 install ok installed libaudit1:amd64 libaudit1 1:2.8.5-3.1 install ok installed libblkid1:amd64 libblkid1 2.36.1-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-5 install ok installed libc6:amd64 libc6 2.31-5 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.45.6-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.17-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.255 install ok installed libext2fs2:amd64 libext2fs2 1.45.6-1 install ok installed libffi7:amd64 libffi7 3.3-5 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.0-23 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1 install ok installed libgnutls30:amd64 libgnutls30 3.6.15-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libhogweed6:amd64 libhogweed6 3.6-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-4 install ok installed liblz4-1:amd64 liblz4-1 1.9.2-2 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+b1 install ok installed libmount1:amd64 libmount1 2.36.1-2 install ok installed libnettle8:amd64 libnettle8 3.6-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.21-2 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.35-2 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.0-3 install ok installed libselinux1:amd64 libselinux1 3.1-2+b1 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b1 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-2 install ok installed libss2:amd64 libss2 1.45.6-1 install ok installed libstdc++6:amd64 libstdc++6 10.2.0-23 install ok installed libsystemd0:amd64 libsystemd0 247.1-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-1 install ok installed libudev1:amd64 libudev1 247.1-3 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-2 install ok installed libzstd1:amd64 libzstd1 1.4.5+dfsg-4 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.45.6-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-2 install ok installed ncurses-base ncurses-base 6.2+20201114-1 install ok installed ncurses-bin ncurses-bin 6.2+20201114-1 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.0-5 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.12+nmu1 install ok installed sysvinit-utils sysvinit-utils 2.96-5 install ok installed tar tar 1.32+dfsg-1 install ok installed tzdata tzdata 2020d-1 install ok installed ucf ucf 3.0043 install ok installed util-linux util-linux 2.36.1-2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg-divert', '--list'] 0m9.9s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg-divert', '--list'] 0m9.9s INFO: Running scripts is_testable 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/is_testable_uninstallable'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/is_testable_uninstallable'] 0m9.9s INFO: apt-cache does not know about any of the requested packages 0m9.9s INFO: Running scripts pre_test 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_test_exceptions'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_test_exceptions'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_test_root_password'] 0m10.0s DUMP: New password: Retype new password: passwd: password updated successfully 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_test_root_password'] 0m10.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiub296s1'] 0m10.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiub296s1'] 0m10.7s DEBUG: No broken symlinks as far as we can find. 0m10.7s INFO: Running scripts pre_install 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_database-server'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_database-server'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_exceptions'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_exceptions'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_extras'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_extras'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'show', '--no-all-versions', 'optimir=1.0-3'] 0m11.5s DUMP: Package: optimir Version: 1.0-3 Installed-Size: 7404 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-en: Integrating genetic variations in miRNA alignment OptimiR is a miRSeq data alignment workflow. It integrates genetic information to assess the impact of variants on miRNA expression. . OptimiR: A bioinformatics pipeline designed to detect and quantify miRNAs, isomiRs and polymiRs from miRSeq data, & study the impact of genetic variations on polymiRs' expression. Description-md5: 759e6ff9eaeea6644852b82160c2085c Homepage: https://github.com/FlorianThibord/OptimiR Section: science Priority: optional Filename: pool/main/o/optimir/optimir_1.0-3_all.deb Size: 1028064 MD5sum: 4ff00e8c13b9c17e3be3b6c1413490bc SHA256: b6550b1083ea4758e73d1d2aec38b609e59d159ff7f9b414524f4f6303a21c94 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'show', '--no-all-versions', 'optimir=1.0-3'] 0m11.5s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: all Maintainer: piuparts developers team Depends: python3-biopython, python3-pysam, python3:any, bowtie2, cutadapt, samtools Description: Dummy package to satisfy dependencies - created by piuparts This package was created automatically by piuparts and can safely be removed 0m11.5s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpy78r4esk/piuparts-depends-dummy'] 0m11.5s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpy78r4esk/piuparts-depends-dummy.deb'. 0m11.5s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpy78r4esk/piuparts-depends-dummy'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m11.5s DUMP: 2.1.12 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m11.5s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpy78r4esk/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpiub296s1/tmp 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m25.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: bowtie2 cutadapt libblas3 libbrotli1 libbsd0 libcurl3-gnutls libdeflate0 libexpat1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libgssapi-krb5-2 libhts3 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libperl5.32 libpng16-16 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libtbb2 libtiff5 libtirpc-common libtirpc3 libwebp6 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support perl perl-modules-5.32 pigz python3 python3-biopython python3-cutadapt python3-dnaio python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pysam python3-reportlab python3-reportlab-accel python3-xopen python3.8 python3.8-minimal python3.9 python3.9-minimal readline-common samtools Suggested packages: bowtie2-examples gdbm-l10n krb5-doc krb5-user liblcms2-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-renderpm python3-psycopg2 python3-scipy raxml t-coffee wise w3-dtd-mathml gcc gfortran python-numpy-doc python3-dev python3-pytest python3-numpy-dbg python-pil-doc python3-pil-dbg python3-setuptools pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python3.8-venv python3.8-doc binutils binfmt-support python3.9-venv python3.9-doc readline-doc cwltool Recommended packages: ca-certificates krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils netbase python-biopython-doc ncbi-blast+ python3-olefile python3-renderpm The following NEW packages will be installed: bowtie2 cutadapt libblas3 libbrotli1 libbsd0 libcurl3-gnutls libdeflate0 libexpat1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libgssapi-krb5-2 libhts3 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libperl5.32 libpng16-16 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libtbb2 libtiff5 libtirpc-common libtirpc3 libwebp6 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support perl perl-modules-5.32 pigz piuparts-depends-dummy python3 python3-biopython python3-cutadapt python3-dnaio python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pysam python3-reportlab python3-reportlab-accel python3-xopen python3.8 python3.8-minimal python3.9 python3.9-minimal readline-common samtools 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. Need to get 38.9 MB/38.9 MB of archives. After this operation, 172 MB of additional disk space will be used. Get:1 /tmp/piuparts-depends-dummy.deb piuparts-depends-dummy all 0.invalid.0 [666 B] Get:2 http://deb.debian.org/debian sid/main amd64 perl-modules-5.32 all 5.32.0-5 [2821 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.18.1-5.1 [64.4 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.18.1-5.1 [44.4 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libperl5.32 amd64 5.32.0-5 [4119 kB] Get:6 http://deb.debian.org/debian sid/main amd64 perl amd64 5.32.0-5 [293 kB] Get:7 http://deb.debian.org/debian sid/main amd64 pigz amd64 2.4-1+b1 [58.3 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libssl1.1 amd64 1.1.1h-1 [1550 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libpython3.9-minimal amd64 3.9.1~rc1-2 [799 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.2.10-1 [96.9 kB] Get:11 http://deb.debian.org/debian sid/main amd64 python3.9-minimal amd64 3.9.1~rc1-2 [1955 kB] Get:12 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amd64 libtirpc3 amd64 1.2.6-3 [83.4 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:25 http://deb.debian.org/debian sid/main amd64 readline-common all 8.1~rc3-1 [73.7 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.1~rc3-1 [168 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.34.0-1 [796 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libpython3.9-stdlib amd64 3.9.1~rc1-2 [1751 kB] Get:29 http://deb.debian.org/debian sid/main amd64 python3.9 amd64 3.9.1~rc1-2 [460 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.9.0-4 [21.0 kB] Get:31 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.9.0-4 [64.1 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libpython3.8-minimal amd64 3.8.6-1 [761 kB] Get:33 http://deb.debian.org/debian sid/main amd64 python3.8-minimal amd64 3.8.6-1 [1863 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libtbb2 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http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 0.6.1-2+b1 [97.9 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.14-2 [139 kB] Get:72 http://deb.debian.org/debian sid/main amd64 python3.8 amd64 3.8.6-1 [422 kB] Get:73 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.19.4-1 [3350 kB] Get:74 http://deb.debian.org/debian sid/main amd64 python3-reportlab-accel amd64 3.5.55-1 [42.4 kB] Get:75 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 8.0.1-1 [467 kB] Get:76 http://deb.debian.org/debian sid/main amd64 python3-reportlab all 3.5.55-1 [573 kB] Get:77 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.78+dfsg-3 [1417 kB] Get:78 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.15.4+ds-3+b1 [2335 kB] Get:79 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.11-1 [545 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 38.9 MB in 1s (66.9 MB/s) Selecting previously unselected package perl-modules-5.32. 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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 ... 9742 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.0-4_amd64.deb ... Unpacking python3 (3.9.0-4) ... Selecting previously unselected package libpython3.8-minimal:amd64. Preparing to unpack .../01-libpython3.8-minimal_3.8.6-1_amd64.deb ... Unpacking libpython3.8-minimal:amd64 (3.8.6-1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../02-python3.8-minimal_3.8.6-1_amd64.deb ... Unpacking python3.8-minimal (3.8.6-1) ... Selecting previously unselected package libtbb2:amd64. Preparing to unpack .../03-libtbb2_2020.3-1_amd64.deb ... Unpacking libtbb2:amd64 (2020.3-1) ... Selecting previously unselected package bowtie2. Preparing to unpack .../04-bowtie2_2.4.2-1_amd64.deb ... Unpacking bowtie2 (2.4.2-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../05-python3-pkg-resources_50.3.0-1_all.deb ... Unpacking python3-pkg-resources (50.3.0-1) ... Selecting previously unselected package python3-xopen. Preparing to unpack .../06-python3-xopen_1.0.1-1_all.deb ... Unpacking python3-xopen (1.0.1-1) ... Selecting previously unselected package python3-dnaio. Preparing to unpack .../07-python3-dnaio_0.4.4-1_amd64.deb ... Unpacking python3-dnaio (0.4.4-1) ... Selecting previously unselected package python3-cutadapt. Preparing to unpack .../08-python3-cutadapt_3.0-1_amd64.deb ... Unpacking python3-cutadapt (3.0-1) ... Selecting previously unselected package cutadapt. Preparing to unpack .../09-cutadapt_3.0-1_all.deb ... Unpacking cutadapt (3.0-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../10-libblas3_3.9.0-3_amd64.deb ... Unpacking libblas3:amd64 (3.9.0-3) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../11-libbrotli1_1.0.9-2+b1_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../12-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../13-libsasl2-modules-db_2.1.27+dfsg-2_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-2) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../14-libsasl2-2_2.1.27+dfsg-2_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-2) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../15-libldap-2.4-2_2.4.56+dfsg-1_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.56+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../16-libnghttp2-14_1.42.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.42.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../17-libpsl5_0.21.0-1.1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.0-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../18-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../19-libssh2-1_1.8.0-2.1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../20-libcurl3-gnutls_7.72.0-1_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.72.0-1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../21-libdeflate0_1.6-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.6-1) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../22-libpng16-16_1.6.37-3_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.37-3) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../23-libfreetype6_2.10.2+dfsg-4_amd64.deb ... Unpacking libfreetype6:amd64 (2.10.2+dfsg-4) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../24-libquadmath0_10.2.0-23_amd64.deb ... Unpacking libquadmath0:amd64 (10.2.0-23) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../25-libgfortran5_10.2.0-23_amd64.deb ... Unpacking libgfortran5:amd64 (10.2.0-23) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../26-libhts3_1.11-2_amd64.deb ... Unpacking libhts3:amd64 (1.11-2) ... Selecting previously unselected package libimagequant0:amd64. Preparing to unpack .../27-libimagequant0_2.12.2-1.1_amd64.deb ... Unpacking libimagequant0:amd64 (2.12.2-1.1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../28-libjbig0_2.1-3.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-3.1+b2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../29-libjpeg62-turbo_1%3a2.0.5-1.1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.0.5-1.1) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../30-liblapack3_3.9.0-3_amd64.deb ... Unpacking liblapack3:amd64 (3.9.0-3) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../31-liblcms2-2_2.9-4+b1_amd64.deb ... Unpacking liblcms2-2:amd64 (2.9-4+b1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../32-libncurses6_6.2+20201114-1_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20201114-1) ... Selecting previously unselected package libpython3.8-stdlib:amd64. Preparing to unpack .../33-libpython3.8-stdlib_3.8.6-1_amd64.deb ... Unpacking libpython3.8-stdlib:amd64 (3.8.6-1) ... Selecting previously unselected package libwebp6:amd64. Preparing to unpack .../34-libwebp6_0.6.1-2+b1_amd64.deb ... Unpacking libwebp6:amd64 (0.6.1-2+b1) ... Selecting previously unselected package libtiff5:amd64. Preparing to unpack .../35-libtiff5_4.1.0+git191117-2_amd64.deb ... Unpacking libtiff5:amd64 (4.1.0+git191117-2) ... Selecting previously unselected package libwebpdemux2:amd64. Preparing to unpack .../36-libwebpdemux2_0.6.1-2+b1_amd64.deb ... Unpacking libwebpdemux2:amd64 (0.6.1-2+b1) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../37-libwebpmux3_0.6.1-2+b1_amd64.deb ... Unpacking libwebpmux3:amd64 (0.6.1-2+b1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../38-libxau6_1%3a1.0.8-1+b2_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../39-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 .../40-libxcb1_1.14-2_amd64.deb ... Unpacking libxcb1:amd64 (1.14-2) ... Selecting previously unselected package python3.8. Preparing to unpack .../41-python3.8_3.8.6-1_amd64.deb ... Unpacking python3.8 (3.8.6-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../42-python3-numpy_1%3a1.19.4-1_amd64.deb ... Unpacking python3-numpy (1:1.19.4-1) ... Selecting previously unselected package python3-reportlab-accel:amd64. Preparing to unpack .../43-python3-reportlab-accel_3.5.55-1_amd64.deb ... Unpacking python3-reportlab-accel:amd64 (3.5.55-1) ... Selecting previously unselected package python3-pil:amd64. Preparing to unpack .../44-python3-pil_8.0.1-1_amd64.deb ... Unpacking python3-pil:amd64 (8.0.1-1) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../45-python3-reportlab_3.5.55-1_all.deb ... Unpacking python3-reportlab (3.5.55-1) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../46-python3-biopython_1.78+dfsg-3_amd64.deb ... Unpacking python3-biopython (1.78+dfsg-3) ... Selecting previously unselected package python3-pysam. Preparing to unpack .../47-python3-pysam_0.15.4+ds-3+b1_amd64.deb ... Unpacking python3-pysam (0.15.4+ds-3+b1) ... Selecting previously unselected package samtools. Preparing to unpack .../48-samtools_1.11-1_amd64.deb ... Unpacking samtools (1.11-1) ... Selecting previously unselected package piuparts-depends-dummy. Preparing to unpack .../49-piuparts-depends-dummy.deb ... Unpacking piuparts-depends-dummy (0.invalid.0) ... Setting up media-types (1.0.1) ... Setting up liblcms2-2:amd64 (2.9-4+b1) ... Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up libkeyutils1:amd64 (1.6.1-2) ... Setting up libpsl5:amd64 (0.21.0-1.1) ... Setting up libpython3.8-minimal:amd64 (3.8.6-1) ... Setting up libtirpc-common (1.2.6-3) ... Setting up perl-modules-5.32 (5.32.0-5) ... Setting up libbrotli1:amd64 (1.0.9-2+b1) ... Setting up libsqlite3-0:amd64 (3.34.0-1) ... Setting up libtbb2:amd64 (2020.3-1) ... Setting up libnghttp2-14:amd64 (1.42.0-1) ... Setting up libdeflate0:amd64 (1.6-1) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libkrb5support0:amd64 (1.18.3-4) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2) ... Setting up libblas3:amd64 (3.9.0-3) ... 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 (1:2.0.5-1.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.2+20201114-1) ... Setting up libquadmath0:amd64 (10.2.0-23) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up libwebp6:amd64 (0.6.1-2+b1) ... Setting up libncursesw6:amd64 (6.2+20201114-1) ... Setting up libk5crypto3:amd64 (1.18.3-4) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2) ... Setting up libgfortran5:amd64 (10.2.0-23) ... Setting up python3.8-minimal (3.8.6-1) ... Setting up pigz (2.4-1+b1) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.18.3-4) ... Setting up libtiff5:amd64 (4.1.0+git191117-2) ... Setting up libwebpmux3:amd64 (0.6.1-2+b1) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up readline-common (8.1~rc3-1) ... Setting up libgdbm6:amd64 (1.18.1-5.1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3) ... 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 (1.14-2) ... Setting up libwebpdemux2:amd64 (0.6.1-2+b1) ... Setting up libreadline8:amd64 (8.1~rc3-1) ... Setting up libldap-2.4-2:amd64 (2.4.56+dfsg-1) ... Setting up libfreetype6:amd64 (2.10.2+dfsg-4) ... Setting up libgssapi-krb5-2:amd64 (1.18.3-4) ... Setting up libgdbm-compat4:amd64 (1.18.1-5.1) ... Setting up libperl5.32:amd64 (5.32.0-5) ... Setting up libtirpc3:amd64 (1.2.6-3) ... Setting up libcurl3-gnutls:amd64 (7.72.0-1) ... Setting up perl (5.32.0-5) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up mailcap (3.67) ... Setting up libpython3.9-stdlib:amd64 (3.9.1~rc1-2) ... Setting up libpython3-stdlib:amd64 (3.9.0-4) ... Setting up libhts3:amd64 (1.11-2) ... Setting up mime-support (3.66) ... Setting up samtools (1.11-1) ... Setting up libpython3.8-stdlib:amd64 (3.8.6-1) ... Setting up python3.8 (3.8.6-1) ... Setting up python3.9 (3.9.1~rc1-2) ... Setting up python3 (3.9.0-4) ... Setting up bowtie2 (2.4.2-1) ... Setting up python3-pil:amd64 (8.0.1-1) ... Setting up python3-reportlab-accel:amd64 (3.5.55-1) ... Setting up python3-reportlab (3.5.55-1) ... Setting up python3-pkg-resources (50.3.0-1) ... Setting up python3-pysam (0.15.4+ds-3+b1) ... Setting up python3-xopen (1.0.1-1) ... Setting up python3-numpy (1:1.19.4-1) ... Setting up python3-biopython (1.78+dfsg-3) ... Setting up python3-dnaio (0.4.4-1) ... Setting up python3-cutadapt (3.0-1) ... Setting up cutadapt (3.0-1) ... Setting up piuparts-depends-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-5) ... 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m25.3s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok 0m25.3s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpiub296s1/./tmp/piuparts-depends-dummy.deb 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m25.3s DUMP: piuparts-depends-dummy install ok installed 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m25.4s DUMP: (Reading database ... 12449 files and directories currently installed.) Removing piuparts-depends-dummy (0.invalid.0) ... 0m25.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m25.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', 'clean'] 0m25.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', 'clean'] 0m25.4s DEBUG: Recording chroot state 0m25.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiub296s1'] 0m26.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiub296s1'] 0m28.5s ERROR: WARN: Broken symlinks: /usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd -> ../../../../../../share/xml/schema/w3c/mathml/dtd/mathml2.dtd 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'policy'] 0m29.1s 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: 0m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'policy'] 0m29.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'policy', 'optimir'] 0m29.1s DUMP: optimir: Installed: (none) Candidate: 1.0-3 Version table: 1.0-3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'policy', 'optimir'] 0m29.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', '-y', 'install', 'optimir=1.0-3'] 0m30.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Recommended packages: r-cran-gridextra r-cran-ggplot2 The following NEW packages will be installed: optimir 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 1028 kB of archives. After this operation, 7582 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 optimir all 1.0-3 [1028 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1028 kB in 0s (6257 kB/s) Selecting previously unselected package optimir. (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 ... 12449 files and directories currently installed.) Preparing to unpack .../archives/optimir_1.0-3_all.deb ... Unpacking optimir (1.0-3) ... Setting up optimir (1.0-3) ... /usr/lib/python3/dist-packages/optimir/libs/get_counts.py:453: SyntaxWarning: "is" with a literal. Did you mean "=="? if prefix is '': 0m30.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', '-y', 'install', 'optimir=1.0-3'] 0m30.3s INFO: Running scripts post_install 0m30.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_install_exceptions'] 0m30.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_install_exceptions'] 0m30.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', 'remove', 'optimir'] 0m30.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: bowtie2 cutadapt libblas3 libbrotli1 libbsd0 libcurl3-gnutls libdeflate0 libexpat1 libfreetype6 libgfortran5 libgssapi-krb5-2 libhts3 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libpng16-16 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libtbb2 libtiff5 libtirpc-common libtirpc3 libwebp6 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support pigz python3 python3-biopython python3-cutadapt python3-dnaio python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pysam python3-reportlab python3-reportlab-accel python3-xopen python3.8 python3.8-minimal python3.9 python3.9-minimal readline-common samtools Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: optimir 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 7582 kB 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 ... 12511 files and directories currently installed.) Removing optimir (1.0-3) ... 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', 'remove', 'optimir'] 0m30.9s INFO: Reinstalling after remove 0m30.9s INFO: Running scripts pre_install 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_database-server'] 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_database-server'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_exceptions'] 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_exceptions'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_extras'] 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_extras'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_foreign_architecture'] 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_foreign_architecture'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'policy'] 0m31.0s 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: 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'policy'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'policy', 'optimir'] 0m31.0s DUMP: optimir: Installed: (none) Candidate: 1.0-3 Version table: 1.0-3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'policy', 'optimir'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', '-y', 'install', 'optimir=1.0-3'] 0m31.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Recommended packages: r-cran-gridextra r-cran-ggplot2 The following NEW packages will be installed: optimir debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/1028 kB of archives. After this operation, 7582 kB of additional disk space will be used. Selecting previously unselected package optimir. (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 ... 12449 files and directories currently installed.) Preparing to unpack .../archives/optimir_1.0-3_all.deb ... Unpacking optimir (1.0-3) ... Setting up optimir (1.0-3) ... /usr/lib/python3/dist-packages/optimir/libs/get_counts.py:453: SyntaxWarning: "is" with a literal. Did you mean "=="? if prefix is '': 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', '-y', 'install', 'optimir=1.0-3'] 0m31.8s INFO: Running scripts post_install 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_install_exceptions'] 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_install_exceptions'] 0m31.8s INFO: Running scripts pre_install 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_database-server'] 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_database-server'] 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_exceptions'] 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_exceptions'] 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_extras'] 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_extras'] 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'policy'] 0m31.9s 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: 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'policy'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'policy', 'optimir'] 0m31.9s DUMP: optimir: Installed: 1.0-3 Candidate: 1.0-3 Version table: *** 1.0-3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-cache', 'policy', 'optimir'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', '-y', 'install', '--reinstall', 'optimir=1.0-3'] 0m32.8s DUMP: Reading package lists... Building dependency tree... Reading state information... debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/1028 kB of archives. After this operation, 0 B of additional disk space will be used. (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 ... 12511 files and directories currently installed.) Preparing to unpack .../archives/optimir_1.0-3_all.deb ... Unpacking optimir (1.0-3) over (1.0-3) ... Setting up optimir (1.0-3) ... /usr/lib/python3/dist-packages/optimir/libs/get_counts.py:453: SyntaxWarning: "is" with a literal. Did you mean "=="? if prefix is '': 0m32.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', '-y', 'install', '--reinstall', 'optimir=1.0-3'] 0m32.8s INFO: Running scripts post_install 0m32.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_install_exceptions'] 0m32.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_install_exceptions'] 0m32.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiub296s1'] 0m33.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiub296s1'] 0m34.3s ERROR: WARN: Broken symlinks: /usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd -> ../../../../../../share/xml/schema/w3c/mathml/dtd/mathml2.dtd (python3-biopython) 0m35.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpiub296s1', '-ac', '--ignore-obsolete'] 0m36.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpiub296s1', '-ac', '--ignore-obsolete'] 0m36.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m36.0s DUMP: 0.15.2 0m36.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m36.0s INFO: Running adequate version 0.15.2 now. 0m36.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'optimir'] 0m36.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'optimir'] 0m36.1s INFO: Running scripts pre_remove 0m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m37.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m37.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m37.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m37.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m37.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m37.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_exceptions'] 0m37.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_exceptions'] 0m37.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_preseed_cleanup'] 0m37.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/pre_remove_preseed_cleanup'] 0m37.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m37.5s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.1.12 install ok installed base-files base-files 11 install ok installed base-passwd base-passwd 3.5.48 install ok installed bash bash 5.1~rc3-1 install ok installed bowtie2 bowtie2 2.4.2-1 install ok installed bsdutils bsdutils 1:2.36.1-2 install ok installed coreutils coreutils 8.32-4+b1 install ok installed cutadapt cutadapt 3.0-1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-2 install ok installed dbconfig-common dbconfig-common 2.0.17 install ok installed debconf debconf 1.5.74 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.20.5 install ok installed e2fsprogs e2fsprogs 1.45.6-1 install ok installed findutils findutils 4.7.0+git20201010-2 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.0-23 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-19 install ok installed gpgv gpgv 2.2.20-1 install ok installed grep grep 3.6-1 install ok installed gzip gzip 1.10-2 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.59 install ok installed libacl1:amd64 libacl1 2.2.53-8 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.1.12 install ok installed libattr1:amd64 libattr1 1:2.4.48-5 install ok installed libaudit-common libaudit-common 1:2.8.5-3.1 install ok installed libaudit1:amd64 libaudit1 1:2.8.5-3.1 install ok installed libblas3:amd64 libblas3 3.9.0-3 install ok installed libblkid1:amd64 libblkid1 2.36.1-2 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b1 install ok installed libbsd0:amd64 libbsd0 0.10.0-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-5 install ok installed libc6:amd64 libc6 2.31-5 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.45.6-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.17-1 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.72.0-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.255 install ok installed libdeflate0:amd64 libdeflate0 1.6-1 install ok installed libexpat1:amd64 libexpat1 2.2.10-1 install ok installed libext2fs2:amd64 libext2fs2 1.45.6-1 install ok installed libffi7:amd64 libffi7 3.3-5 install ok installed libfreetype6:amd64 libfreetype6 2.10.2+dfsg-4 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.0-23 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.18.1-5.1 install ok installed libgdbm6:amd64 libgdbm6 1.18.1-5.1 install ok installed libgfortran5:amd64 libgfortran5 10.2.0-23 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1 install ok installed libgnutls30:amd64 libgnutls30 3.6.15-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-4 install ok installed libhogweed6:amd64 libhogweed6 3.6-2 install ok installed libhts3:amd64 libhts3 1.11-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-4 install ok installed libimagequant0:amd64 libimagequant0 2.12.2-1.1 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.0.5-1.1 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-4 install ok installed liblapack3:amd64 liblapack3 3.9.0-3 install ok installed liblcms2-2:amd64 liblcms2-2 2.9-4+b1 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.56+dfsg-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.2-2 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+b1 install ok installed libmount1:amd64 libmount1 2.36.1-2 install ok installed libncurses6:amd64 libncurses6 6.2+20201114-1 install ok installed libncursesw6:amd64 libncursesw6 6.2+20201114-1 install ok installed libnettle8:amd64 libnettle8 3.6-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.42.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.21-2 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.35-2 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libperl5.32:amd64 libperl5.32 5.32.0-5 install ok installed libpng16-16:amd64 libpng16-16 1.6.37-3 install ok installed libpsl5:amd64 libpsl5 0.21.0-1.1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.9.0-4 install ok installed libpython3.8-minimal:amd64 libpython3.8-minimal 3.8.6-1 install ok installed libpython3.8-stdlib:amd64 libpython3.8-stdlib 3.8.6-1 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.1~rc1-2 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.1~rc1-2 install ok installed libquadmath0:amd64 libquadmath0 10.2.0-23 install ok installed libreadline8:amd64 libreadline8 8.1~rc3-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-2 install ok installed libseccomp2:amd64 libseccomp2 2.5.0-3 install ok installed libselinux1:amd64 libselinux1 3.1-2+b1 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b1 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-2 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.34.0-1 install ok installed libss2:amd64 libss2 1.45.6-1 install ok installed libssh2-1:amd64 libssh2-1 1.8.0-2.1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1h-1 install ok installed libstdc++6:amd64 libstdc++6 10.2.0-23 install ok installed libsystemd0:amd64 libsystemd0 247.1-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2 install ok installed libtbb2:amd64 libtbb2 2020.3-1 install ok installed libtiff5:amd64 libtiff5 4.1.0+git191117-2 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-1 install ok installed libtirpc-common libtirpc-common 1.2.6-3 install ok installed libtirpc3:amd64 libtirpc3 1.2.6-3 install ok installed libudev1:amd64 libudev1 247.1-3 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-2 install ok installed libwebp6:amd64 libwebp6 0.6.1-2+b1 install ok installed libwebpdemux2:amd64 libwebpdemux2 0.6.1-2+b1 install ok installed libwebpmux3:amd64 libwebpmux3 0.6.1-2+b1 install ok installed libxau6:amd64 libxau6 1:1.0.8-1+b2 install ok installed libxcb1:amd64 libxcb1 1.14-2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libzstd1:amd64 libzstd1 1.4.5+dfsg-4 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.45.6-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mailcap mailcap 3.67 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed media-types media-types 1.0.1 install ok installed mime-support mime-support 3.66 install ok installed mount mount 2.36.1-2 install ok installed ncurses-base ncurses-base 6.2+20201114-1 install ok installed ncurses-bin ncurses-bin 6.2+20201114-1 install ok installed optimir optimir 1.0-3 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl perl 5.32.0-5 install ok installed perl-base perl-base 5.32.0-5 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.0-5 install ok installed pigz pigz 2.4-1+b1 install ok installed python3 python3 3.9.0-4 install ok installed python3-biopython python3-biopython 1.78+dfsg-3 install ok installed python3-cutadapt python3-cutadapt 3.0-1 install ok installed python3-dnaio python3-dnaio 0.4.4-1 install ok installed python3-minimal python3-minimal 3.9.0-4 install ok installed python3-numpy python3-numpy 1:1.19.4-1 install ok installed python3-pil:amd64 python3-pil 8.0.1-1 install ok installed python3-pkg-resources python3-pkg-resources 50.3.0-1 install ok installed python3-pysam python3-pysam 0.15.4+ds-3+b1 install ok installed python3-reportlab python3-reportlab 3.5.55-1 install ok installed python3-reportlab-accel:amd64 python3-reportlab-accel 3.5.55-1 install ok installed python3-xopen python3-xopen 1.0.1-1 install ok installed python3.8 python3.8 3.8.6-1 install ok installed python3.8-minimal python3.8-minimal 3.8.6-1 install ok installed python3.9 python3.9 3.9.1~rc1-2 install ok installed python3.9-minimal python3.9-minimal 3.9.1~rc1-2 install ok installed readline-common readline-common 8.1~rc3-1 install ok installed samtools samtools 1.11-1 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.12+nmu1 install ok installed sysvinit-utils sysvinit-utils 2.96-5 install ok installed tar tar 1.32+dfsg-1 install ok installed tzdata tzdata 2020d-1 install ok installed ucf ucf 3.0043 install ok installed util-linux util-linux 2.36.1-2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m37.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m37.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', 'remove', 'bowtie2', 'cutadapt', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhts3:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.8-minimal:amd64', 'libpython3.8-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'libtiff5:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.32', 'pigz', 'python3', 'python3-biopython', 'python3-cutadapt', 'python3-dnaio', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-xopen', 'python3.8', 'python3.8-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'optimir'] 0m40.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bowtie2 cutadapt libblas3 libbrotli1 libbsd0 libcurl3-gnutls libdeflate0 libexpat1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libgssapi-krb5-2 libhts3 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libperl5.32 libpng16-16 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libtbb2 libtiff5 libtirpc-common libtirpc3 libwebp6 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support optimir perl perl-modules-5.32 pigz python3 python3-biopython python3-cutadapt python3-dnaio python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pysam python3-reportlab python3-reportlab-accel python3-xopen python3.8 python3.8-minimal python3.9 python3.9-minimal readline-common samtools 0 upgraded, 0 newly installed, 79 to remove and 0 not upgraded. After this operation, 180 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 ... 12511 files and directories currently installed.) Removing optimir (1.0-3) ... Removing bowtie2 (2.4.2-1) ... Removing cutadapt (3.0-1) ... Removing python3-biopython (1.78+dfsg-3) ... Removing python3-numpy (1:1.19.4-1) ... Removing liblapack3:amd64 (3.9.0-3) ... Removing libblas3:amd64 (3.9.0-3) ... Removing python3-reportlab (3.5.55-1) ... Removing python3-pil:amd64 (8.0.1-1) ... Removing libfreetype6:amd64 (2.10.2+dfsg-4) ... Removing samtools (1.11-1) ... Removing libxcb1:amd64 (1.14-2) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.10.0-1) ... Removing python3-reportlab-accel:amd64 (3.5.55-1) ... Removing python3-cutadapt (3.0-1) ... Removing python3-dnaio (0.4.4-1) ... Removing python3-xopen (1.0.1-1) ... Removing python3-pkg-resources (50.3.0-1) ... Removing python3-pysam (0.15.4+ds-3+b1) ... Removing python3 (3.9.0-4) ... Removing python3.9 (3.9.1~rc1-2) ... Removing python3-minimal (3.9.0-4) ... Removing python3.9-minimal (3.9.1~rc1-2) ... Removing python3.8 (3.8.6-1) ... Removing python3.8-minimal (3.8.6-1) ... Removing libexpat1:amd64 (2.2.10-1) ... Removing libpython3-stdlib:amd64 (3.9.0-4) ... Removing libpython3.9-stdlib:amd64 (3.9.1~rc1-2) ... find: '/usr/lib/python3': No such file or directory Removing libpython3.8-stdlib:amd64 (3.8.6-1) ... find: '/usr/lib/python3': No such file or directory Removing mime-support (3.66) ... Removing mailcap (3.67) ... Removing perl (5.32.0-5) ... Removing libperl5.32:amd64 (5.32.0-5) ... Removing libgdbm-compat4:amd64 (1.18.1-5.1) ... Removing libgdbm6:amd64 (1.18.1-5.1) ... Removing libgfortran5:amd64 (10.2.0-23) ... Removing libnsl2:amd64 (1.3.0-2) ... Removing libtirpc3:amd64 (1.2.6-3) ... Removing libimagequant0:amd64 (2.12.2-1.1) ... Removing libtiff5:amd64 (4.1.0+git191117-2) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.0.5-1.1) ... Removing liblcms2-2:amd64 (2.9-4+b1) ... Removing libncurses6:amd64 (6.2+20201114-1) ... Removing libncursesw6:amd64 (6.2+20201114-1) ... Removing libpng16-16:amd64 (1.6.37-3) ... Removing libpython3.8-minimal:amd64 (3.8.6-1) ... find: '/usr/lib/python3': No such file or directory Removing libpython3.9-minimal:amd64 (3.9.1~rc1-2) ... find: '/usr/lib/python3': No such file or directory Removing libquadmath0:amd64 (10.2.0-23) ... Removing libreadline8:amd64 (8.1~rc3-1) ... Removing libsqlite3-0:amd64 (3.34.0-1) ... Removing libtbb2:amd64 (2020.3-1) ... Removing libtirpc-common (1.2.6-3) ... Removing libwebpmux3:amd64 (0.6.1-2+b1) ... Removing libwebpdemux2:amd64 (0.6.1-2+b1) ... Removing libwebp6:amd64 (0.6.1-2+b1) ... Removing libxau6:amd64 (1:1.0.8-1+b2) ... Removing media-types (1.0.1) ... Removing perl-modules-5.32 (5.32.0-5) ... Removing pigz (2.4-1+b1) ... Removing readline-common (8.1~rc3-1) ... Removing libhts3:amd64 (1.11-2) ... Removing libcurl3-gnutls:amd64 (7.72.0-1) ... Removing libbrotli1:amd64 (1.0.9-2+b1) ... Removing libdeflate0:amd64 (1.6-1) ... Removing libgssapi-krb5-2:amd64 (1.18.3-4) ... Removing libkrb5-3:amd64 (1.18.3-4) ... Removing libk5crypto3:amd64 (1.18.3-4) ... Removing libkeyutils1:amd64 (1.6.1-2) ... Removing libkrb5support0:amd64 (1.18.3-4) ... Removing libldap-2.4-2:amd64 (2.4.56+dfsg-1) ... Removing libnghttp2-14:amd64 (1.42.0-1) ... Removing libpsl5:amd64 (0.21.0-1.1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-2) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-2) ... Removing libssh2-1:amd64 (1.8.0-2.1) ... Removing libssl1.1:amd64 (1.1.1h-1) ... Processing triggers for libc-bin (2.31-5) ... 0m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', 'remove', 'bowtie2', 'cutadapt', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhts3:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.8-minimal:amd64', 'libpython3.8-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'libtiff5:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.32', 'pigz', 'python3', 'python3-biopython', 'python3-cutadapt', 'python3-dnaio', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-xopen', 'python3.8', 'python3.8-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'optimir'] 0m40.0s INFO: Running scripts post_remove 0m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_remove_cleanup'] 0m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_remove_cleanup'] 0m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_remove_exceptions'] 0m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_remove_exceptions'] 0m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg', '--purge', 'bowtie2', 'cutadapt', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhts3:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.8-minimal:amd64', 'libpython3.8-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'libtiff5:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.32', 'pigz', 'python3', 'python3-biopython', 'python3-cutadapt', 'python3-dnaio', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-xopen', 'python3.8', 'python3.8-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools'] 0m40.2s 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 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 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 libfreetype6 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 (Reading database ... 6959 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.18.3-4) ... dpkg: warning: ignoring request to remove libhts3 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-2.4-2 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 libperl5.32 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 libpython3.8-minimal:amd64 (3.8.6-1) ... dpkg: warning: ignoring request to remove libpython3.8-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.1~rc1-2) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 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 Purging configuration files for libssl1.1:amd64 (1.1.1h-1) ... dpkg: warning: ignoring request to remove libtbb2 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed Purging configuration files for libtirpc-common (1.2.6-3) ... dpkg: warning: ignoring request to remove libtirpc3 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove 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 (3.67) ... Purging configuration files for media-types (1.0.1) ... dpkg: warning: ignoring request to remove mime-support which isn't installed Purging configuration files for perl (5.32.0-5) ... dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed dpkg: warning: ignoring request to remove pigz which isn't installed Purging configuration files for python3 (3.9.0-4) ... dpkg: warning: ignoring request to remove python3-biopython 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-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-reportlab-accel which isn't installed dpkg: warning: ignoring request to remove python3-xopen which isn't installed dpkg: warning: ignoring request to remove python3.8 which isn't installed Purging configuration files for python3.8-minimal (3.8.6-1) ... dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.1~rc1-2) ... Purging configuration files for readline-common (8.1~rc3-1) ... dpkg: warning: ignoring request to remove samtools which isn't installed 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg', '--purge', 'bowtie2', 'cutadapt', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhts3:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.8-minimal:amd64', 'libpython3.8-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'libtiff5:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.32', 'pigz', 'python3', 'python3-biopython', 'python3-cutadapt', 'python3-dnaio', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-xopen', 'python3.8', 'python3.8-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools'] 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg', '--purge', 'optimir'] 0m40.2s DUMP: dpkg: warning: ignoring request to remove optimir which isn't installed 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg', '--purge', 'optimir'] 0m40.2s INFO: Running scripts post_purge 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_purge_exceptions'] 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_purge_exceptions'] 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_purge_manual_cleanup'] 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_purge_manual_cleanup'] 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg', '--purge', '--pending'] 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg', '--purge', '--pending'] 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg', '--remove', '--pending'] 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg', '--remove', '--pending'] 0m40.2s INFO: Running scripts post_test 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_test_exceptions'] 0m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'tmp/scripts/post_test_exceptions'] 0m40.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiub296s1'] 0m40.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiub296s1'] 0m41.6s DEBUG: No broken symlinks as far as we can find. 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg-divert', '--list'] 0m41.7s 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 0m41.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'dpkg-divert', '--list'] 0m41.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', 'clean'] 0m41.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiub296s1', 'apt-get', 'clean'] 0m41.7s DEBUG: Recording chroot state 0m42.4s INFO: PASS: Installation and purging test. 0m42.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/shm'] 0m42.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/shm'] 0m42.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/console'] 0m42.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/console'] 0m42.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/ptmx'] 0m42.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/ptmx'] 0m42.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/pts'] 0m43.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpiub296s1/dev/pts'] 0m43.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpiub296s1/proc'] 0m43.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpiub296s1/proc'] 0m43.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpiub296s1'] 0m43.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpiub296s1'] 0m43.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpiub296s1 0m43.1s INFO: PASS: All tests. 0m43.1s INFO: piuparts run ends. ret=0 End: 2020-12-06 22:16:56 GMT