Start: 2019-12-13 15:15:02 UTC [testing] Package: python3-biotools Source: python-biotools Version: 1.2.12-4 Installed-Size: 127 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-matplotlib, python3-numpy, python3:any, python:any, clustalw, ncbi-blast+ | ncbi-blast+-legacy Description: Python3 bioinformatics utilities for high-throughput genomic sequencing Homepage: https://github.com/sonwell/biotools Description-md5: fd0c541879ac3385f0f3a9d4fa00e433 Section: python Priority: optional Filename: pool/main/p/python-biotools/python3-biotools_1.2.12-4_all.deb Size: 28872 MD5sum: 7750f844540950657ed4fec6b071a64e SHA256: e621ef71f16d47b36adf8f390e1909494913c7aaf22a80825dbacc39cd7a2c3b [sid] Package: python3-biotools Source: python-biotools Version: 1.2.12-5 Installed-Size: 127 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-matplotlib, python3-numpy, python3:any, clustalw, ncbi-blast+ | ncbi-blast+-legacy Description: Python3 bioinformatics utilities for high-throughput genomic sequencing Homepage: https://github.com/sonwell/biotools Description-md5: fd0c541879ac3385f0f3a9d4fa00e433 Section: python Priority: optional Filename: pool/main/p/python-biotools/python3-biotools_1.2.12-5_all.deb Size: 28880 MD5sum: b5634110e222bb7ec84fbf03d604d983 SHA256: 62e7f00a2f1019d9ae17412a78063ac4ebccef5b83d6ed82f4d0db05276eaeec Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python2.7/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://mirror-ubc.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt python3-biotools=1.2.12-5 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.0.2~201909101611~1.0.1-11-g98f8c745 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://mirror-ubc.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt python3-biotools=1.2.12-5 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.19.0-6-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpKCn7vU 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpKCn7vU 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m3.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m3.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/proc'] 0m3.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/proc'] 0m3.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/pts'] 0m3.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/pts'] 0m3.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/ptmx'] 0m3.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/ptmx'] 0m3.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/console'] 0m3.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/console'] 0m3.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/shm'] 0m3.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/shm'] 0m3.5s DEBUG: sources.list: deb http://mirror-ubc.debian.org/debian/ bullseye main 0m3.6s DEBUG: Created policy-rc.d and chmodded it. 0m3.6s DEBUG: Created resolv.conf. 0m3.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpKCn7vU/tmp/scripts/ 0m3.6s INFO: Running scripts post_chroot_unpack 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', 'update'] 0m9.3s DUMP: Get:1 http://mirror-ubc.debian.org/debian bullseye InRelease [113 kB] Get:2 http://mirror-ubc.debian.org/debian bullseye/main amd64 Packages [7677 kB] Get:3 http://mirror-ubc.debian.org/debian bullseye/main Translation-en [5832 kB] Fetched 13.6 MB in 4s (3104 kB/s) Reading package lists... 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', 'update'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', '-yf', 'dist-upgrade'] 0m10.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: debianutils libtasn1-6 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 155 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian bullseye/main amd64 debianutils amd64 4.9.1 [101 kB] Get:2 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtasn1-6 amd64 4.15.0-2 [53.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 155 kB in 0s (15.0 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6532 files and directories currently installed.) Preparing to unpack .../debianutils_4.9.1_amd64.deb ... Unpacking debianutils (4.9.1) over (4.9) ... Setting up debianutils (4.9.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6532 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.15.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.15.0-2) over (4.14-3) ... Setting up libtasn1-6:amd64 (4.15.0-2) ... Processing triggers for libc-bin (2.29-3) ... 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', '-yf', 'dist-upgrade'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m10.8s DUMP: a0cb77e631631575455d8acb6d38227d - 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m10.8s INFO: Running scripts post_setup 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_setup_dummy_users'] 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_setup_dummy_users'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_setup_forbid_home'] 0m12.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_setup_forbid_home'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_setup_force-unsafe-io'] 0m12.3s 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' 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_setup_force-unsafe-io'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_setup_minimize'] 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_setup_minimize'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_setup_squeeze-backports'] 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_setup_squeeze-backports'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_setup_zz_backports'] 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_setup_zz_backports'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m12.4s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.4 install ok installed base-files base-files 11 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-5 install ok installed bsdutils bsdutils 1:2.34-0.1 install ok installed coreutils coreutils 8.30-3+b1 install ok installed dash dash 0.5.10.2-6 install ok installed debconf debconf 1.5.73 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.9.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.7 install ok installed e2fsprogs e2fsprogs 1.45.4-1 install ok installed fdisk fdisk 2.34-0.1 install ok installed findutils findutils 4.7.0-1 install ok installed gcc-9-base:amd64 gcc-9-base 9.2.1-21 install ok installed gpgv gpgv 2.2.17-3 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+b1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.57 install ok installed libacl1:amd64 libacl1 2.2.53-5 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-5 install ok installed libaudit-common libaudit-common 1:2.8.5-2 install ok installed libaudit1:amd64 libaudit1 1:2.8.5-2+b1 install ok installed libblkid1:amd64 libblkid1 2.34-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-2 install ok installed libc-bin libc-bin 2.29-3 install ok installed libc6:amd64 libc6 2.29-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.1+b1 install ok installed libcom-err2:amd64 libcom-err2 1.45.4-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.250 install ok installed libext2fs2:amd64 libext2fs2 1.45.4-1 install ok installed libfdisk1:amd64 libfdisk1 2.34-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:9.2.1-21 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.5-3 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4 install ok installed libgnutls30:amd64 libgnutls30 3.6.10-5 install ok installed libgpg-error0:amd64 libgpg-error0 1.36-7 install ok installed libhogweed5:amd64 libhogweed5 3.5.1+really3.5.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.2.0-2 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 2.34-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20191019-1 install ok installed libnettle7:amd64 libnettle7 3.5.1+really3.5.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.18.1-2 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 10.34-7 install ok installed libpcre3:amd64 libpcre3 2:8.39-12+b1 install ok installed libseccomp2:amd64 libseccomp2 2.4.2-2 install ok installed libselinux1:amd64 libselinux1 2.9-3+b1 install ok installed libsemanage-common libsemanage-common 2.9-3 install ok installed libsemanage1:amd64 libsemanage1 2.9-3+b1 install ok installed libsepol1:amd64 libsepol1 2.9-2+b2 install ok installed libsmartcols1:amd64 libsmartcols1 2.34-0.1 install ok installed libss2:amd64 libss2 1.45.4-1 install ok installed libstdc++6:amd64 libstdc++6 9.2.1-21 install ok installed libsystemd0:amd64 libsystemd0 244-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.15.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.1+20191019-1 install ok installed libudev1:amd64 libudev1 244-3 install ok installed libunistring2:amd64 libunistring2 0.9.10-2 install ok installed libuuid1:amd64 libuuid1 2.34-0.1 install ok installed libzstd1:amd64 libzstd1 1.4.4+dfsg-1 install ok installed login login 1:4.7-2 install ok installed logsave logsave 1.45.4-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.34-0.1 install ok installed ncurses-base ncurses-base 6.1+20191019-1 install ok installed ncurses-bin ncurses-bin 6.1+20191019-1 install ok installed passwd passwd 1:4.7-2 install ok installed perl-base perl-base 5.30.0-9 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-1 install ok installed tar tar 1.30+dfsg-6+b1 install ok installed tzdata tzdata 2019c-3 install ok installed util-linux util-linux 2.34-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+b1 0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m12.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m13.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 0m13.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 0m13.8s INFO: Running scripts is_testable 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/is_testable_uninstallable'] 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/is_testable_uninstallable'] 0m13.8s INFO: Running scripts pre_test 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_test_exceptions'] 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_test_exceptions'] 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_test_root_password'] 0m13.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_test_root_password'] 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'show', '--no-all-versions', 'python3-biotools'] 0m14.2s DUMP: Package: python3-biotools Source: python-biotools Version: 1.2.12-4 Installed-Size: 127 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-matplotlib, python3-numpy, python3:any, python:any, clustalw, ncbi-blast+ | ncbi-blast+-legacy Description-en: Python3 bioinformatics utilities for high-throughput genomic sequencing This package contains utilities like biotools.align - align sequences (hybrid between Needleman-Wunsch and Smith-Waterman which is used to find the subsequence within a larger sequence that best aligns to a reference) biotools.annotation - create annotation files. The annotations can be used to create a hierarchy among the annotations biotools.BLAST - manage BLAST databases and interface with the BLAST+ standalone program available from NCBI. biotools.clustal - interface to clustalw global (multiple nucleotide or peptide sequence alignment) biotools.complement - creates the complement of a sequence, which can then be reversed biotools.sequence - various tools to deal with sequences biotools.translate - translate a nucleotide using the standard genetic code . This package contains the Python3 module. Description-md5: fd0c541879ac3385f0f3a9d4fa00e433 Homepage: https://github.com/sonwell/biotools Section: python Priority: optional Filename: pool/main/p/python-biotools/python3-biotools_1.2.12-4_all.deb Size: 28872 MD5sum: 7750f844540950657ed4fec6b071a64e SHA256: e621ef71f16d47b36adf8f390e1909494913c7aaf22a80825dbacc39cd7a2c3b 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'show', '--no-all-versions', 'python3-biotools'] 0m14.2s INFO: apt-cache knows about the following packages: python3-biotools 0m14.2s INFO: Running scripts pre_install 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_database-server'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_database-server'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_exceptions'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_exceptions'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_extras'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_extras'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'policy'] 0m14.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian bullseye/main amd64 Packages release o=Debian,a=testing,n=bullseye,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'policy'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'policy', 'python3-biotools'] 0m14.4s DUMP: python3-biotools: Installed: (none) Candidate: 1.2.12-4 Version table: 1.2.12-4 500 500 http://mirror-ubc.debian.org/debian bullseye/main amd64 Packages 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'policy', 'python3-biotools'] 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', '-y', 'install', 'python3-biotools'] 0m41.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: clustalw fonts-lyx libblas3 libexpat1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libgomp1 libjs-jquery libjs-jquery-ui liblapack3 liblmdb0 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec2 libperl5.30 libpng16-16 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl1.1 mime-support ncbi-blast+ ncbi-data perl perl-modules-5.30 python python-matplotlib-data python-minimal python2 python2-minimal python2.7 python2.7-minimal python3 python3-cycler python3-dateutil python3-kiwisolver python3-matplotlib python3-minimal python3-numpy python3-pkg-resources python3-pyparsing python3-six python3.7 python3.7-minimal readline-common ttf-bitstream-vera Suggested packages: clustalx seaview gdbm-l10n libjs-jquery-ui-docs sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libb-debug-perl liblocale-codes-perl python-doc python-tk python2-doc python2.7-doc binutils binfmt-support python3-doc python3-tk python3-venv python-cycler-doc dvipng ffmpeg gir1.2-gtk-3.0 ghostscript inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-nose python3-pyqt4 python3-scipy python3-sip python3-tornado texlive-extra-utils texlive-latex-extra ttf-staypuft gcc gfortran python-numpy-doc python3-dev python3-pytest python3-numpy-dbg python3-setuptools python-pyparsing-doc python3.7-venv python3.7-doc readline-doc Recommended packages: javascript-common bzip2 file xz-utils netbase python3-pil python3-tk The following NEW packages will be installed: clustalw fonts-lyx libblas3 libexpat1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libgomp1 libjs-jquery libjs-jquery-ui liblapack3 liblmdb0 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec2 libperl5.30 libpng16-16 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl1.1 mime-support ncbi-blast+ ncbi-data perl perl-modules-5.30 python python-matplotlib-data python-minimal python2 python2-minimal python2.7 python2.7-minimal python3 python3-biotools python3-cycler python3-dateutil python3-kiwisolver python3-matplotlib python3-minimal python3-numpy python3-pkg-resources python3-pyparsing python3-six python3.7 python3.7-minimal readline-common ttf-bitstream-vera 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. Need to get 51.1 MB of archives. After this operation, 226 MB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian bullseye/main amd64 perl-modules-5.30 all 5.30.0-9 [2803 kB] Get:2 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.18.1-5 [64.5 kB] Get:3 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.18.1-5 [44.2 kB] Get:4 http://mirror-ubc.debian.org/debian bullseye/main amd64 libperl5.30 amd64 5.30.0-9 [4008 kB] Get:5 http://mirror-ubc.debian.org/debian bullseye/main amd64 perl amd64 5.30.0-9 [290 kB] Get:6 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython2.7-minimal amd64 2.7.17-1 [395 kB] Get:7 http://mirror-ubc.debian.org/debian bullseye/main amd64 python2.7-minimal amd64 2.7.17-1 [1363 kB] Get:8 http://mirror-ubc.debian.org/debian bullseye/main amd64 python2-minimal amd64 2.7.17-2 [41.4 kB] Get:9 http://mirror-ubc.debian.org/debian bullseye/main amd64 python-minimal amd64 2.7.17-2 [21.1 kB] Get:10 http://mirror-ubc.debian.org/debian bullseye/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB] Get:11 http://mirror-ubc.debian.org/debian bullseye/main amd64 mime-support all 3.64 [37.8 kB] Get:12 http://mirror-ubc.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:13 http://mirror-ubc.debian.org/debian bullseye/main amd64 readline-common all 8.0-3 [72.5 kB] Get:14 http://mirror-ubc.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.0-3 [160 kB] Get:15 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.30.1-1 [649 kB] Get:16 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython2.7-stdlib amd64 2.7.17-1 [1885 kB] Get:17 http://mirror-ubc.debian.org/debian bullseye/main amd64 python2.7 amd64 2.7.17-1 [309 kB] Get:18 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython2-stdlib amd64 2.7.17-2 [20.9 kB] Get:19 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython-stdlib amd64 2.7.17-2 [20.9 kB] Get:20 http://mirror-ubc.debian.org/debian bullseye/main amd64 python2 amd64 2.7.17-2 [41.7 kB] Get:21 http://mirror-ubc.debian.org/debian bullseye/main amd64 python amd64 2.7.17-2 [22.9 kB] Get:22 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython3.7-minimal amd64 3.7.5-2 [590 kB] Get:23 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3.7-minimal amd64 3.7.5-2 [1812 kB] Get:24 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.7.5-1 [36.6 kB] Get:25 http://mirror-ubc.debian.org/debian bullseye/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:26 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython3.7-stdlib amd64 3.7.5-2 [1732 kB] Get:27 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3.7 amd64 3.7.5-2 [347 kB] Get:28 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.7.5-1 [20.1 kB] Get:29 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3 amd64 3.7.5-1 [61.5 kB] Get:30 http://mirror-ubc.debian.org/debian bullseye/main amd64 clustalw amd64 2.1+lgpl-6 [282 kB] Get:31 http://mirror-ubc.debian.org/debian bullseye/main amd64 fonts-lyx all 2.3.3-2 [199 kB] Get:32 http://mirror-ubc.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-1 [153 kB] Get:33 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-1 [292 kB] Get:34 http://mirror-ubc.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.1-2 [392 kB] Get:35 http://mirror-ubc.debian.org/debian bullseye/main amd64 libquadmath0 amd64 9.2.1-21 [145 kB] Get:36 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgfortran5 amd64 9.2.1-21 [634 kB] Get:37 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgomp1 amd64 9.2.1-21 [88.1 kB] Get:38 http://mirror-ubc.debian.org/debian bullseye/main amd64 libjs-jquery all 3.3.1~dfsg-3 [332 kB] Get:39 http://mirror-ubc.debian.org/debian bullseye/main amd64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get:40 http://mirror-ubc.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-1 [2168 kB] Get:41 http://mirror-ubc.debian.org/debian bullseye/main amd64 liblmdb0 amd64 0.9.22-1 [45.0 kB] Get:42 http://mirror-ubc.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.3-1 [212 kB] Get:43 http://mirror-ubc.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.3-1 [104 kB] Get:44 http://mirror-ubc.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.3-1 [133 kB] Get:45 http://mirror-ubc.debian.org/debian bullseye/main amd64 ncbi-data all 6.1.20170106+dfsg1-7 [3555 kB] Get:46 http://mirror-ubc.debian.org/debian bullseye/main amd64 ncbi-blast+ amd64 2.8.1-2 [11.1 MB] Get:47 http://mirror-ubc.debian.org/debian bullseye/main amd64 ttf-bitstream-vera all 1.10-8 [352 kB] Get:48 http://mirror-ubc.debian.org/debian bullseye/main amd64 python-matplotlib-data all 3.0.2-2 [4138 kB] Get:49 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3-six all 1.13.0-1 [16.2 kB] Get:50 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3-dateutil all 2.7.3-3 [64.5 kB] Get:51 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3-pyparsing all 2.4.2-1 [106 kB] Get:52 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3-pkg-resources all 41.2.0-1 [154 kB] Get:53 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.16.5-1 [2142 kB] Get:54 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3-cycler all 0.10.0-1 [7556 B] Get:55 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3-kiwisolver amd64 1.0.1-2+b2 [86.8 kB] Get:56 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3-matplotlib amd64 3.0.2-2+b2 [5458 kB] Get:57 http://mirror-ubc.debian.org/debian bullseye/main amd64 python3-biotools all 1.2.12-4 [28.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 51.1 MB in 2s (21.5 MB/s) Selecting previously unselected package perl-modules-5.30. (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 ... 6534 files and directories currently installed.) Preparing to unpack .../00-perl-modules-5.30_5.30.0-9_all.deb ... Unpacking perl-modules-5.30 (5.30.0-9) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../01-libgdbm6_1.18.1-5_amd64.deb ... Unpacking libgdbm6:amd64 (1.18.1-5) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Unpacking python3.7-minimal (3.7.5-2) ... Setting up libssl1.1:amd64 (1.1.1d-2) ... Setting up libpython3.7-minimal:amd64 (3.7.5-2) ... Setting up libexpat1:amd64 (2.2.9-1) ... Setting up python3.7-minimal (3.7.5-2) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9606 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.7.5-1_amd64.deb ... Unpacking python3-minimal (3.7.5-1) ... 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Selecting previously unselected package libblas3:amd64. Preparing to unpack .../03-libblas3_3.9.0-1_amd64.deb ... Unpacking libblas3:amd64 (3.9.0-1) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../04-libpng16-16_1.6.37-1_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.37-1) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../05-libfreetype6_2.10.1-2_amd64.deb ... Unpacking libfreetype6:amd64 (2.10.1-2) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../06-libquadmath0_9.2.1-21_amd64.deb ... Unpacking libquadmath0:amd64 (9.2.1-21) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../07-libgfortran5_9.2.1-21_amd64.deb ... Unpacking libgfortran5:amd64 (9.2.1-21) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../08-libgomp1_9.2.1-21_amd64.deb ... Unpacking libgomp1:amd64 (9.2.1-21) ... 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Selecting previously unselected package libmbedtls12:amd64. Preparing to unpack .../15-libmbedtls12_2.16.3-1_amd64.deb ... Unpacking libmbedtls12:amd64 (2.16.3-1) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../16-ncbi-data_6.1.20170106+dfsg1-7_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg1-7) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../17-ncbi-blast+_2.8.1-2_amd64.deb ... Unpacking ncbi-blast+ (2.8.1-2) ... Selecting previously unselected package ttf-bitstream-vera. Preparing to unpack .../18-ttf-bitstream-vera_1.10-8_all.deb ... Unpacking ttf-bitstream-vera (1.10-8) ... Selecting previously unselected package python-matplotlib-data. Preparing to unpack .../19-python-matplotlib-data_3.0.2-2_all.deb ... Unpacking python-matplotlib-data (3.0.2-2) ... Selecting previously unselected package python3-six. Preparing to unpack .../20-python3-six_1.13.0-1_all.deb ... Unpacking python3-six (1.13.0-1) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../21-python3-dateutil_2.7.3-3_all.deb ... Unpacking python3-dateutil (2.7.3-3) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../22-python3-pyparsing_2.4.2-1_all.deb ... Unpacking python3-pyparsing (2.4.2-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../23-python3-pkg-resources_41.2.0-1_all.deb ... Unpacking python3-pkg-resources (41.2.0-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../24-python3-numpy_1%3a1.16.5-1_amd64.deb ... Unpacking python3-numpy (1:1.16.5-1) ... Selecting previously unselected package python3-cycler. Preparing to unpack .../25-python3-cycler_0.10.0-1_all.deb ... Unpacking python3-cycler (0.10.0-1) ... Selecting previously unselected package python3-kiwisolver. Preparing to unpack .../26-python3-kiwisolver_1.0.1-2+b2_amd64.deb ... Unpacking python3-kiwisolver (1.0.1-2+b2) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../27-python3-matplotlib_3.0.2-2+b2_amd64.deb ... Unpacking python3-matplotlib (3.0.2-2+b2) ... Selecting previously unselected package python3-biotools. Preparing to unpack .../28-python3-biotools_1.2.12-4_all.deb ... Unpacking python3-biotools (1.2.12-4) ... Setting up liblmdb0:amd64 (0.9.22-1) ... Setting up ncbi-data (6.1.20170106+dfsg1-7) ... Setting up ttf-bitstream-vera (1.10-8) ... Setting up perl-modules-5.30 (5.30.0-9) ... Setting up mime-support (3.64) ... Setting up fonts-lyx (2.3.3-2) ... Setting up libsqlite3-0:amd64 (3.30.1-1) ... Setting up libgomp1:amd64 (9.2.1-21) ... Setting up libblas3:amd64 (3.9.0-1) ... 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 libquadmath0:amd64 (9.2.1-21) ... Setting up libpng16-16:amd64 (1.6.37-1) ... Setting up libgfortran5:amd64 (9.2.1-21) ... Setting up clustalw (2.1+lgpl-6) ... Setting up libmbedcrypto3:amd64 (2.16.3-1) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3) ... Setting up python-matplotlib-data (3.0.2-2) ... Setting up readline-common (8.0-3) ... Setting up libgdbm6:amd64 (1.18.1-5) ... Setting up liblapack3:amd64 (3.9.0-1) ... 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 libmbedx509-0:amd64 (2.16.3-1) ... Setting up libreadline8:amd64 (8.0-3) ... Setting up libmbedtls12:amd64 (2.16.3-1) ... Setting up libpython2.7-stdlib:amd64 (2.7.17-1) ... Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up libfreetype6:amd64 (2.10.1-2) ... Setting up libgdbm-compat4:amd64 (1.18.1-5) ... Setting up libperl5.30:amd64 (5.30.0-9) ... Setting up libpython3.7-stdlib:amd64 (3.7.5-2) ... Setting up python2.7 (2.7.17-1) ... Setting up libpython2-stdlib:amd64 (2.7.17-2) ... Setting up python2 (2.7.17-2) ... Setting up libpython-stdlib:amd64 (2.7.17-2) ... Setting up perl (5.30.0-9) ... Setting up python (2.7.17-2) ... Setting up libpython3-stdlib:amd64 (3.7.5-1) ... Setting up python3.7 (3.7.5-2) ... Setting up python3 (3.7.5-1) ... Setting up ncbi-blast+ (2.8.1-2) ... Setting up python3-six (1.13.0-1) ... Setting up python3-pyparsing (2.4.2-1) ... Setting up python3-cycler (0.10.0-1) ... Setting up python3-dateutil (2.7.3-3) ... Setting up python3-pkg-resources (41.2.0-1) ... Setting up python3-kiwisolver (1.0.1-2+b2) ... Setting up python3-numpy (1:1.16.5-1) ... Setting up python3-matplotlib (3.0.2-2+b2) ... Setting up python3-biotools (1.2.12-4) ... Processing triggers for libc-bin (2.29-3) ... 0m41.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', '-y', 'install', 'python3-biotools'] 0m41.4s INFO: Running scripts post_install 0m41.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_install_exceptions'] 0m41.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_install_exceptions'] 0m41.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 0m42.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 0m42.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpKCn7vU to sid 0m42.0s DEBUG: sources.list: deb http://mirror-ubc.debian.org/debian/ sid main 0m42.0s INFO: Running scripts pre_distupgrade 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_distupgrade_exceptions'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_distupgrade_exceptions'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', 'update'] 0m47.5s DUMP: Get:1 http://mirror-ubc.debian.org/debian sid InRelease [142 kB] Get:2 http://mirror-ubc.debian.org/debian sid/main amd64 Packages [8206 kB] Get:3 http://mirror-ubc.debian.org/debian sid/main Translation-en [6164 kB] Fetched 14.5 MB in 4s (3738 kB/s) Reading package lists... 0m47.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', 'update'] 0m47.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', '-yf', 'dist-upgrade'] 1m2.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python python-minimal python2 python2-minimal python2.7 python2.7-minimal Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libcrypt1 libpython3.8-minimal libpython3.8-stdlib python3.8 python3.8-minimal The following packages will be upgraded: libc-bin libc6 libpython3-stdlib libselinux1 libsemanage-common libsemanage1 libsepol1 ncbi-blast+ python3 python3-biotools python3-minimal python3-numpy python3-pkg-resources 13 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 26.5 MB of archives. After this operation, 41.8 MB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.10-5 [84.8 kB] Get:2 http://mirror-ubc.debian.org/debian sid/main amd64 libc6 amd64 2.29-6 [2806 kB] Get:3 http://mirror-ubc.debian.org/debian sid/main amd64 libc-bin amd64 2.29-6 [806 kB] Get:4 http://mirror-ubc.debian.org/debian sid/main amd64 python3-minimal amd64 3.7.5-3 [36.8 kB] Get:5 http://mirror-ubc.debian.org/debian sid/main amd64 python3 amd64 3.7.5-3 [62.1 kB] Get:6 http://mirror-ubc.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.7.5-3 [20.2 kB] Get:7 http://mirror-ubc.debian.org/debian sid/main amd64 libpython3.8-minimal amd64 3.8.1~rc1-1 [749 kB] Get:8 http://mirror-ubc.debian.org/debian sid/main amd64 python3.8-minimal amd64 3.8.1~rc1-1 [1939 kB] Get:9 http://mirror-ubc.debian.org/debian sid/main amd64 libselinux1 amd64 3.0-1 [86.6 kB] Get:10 http://mirror-ubc.debian.org/debian sid/main amd64 libsepol1 amd64 3.0-1 [262 kB] Get:11 http://mirror-ubc.debian.org/debian sid/main amd64 libsemanage-common all 3.0-1 [20.9 kB] Get:12 http://mirror-ubc.debian.org/debian sid/main amd64 libsemanage1 amd64 3.0-1 [96.8 kB] Get:13 http://mirror-ubc.debian.org/debian sid/main amd64 libpython3.8-stdlib amd64 3.8.1~rc1-1 [1666 kB] Get:14 http://mirror-ubc.debian.org/debian sid/main amd64 ncbi-blast+ amd64 2.9.0-3 [11.2 MB] Get:15 http://mirror-ubc.debian.org/debian sid/main amd64 python3.8 amd64 3.8.1~rc1-1 [405 kB] Get:16 http://mirror-ubc.debian.org/debian sid/main amd64 python3-pkg-resources all 41.4.0-1 [154 kB] Get:17 http://mirror-ubc.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.17.4-4 [6150 kB] Get:18 http://mirror-ubc.debian.org/debian sid/main amd64 python3-biotools all 1.2.12-5 [28.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 26.5 MB in 1s (35.0 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12027 files and directories currently installed.) Preparing to unpack .../libc6_2.29-6_amd64.deb ... Unpacking libc6:amd64 (2.29-6) over (2.29-3) ... Selecting previously unselected package libcrypt1:amd64. Preparing to unpack .../libcrypt1_1%3a4.4.10-5_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.10-5) ... Setting up libcrypt1:amd64 (1:4.4.10-5) ... Setting up libc6:amd64 (2.29-6) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12031 files and directories currently installed.) Preparing to unpack .../python3_3.7.5-3_amd64.deb ... Unpacking python3 (3.7.5-3) over (3.7.5-1) ... Preparing to unpack .../libpython3-stdlib_3.7.5-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.7.5-3) over (3.7.5-1) ... Selecting previously unselected package libpython3.8-minimal:amd64. Preparing to unpack .../libpython3.8-minimal_3.8.1~rc1-1_amd64.deb ... Unpacking libpython3.8-minimal:amd64 (3.8.1~rc1-1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.1~rc1-1_amd64.deb ... Unpacking python3.8-minimal (3.8.1~rc1-1) ... Preparing to unpack .../libselinux1_3.0-1_amd64.deb ... Unpacking libselinux1:amd64 (3.0-1) over (2.9-3+b1) ... Setting up libselinux1:amd64 (3.0-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12312 files and directories currently installed.) Preparing to unpack .../libsepol1_3.0-1_amd64.deb ... Unpacking libsepol1:amd64 (3.0-1) over (2.9-2+b2) ... Setting up libsepol1:amd64 (3.0-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12311 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.0-1_all.deb ... Unpacking libsemanage-common (3.0-1) over (2.9-3) ... Setting up libsemanage-common (3.0-1) ... (Reading database ... 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Preparing to unpack .../3-python3-pkg-resources_41.4.0-1_all.deb ... Unpacking python3-pkg-resources (41.4.0-1) over (41.2.0-1) ... Preparing to unpack .../4-python3-numpy_1%3a1.17.4-4_amd64.deb ... Unpacking python3-numpy (1:1.17.4-4) over (1:1.16.5-1) ... Preparing to unpack .../5-python3-biotools_1.2.12-5_all.deb ... Unpacking python3-biotools (1.2.12-5) over (1.2.12-4) ... Setting up libpython3.8-minimal:amd64 (3.8.1~rc1-1) ... Setting up python3.8-minimal (3.8.1~rc1-1) ... Setting up libpython3.8-stdlib:amd64 (3.8.1~rc1-1) ... Setting up python3.8 (3.8.1~rc1-1) ... Setting up libpython3-stdlib:amd64 (3.7.5-3) ... Setting up python3 (3.7.5-3) ... Setting up ncbi-blast+ (2.9.0-3) ... Setting up python3-pkg-resources (41.4.0-1) ... Setting up python3-numpy (1:1.17.4-4) ... Setting up python3-biotools (1.2.12-5) ... Processing triggers for libc-bin (2.29-6) ... Processing triggers for mime-support (3.64) ... 1m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', '-yf', 'dist-upgrade'] 1m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m2.5s DUMP: b6bf0481e8f7e895a746087309f6c245 - 1m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'show', '--no-all-versions', 'python3-biotools'] 1m2.8s DUMP: Package: python3-biotools Source: python-biotools Version: 1.2.12-5 Installed-Size: 127 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-matplotlib, python3-numpy, python3:any, clustalw, ncbi-blast+ | ncbi-blast+-legacy Description-en: Python3 bioinformatics utilities for high-throughput genomic sequencing This package contains utilities like biotools.align - align sequences (hybrid between Needleman-Wunsch and Smith-Waterman which is used to find the subsequence within a larger sequence that best aligns to a reference) biotools.annotation - create annotation files. The annotations can be used to create a hierarchy among the annotations biotools.BLAST - manage BLAST databases and interface with the BLAST+ standalone program available from NCBI. biotools.clustal - interface to clustalw global (multiple nucleotide or peptide sequence alignment) biotools.complement - creates the complement of a sequence, which can then be reversed biotools.sequence - various tools to deal with sequences biotools.translate - translate a nucleotide using the standard genetic code . This package contains the Python3 module. Description-md5: fd0c541879ac3385f0f3a9d4fa00e433 Homepage: https://github.com/sonwell/biotools Section: python Priority: optional Filename: pool/main/p/python-biotools/python3-biotools_1.2.12-5_all.deb Size: 28880 MD5sum: b5634110e222bb7ec84fbf03d604d983 SHA256: 62e7f00a2f1019d9ae17412a78063ac4ebccef5b83d6ed82f4d0db05276eaeec 1m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'show', '--no-all-versions', 'python3-biotools'] 1m2.8s INFO: apt-cache knows about the following packages: python3-biotools 1m2.8s INFO: Running scripts pre_install 1m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_database-server'] 1m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_database-server'] 1m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_exceptions'] 1m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_exceptions'] 1m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_extras'] 1m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_extras'] 1m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_foreign_architecture'] 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_foreign_architecture'] 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'policy'] 1m2.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'policy'] 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'policy', 'python3-biotools'] 1m3.0s DUMP: python3-biotools: Installed: 1.2.12-5 Candidate: 1.2.12-5 Version table: *** 1.2.12-5 500 500 http://mirror-ubc.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'policy', 'python3-biotools'] 1m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', '-y', 'install', 'python3-biotools'] 1m3.5s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-biotools is already the newest version (1.2.12-5). The following packages were automatically installed and are no longer required: libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python python-minimal python2 python2-minimal python2.7 python2.7-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', '-y', 'install', 'python3-biotools'] 1m3.5s INFO: Running scripts post_install 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_install_exceptions'] 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_install_exceptions'] 1m3.5s INFO: Running scripts post_distupgrade 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_distupgrade_exceptions'] 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_distupgrade_exceptions'] 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_distupgrade_zz_backports'] 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_distupgrade_zz_backports'] 1m3.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 1m4.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 1m4.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 1m5.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 1m5.0s INFO: Running scripts pre_install 1m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_database-server'] 1m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_database-server'] 1m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_exceptions'] 1m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_exceptions'] 1m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_extras'] 1m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_extras'] 1m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_foreign_architecture'] 1m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_foreign_architecture'] 1m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'policy'] 1m5.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 1m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'policy'] 1m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'policy', 'python3-biotools'] 1m5.2s DUMP: python3-biotools: Installed: 1.2.12-5 Candidate: 1.2.12-5 Version table: *** 1.2.12-5 500 500 http://mirror-ubc.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-cache', 'policy', 'python3-biotools'] 1m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', '-y', 'install', 'python3-biotools=1.2.12-5'] 1m5.8s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-biotools is already the newest version (1.2.12-5). The following packages were automatically installed and are no longer required: libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python python-minimal python2 python2-minimal python2.7 python2.7-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', '-y', 'install', 'python3-biotools=1.2.12-5'] 1m5.8s INFO: Running scripts post_install 1m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_install_exceptions'] 1m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_install_exceptions'] 1m5.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 1m6.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 1m7.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', '-ac', '--ignore-obsolete'] 1m9.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', '-ac', '--ignore-obsolete'] 1m9.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m9.3s DUMP: 0.15.2 1m9.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m9.3s INFO: Running adequate version 0.15.2 now. 1m9.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'python3-biotools'] 1m9.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'python3-biotools'] 1m9.4s INFO: Running scripts pre_remove 1m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_remove_exceptions'] 1m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/pre_remove_exceptions'] 1m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m11.6s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.4 install ok installed base-files base-files 11 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-5 install ok installed bsdutils bsdutils 1:2.34-0.1 install ok installed clustalw clustalw 2.1+lgpl-6 install ok installed coreutils coreutils 8.30-3+b1 install ok installed dash dash 0.5.10.2-6 install ok installed debconf debconf 1.5.73 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.9.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.7 install ok installed e2fsprogs e2fsprogs 1.45.4-1 install ok installed fdisk fdisk 2.34-0.1 install ok installed findutils findutils 4.7.0-1 install ok installed fonts-lyx fonts-lyx 2.3.3-2 install ok installed gcc-9-base:amd64 gcc-9-base 9.2.1-21 install ok installed gpgv gpgv 2.2.17-3 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+b1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.57 install ok installed libacl1:amd64 libacl1 2.2.53-5 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-5 install ok installed libaudit-common libaudit-common 1:2.8.5-2 install ok installed libaudit1:amd64 libaudit1 1:2.8.5-2+b1 install ok installed libblas3:amd64 libblas3 3.9.0-1 install ok installed libblkid1:amd64 libblkid1 2.34-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-2 install ok installed libc-bin libc-bin 2.29-6 install ok installed libc6:amd64 libc6 2.29-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.1+b1 install ok installed libcom-err2:amd64 libcom-err2 1.45.4-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.10-5 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.250 install ok installed libexpat1:amd64 libexpat1 2.2.9-1 install ok installed libext2fs2:amd64 libext2fs2 1.45.4-1 install ok installed libfdisk1:amd64 libfdisk1 2.34-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libfreetype6:amd64 libfreetype6 2.10.1-2 install ok installed libgcc1:amd64 libgcc1 1:9.2.1-21 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.5-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.18.1-5 install ok installed libgdbm6:amd64 libgdbm6 1.18.1-5 install ok installed libgfortran5:amd64 libgfortran5 9.2.1-21 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4 install ok installed libgnutls30:amd64 libgnutls30 3.6.10-5 install ok installed libgomp1:amd64 libgomp1 9.2.1-21 install ok installed libgpg-error0:amd64 libgpg-error0 1.36-7 install ok installed libhogweed5:amd64 libhogweed5 3.5.1+really3.5.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.2.0-2 install ok installed libjs-jquery libjs-jquery 3.3.1~dfsg-3 install ok installed libjs-jquery-ui libjs-jquery-ui 1.12.1+dfsg-5 install ok installed liblapack3:amd64 liblapack3 3.9.0-1 install ok installed liblmdb0:amd64 liblmdb0 0.9.22-1 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 libmbedcrypto3:amd64 libmbedcrypto3 2.16.3-1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.3-1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.3-1 install ok installed libmount1:amd64 libmount1 2.34-0.1 install ok installed libmpdec2:amd64 libmpdec2 2.4.2-2 install ok installed libncursesw6:amd64 libncursesw6 6.1+20191019-1 install ok installed libnettle7:amd64 libnettle7 3.5.1+really3.5.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.18.1-2 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 10.34-7 install ok installed libpcre3:amd64 libpcre3 2:8.39-12+b1 install ok installed libperl5.30:amd64 libperl5.30 5.30.0-9 install ok installed libpng16-16:amd64 libpng16-16 1.6.37-1 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.17-2 install ok installed libpython2-stdlib:amd64 libpython2-stdlib 2.7.17-2 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.17-1 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.17-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.7.5-3 install ok installed libpython3.7-minimal:amd64 libpython3.7-minimal 3.7.5-2 install ok installed libpython3.7-stdlib:amd64 libpython3.7-stdlib 3.7.5-2 install ok installed libpython3.8-minimal:amd64 libpython3.8-minimal 3.8.1~rc1-1 install ok installed libpython3.8-stdlib:amd64 libpython3.8-stdlib 3.8.1~rc1-1 install ok installed libquadmath0:amd64 libquadmath0 9.2.1-21 install ok installed libreadline8:amd64 libreadline8 8.0-3 install ok installed libseccomp2:amd64 libseccomp2 2.4.2-2 install ok installed libselinux1:amd64 libselinux1 3.0-1 install ok installed libsemanage-common libsemanage-common 3.0-1 install ok installed libsemanage1:amd64 libsemanage1 3.0-1 install ok installed libsepol1:amd64 libsepol1 3.0-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.34-0.1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.30.1-1 install ok installed libss2:amd64 libss2 1.45.4-1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1d-2 install ok installed libstdc++6:amd64 libstdc++6 9.2.1-21 install ok installed libsystemd0:amd64 libsystemd0 244-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.15.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.1+20191019-1 install ok installed libudev1:amd64 libudev1 244-3 install ok installed libunistring2:amd64 libunistring2 0.9.10-2 install ok installed libuuid1:amd64 libuuid1 2.34-0.1 install ok installed libzstd1:amd64 libzstd1 1.4.4+dfsg-1 install ok installed login login 1:4.7-2 install ok installed logsave logsave 1.45.4-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mime-support mime-support 3.64 install ok installed mount mount 2.34-0.1 install ok installed ncbi-blast+ ncbi-blast+ 2.9.0-3 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-7 install ok installed ncurses-base ncurses-base 6.1+20191019-1 install ok installed ncurses-bin ncurses-bin 6.1+20191019-1 install ok installed passwd passwd 1:4.7-2 install ok installed perl perl 5.30.0-9 install ok installed perl-base perl-base 5.30.0-9 install ok installed perl-modules-5.30 perl-modules-5.30 5.30.0-9 install ok installed python python 2.7.17-2 install ok installed python-matplotlib-data python-matplotlib-data 3.0.2-2 install ok installed python-minimal python-minimal 2.7.17-2 install ok installed python2 python2 2.7.17-2 install ok installed python2-minimal python2-minimal 2.7.17-2 install ok installed python2.7 python2.7 2.7.17-1 install ok installed python2.7-minimal python2.7-minimal 2.7.17-1 install ok installed python3 python3 3.7.5-3 install ok installed python3-biotools python3-biotools 1.2.12-5 install ok installed python3-cycler python3-cycler 0.10.0-1 install ok installed python3-dateutil python3-dateutil 2.7.3-3 install ok installed python3-kiwisolver python3-kiwisolver 1.0.1-2+b2 install ok installed python3-matplotlib python3-matplotlib 3.0.2-2+b2 install ok installed python3-minimal python3-minimal 3.7.5-3 install ok installed python3-numpy python3-numpy 1:1.17.4-4 install ok installed python3-pkg-resources python3-pkg-resources 41.4.0-1 install ok installed python3-pyparsing python3-pyparsing 2.4.2-1 install ok installed python3-six python3-six 1.13.0-1 install ok installed python3.7 python3.7 3.7.5-2 install ok installed python3.7-minimal python3.7-minimal 3.7.5-2 install ok installed python3.8 python3.8 3.8.1~rc1-1 install ok installed python3.8-minimal python3.8-minimal 3.8.1~rc1-1 install ok installed readline-common readline-common 8.0-3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-1 install ok installed tar tar 1.30+dfsg-6+b1 install ok installed ttf-bitstream-vera ttf-bitstream-vera 1.10-8 install ok installed tzdata tzdata 2019c-3 install ok installed util-linux util-linux 2.34-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+b1 1m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', 'remove', 'libfreetype6:amd64', 'libmbedx509-0:amd64', 'libmbedcrypto3:amd64', 'liblmdb0:amd64', 'python3.7-minimal', 'python3-matplotlib', 'python2-minimal', 'libblas3:amd64', 'ttf-bitstream-vera', 'libpython2.7-minimal:amd64', 'libjs-jquery', 'libpython3-stdlib:amd64', 'libgdbm-compat4:amd64', 'libgfortran5:amd64', 'python3-cycler', 'python3-kiwisolver', 'libgdbm6:amd64', 'libpython2-stdlib:amd64', 'libpython3.7-stdlib:amd64', 'python3-pyparsing', 'perl', 'libssl1.1:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libpython3.8-stdlib:amd64', 'mime-support', 'libpython3.8-minimal:amd64', 'libsqlite3-0:amd64', 'libpython3.7-minimal:amd64', 'libperl5.30:amd64', 'libpng16-16:amd64', 'python3-pkg-resources', 'python3-dateutil', 'perl-modules-5.30', 'python', 'liblapack3:amd64', 'libexpat1:amd64', 'python2.7', 'python3-six', 'python3-minimal', 'python3.7', 'ncbi-data', 'libmpdec2:amd64', 'readline-common', 'python-matplotlib-data', 'ncbi-blast+-', 'python-minimal', 'python2', 'python3.8-minimal', 'libpython-stdlib:amd64', 'clustalw', 'libpython2.7-stdlib:amd64', 'libjs-jquery-ui', 'fonts-lyx', 'libmbedtls12:amd64', 'libgomp1:amd64', 'python2.7-minimal', 'python3.8', 'python3-numpy', 'python3', 'python3-biotools'] 1m15.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: clustalw fonts-lyx libblas3 libexpat1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libgomp1 libjs-jquery libjs-jquery-ui liblapack3 liblmdb0 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec2 libperl5.30 libpng16-16 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.8-minimal libpython3.8-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl1.1 mime-support ncbi-blast+ ncbi-data perl perl-modules-5.30 python python-matplotlib-data python-minimal python2 python2-minimal python2.7 python2.7-minimal python3 python3-biotools python3-cycler python3-dateutil python3-kiwisolver python3-matplotlib python3-minimal python3-numpy python3-pkg-resources python3-pyparsing python3-six python3.7 python3.7-minimal python3.8 python3.8-minimal readline-common ttf-bitstream-vera 0 upgraded, 0 newly installed, 61 to remove and 0 not upgraded. After this operation, 267 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 ... 12772 files and directories currently installed.) Removing python3-biotools (1.2.12-5) ... Removing clustalw (2.1+lgpl-6) ... Removing python3-matplotlib (3.0.2-2+b2) ... Removing python-matplotlib-data (3.0.2-2) ... Removing fonts-lyx (2.3.3-2) ... Removing python3-numpy (1:1.17.4-4) ... Removing liblapack3:amd64 (3.9.0-1) ... Removing libblas3:amd64 (3.9.0-1) ... Removing python3.8 (3.8.1~rc1-1) ... Removing python3.8-minimal (3.8.1~rc1-1) ... Removing ncbi-blast+ (2.9.0-3) ... Removing python3-dateutil (2.7.3-3) ... Removing libfreetype6:amd64 (2.10.1-2) ... Removing perl (5.30.0-9) ... Removing libperl5.30:amd64 (5.30.0-9) ... Removing libgdbm-compat4:amd64 (1.18.1-5) ... Removing libgdbm6:amd64 (1.18.1-5) ... Removing libgfortran5:amd64 (9.2.1-21) ... Removing libgomp1:amd64 (9.2.1-21) ... Removing libjs-jquery-ui (1.12.1+dfsg-5) ... Removing libjs-jquery (3.3.1~dfsg-3) ... Removing liblmdb0:amd64 (0.9.22-1) ... Removing libmbedtls12:amd64 (2.16.3-1) ... Removing libmbedx509-0:amd64 (2.16.3-1) ... Removing libmbedcrypto3:amd64 (2.16.3-1) ... Removing libpython3.8-stdlib:amd64 (3.8.1~rc1-1) ... Removing libpng16-16:amd64 (1.6.37-1) ... Removing python (2.7.17-2) ... Removing libpython-stdlib:amd64 (2.7.17-2) ... Removing python2 (2.7.17-2) ... Removing libpython2-stdlib:amd64 (2.7.17-2) ... Removing python2.7 (2.7.17-1) ... Removing libpython2.7-stdlib:amd64 (2.7.17-1) ... Removing python-minimal (2.7.17-2) ... Removing python3-kiwisolver (1.0.1-2+b2) ... Removing libpython3.8-minimal:amd64 (3.8.1~rc1-1) ... Removing libquadmath0:amd64 (9.2.1-21) ... Removing ncbi-data (6.1.20170106+dfsg1-7) ... Removing perl-modules-5.30 (5.30.0-9) ... Removing python2-minimal (2.7.17-2) ... Removing python3-cycler (0.10.0-1) ... Removing python3-pkg-resources (41.4.0-1) ... Removing python3-pyparsing (2.4.2-1) ... Removing ttf-bitstream-vera (1.10-8) ... Removing python3-six (1.13.0-1) ... Removing python3 (3.7.5-3) ... Removing python3-minimal (3.7.5-3) ... Removing python3.7 (3.7.5-2) ... Removing python2.7-minimal (2.7.17-1) ... Removing libpython2.7-minimal:amd64 (2.7.17-1) ... find: '/usr/lib/python2.7': No such file or directory Removing libpython3-stdlib:amd64 (3.7.5-3) ... Removing python3.7-minimal (3.7.5-2) ... Removing libexpat1:amd64 (2.2.9-1) ... Removing libpython3.7-stdlib:amd64 (3.7.5-2) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec2:amd64 (2.4.2-2) ... Removing libpython3.7-minimal:amd64 (3.7.5-2) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.0-3) ... Removing libsqlite3-0:amd64 (3.30.1-1) ... Removing libssl1.1:amd64 (1.1.1d-2) ... Removing mime-support (3.64) ... Removing readline-common (8.0-3) ... Processing triggers for libc-bin (2.29-6) ... 1m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', 'remove', 'libfreetype6:amd64', 'libmbedx509-0:amd64', 'libmbedcrypto3:amd64', 'liblmdb0:amd64', 'python3.7-minimal', 'python3-matplotlib', 'python2-minimal', 'libblas3:amd64', 'ttf-bitstream-vera', 'libpython2.7-minimal:amd64', 'libjs-jquery', 'libpython3-stdlib:amd64', 'libgdbm-compat4:amd64', 'libgfortran5:amd64', 'python3-cycler', 'python3-kiwisolver', 'libgdbm6:amd64', 'libpython2-stdlib:amd64', 'libpython3.7-stdlib:amd64', 'python3-pyparsing', 'perl', 'libssl1.1:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libpython3.8-stdlib:amd64', 'mime-support', 'libpython3.8-minimal:amd64', 'libsqlite3-0:amd64', 'libpython3.7-minimal:amd64', 'libperl5.30:amd64', 'libpng16-16:amd64', 'python3-pkg-resources', 'python3-dateutil', 'perl-modules-5.30', 'python', 'liblapack3:amd64', 'libexpat1:amd64', 'python2.7', 'python3-six', 'python3-minimal', 'python3.7', 'ncbi-data', 'libmpdec2:amd64', 'readline-common', 'python-matplotlib-data', 'ncbi-blast+-', 'python-minimal', 'python2', 'python3.8-minimal', 'libpython-stdlib:amd64', 'clustalw', 'libpython2.7-stdlib:amd64', 'libjs-jquery-ui', 'fonts-lyx', 'libmbedtls12:amd64', 'libgomp1:amd64', 'python2.7-minimal', 'python3.8', 'python3-numpy', 'python3', 'python3-biotools'] 1m15.7s INFO: Running scripts post_remove 1m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_remove_exceptions'] 1m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_remove_exceptions'] 1m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg', '--purge', 'libfreetype6:amd64', 'libmbedx509-0:amd64', 'libmbedcrypto3:amd64', 'liblmdb0:amd64', 'python3.7-minimal', 'python3-matplotlib', 'python2-minimal', 'libblas3:amd64', 'ttf-bitstream-vera', 'libpython2.7-minimal:amd64', 'libjs-jquery', 'libpython3-stdlib:amd64', 'libgdbm-compat4:amd64', 'libgfortran5:amd64', 'python3-cycler', 'python3-kiwisolver', 'libgdbm6:amd64', 'libpython2-stdlib:amd64', 'libpython3.7-stdlib:amd64', 'python3-pyparsing', 'perl', 'libssl1.1:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libpython3.8-stdlib:amd64', 'mime-support', 'libpython3.8-minimal:amd64', 'libsqlite3-0:amd64', 'libpython3.7-minimal:amd64', 'libperl5.30:amd64', 'libpng16-16:amd64', 'python3-pkg-resources', 'python3-dateutil', 'perl-modules-5.30', 'python', 'liblapack3:amd64', 'libexpat1:amd64', 'python2.7', 'python3-six', 'python3-minimal', 'python3.7', 'ncbi-data', 'libmpdec2:amd64', 'readline-common', 'python-matplotlib-data', 'ncbi-blast+', 'python-minimal', 'python2', 'python3.8-minimal', 'libpython-stdlib:amd64', 'clustalw', 'libpython2.7-stdlib:amd64', 'libjs-jquery-ui', 'fonts-lyx', 'libmbedtls12:amd64', 'libgomp1:amd64', 'python2.7-minimal', 'python3.8', 'python3-numpy', 'python3'] 1m15.9s DUMP: dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed (Reading database ... 6550 files and directories currently installed.) Purging configuration files for python3.7-minimal (3.7.5-2) ... dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python2-minimal which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove ttf-bitstream-vera which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.17-1) ... dpkg: warning: ignoring request to remove libjs-jquery which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libpython2-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.7-stdlib which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed Purging configuration files for perl (5.30.0-9) ... Purging configuration files for libssl1.1:amd64 (1.1.1d-2) ... 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 libpython3.8-stdlib which isn't installed Purging configuration files for mime-support (3.64) ... Purging configuration files for libpython3.8-minimal:amd64 (3.8.1~rc1-1) ... dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed Purging configuration files for libpython3.7-minimal:amd64 (3.7.5-2) ... dpkg: warning: ignoring request to remove libperl5.30 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove perl-modules-5.30 which isn't installed Purging configuration files for python (2.7.17-2) ... dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.7 which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-7) ... dpkg: warning: ignoring request to remove libmpdec2 which isn't installed Purging configuration files for readline-common (8.0-3) ... Purging configuration files for python-matplotlib-data (3.0.2-2) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python2 which isn't installed Purging configuration files for python3.8-minimal (3.8.1~rc1-1) ... dpkg: warning: ignoring request to remove libpython-stdlib which isn't installed Purging configuration files for clustalw (2.1+lgpl-6) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed Purging configuration files for libjs-jquery-ui (1.12.1+dfsg-5) ... dpkg: warning: ignoring request to remove fonts-lyx which isn't installed dpkg: warning: ignoring request to remove libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed Purging configuration files for python2.7-minimal (2.7.17-1) ... dpkg: warning: ignoring request to remove python3.8 which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed Purging configuration files for python3 (3.7.5-3) ... 1m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg', '--purge', 'libfreetype6:amd64', 'libmbedx509-0:amd64', 'libmbedcrypto3:amd64', 'liblmdb0:amd64', 'python3.7-minimal', 'python3-matplotlib', 'python2-minimal', 'libblas3:amd64', 'ttf-bitstream-vera', 'libpython2.7-minimal:amd64', 'libjs-jquery', 'libpython3-stdlib:amd64', 'libgdbm-compat4:amd64', 'libgfortran5:amd64', 'python3-cycler', 'python3-kiwisolver', 'libgdbm6:amd64', 'libpython2-stdlib:amd64', 'libpython3.7-stdlib:amd64', 'python3-pyparsing', 'perl', 'libssl1.1:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libpython3.8-stdlib:amd64', 'mime-support', 'libpython3.8-minimal:amd64', 'libsqlite3-0:amd64', 'libpython3.7-minimal:amd64', 'libperl5.30:amd64', 'libpng16-16:amd64', 'python3-pkg-resources', 'python3-dateutil', 'perl-modules-5.30', 'python', 'liblapack3:amd64', 'libexpat1:amd64', 'python2.7', 'python3-six', 'python3-minimal', 'python3.7', 'ncbi-data', 'libmpdec2:amd64', 'readline-common', 'python-matplotlib-data', 'ncbi-blast+', 'python-minimal', 'python2', 'python3.8-minimal', 'libpython-stdlib:amd64', 'clustalw', 'libpython2.7-stdlib:amd64', 'libjs-jquery-ui', 'fonts-lyx', 'libmbedtls12:amd64', 'libgomp1:amd64', 'python2.7-minimal', 'python3.8', 'python3-numpy', 'python3'] 1m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg', '--purge', 'python3-biotools'] 1m16.0s DUMP: dpkg: warning: ignoring request to remove python3-biotools which isn't installed 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg', '--purge', 'python3-biotools'] 1m16.0s INFO: Running scripts post_purge 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_purge_exceptions'] 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_purge_exceptions'] 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg', '--purge', '--pending'] 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg', '--purge', '--pending'] 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg', '--remove', '--pending'] 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg', '--remove', '--pending'] 1m16.0s INFO: Running scripts post_test 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_test_exceptions'] 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'tmp/scripts/post_test_exceptions'] 1m16.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 1m16.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 1m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg-divert', '--list'] 1m16.5s 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 1m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'dpkg-divert', '--list'] 1m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', 'clean'] 1m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKCn7vU', 'apt-get', 'clean'] 1m16.5s DEBUG: Recording chroot state 1m18.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/shm'] 1m18.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/shm'] 1m18.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/console'] 1m18.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/console'] 1m18.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/ptmx'] 1m18.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/ptmx'] 1m18.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/pts'] 1m18.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/dev/pts'] 1m18.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/proc'] 1m18.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpKCn7vU/proc'] 1m18.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 1m18.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpKCn7vU'] 1m18.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpKCn7vU 1m18.5s INFO: PASS: Upgrading between Debian distributions. 1m18.5s INFO: PASS: All tests. 1m18.5s INFO: piuparts run ends. ret=0 End: 2019-12-13 15:16:20 UTC