Start: 2023-01-18 13:44:04 GMT [stretch] Package: pbgenomicconsensus Version: 2.1.0-1 Installed-Size: 67 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any, python-pkg-resources, python-pbgenomicconsensus (= 2.1.0-1) Recommends: python-consensuscore2 Description: Pacific Biosciences variant and consensus caller Homepage: https://github.com/PacificBiosciences/GenomicConsensus Description-md5: eb02e6be4887292eba0a2cc667e114d6 Section: science Priority: optional Filename: pool/main/p/pbgenomicconsensus/pbgenomicconsensus_2.1.0-1_all.deb Size: 26556 MD5sum: e310a37b7b32d8e2730cb690d99377f7 SHA256: 3b4e1676e11f5df9a439ae1302a89c20e173612e4f9062e95c67076188efab53 [stretch-lts] Package: pbgenomicconsensus Version: 2.1.0-1 Installed-Size: 67 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any, python-pkg-resources, python-pbgenomicconsensus (= 2.1.0-1) Recommends: python-consensuscore2 Description: Pacific Biosciences variant and consensus caller Homepage: https://github.com/PacificBiosciences/GenomicConsensus Description-md5: eb02e6be4887292eba0a2cc667e114d6 Section: science Priority: optional Filename: pool/main/p/pbgenomicconsensus/pbgenomicconsensus_2.1.0-1_all.deb Size: 26556 MD5sum: e310a37b7b32d8e2730cb690d99377f7 SHA256: 3b4e1676e11f5df9a439ae1302a89c20e173612e4f9062e95c67076188efab53 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d stretch-lts -B /srv/piuparts.debian.org/slave/refchroot/stretch2next/reference-chroot-metadata.dat --apt pbgenomicconsensus=2.1.0-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d stretch-lts -B /srv/piuparts.debian.org/slave/refchroot/stretch2next/reference-chroot-metadata.dat --apt pbgenomicconsensus=2.1.0-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpuxl56u32 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpuxl56u32 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.8s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/proc'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/proc'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/pts'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/pts'] 0m1.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/ptmx'] 0m1.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/ptmx'] 0m1.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/console'] 0m1.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/console'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/shm'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/shm'] 0m1.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.8s DEBUG: Created policy-rc.d and chmodded it. 0m1.8s DEBUG: Created resolv.conf. 0m1.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpuxl56u32/tmp/scripts/ 0m1.8s INFO: Running scripts post_chroot_unpack 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', 'update'] 0m3.0s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', 'update'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.6s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.6s INFO: Running scripts post_setup 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_setup_dummy_users'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_setup_dummy_users'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_setup_forbid_home'] 0m4.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_setup_forbid_home'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_setup_zz_backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_setup_zz_backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.8s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2next/reference-chroot-metadata.dat 0m4.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m5.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m5.1s INFO: Running scripts is_testable 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/is_testable_uninstallable'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/is_testable_uninstallable'] 0m5.1s INFO: Running scripts pre_test 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_test_exceptions'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_test_exceptions'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_test_root_password'] 0m5.1s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_test_root_password'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'show', '--no-all-versions', 'pbgenomicconsensus'] 0m5.3s DUMP: Package: pbgenomicconsensus Version: 2.1.0-1 Installed-Size: 67 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any, python-pkg-resources, python-pbgenomicconsensus (= 2.1.0-1) Recommends: python-consensuscore2 Description-en: Pacific Biosciences variant and consensus caller The GenomicConsensus package provides Quiver, Pacific Biosciences' flagship consensus and variant caller. Quiver is an algorithm that finds the maximum likelihood template sequence given PacBio reads of the template. These reads are modeled using a conditional random field approach that prescribes a probability to a read given a template sequence. In addition to the base sequence of each read, Quiver uses several additional quality value covariates that the base caller provides. . This package is part of the SMRTAnalysis suite Description-md5: eb02e6be4887292eba0a2cc667e114d6 Homepage: https://github.com/PacificBiosciences/GenomicConsensus Section: science Priority: optional Filename: pool/main/p/pbgenomicconsensus/pbgenomicconsensus_2.1.0-1_all.deb Size: 26556 MD5sum: e310a37b7b32d8e2730cb690d99377f7 SHA256: 3b4e1676e11f5df9a439ae1302a89c20e173612e4f9062e95c67076188efab53 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'show', '--no-all-versions', 'pbgenomicconsensus'] 0m5.3s INFO: apt-cache knows about the following packages: pbgenomicconsensus 0m5.3s INFO: Running scripts pre_install 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_database-server'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_database-server'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_exceptions'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_exceptions'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_extras'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_extras'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'policy'] 0m5.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'policy'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'policy', 'pbgenomicconsensus'] 0m5.5s DUMP: pbgenomicconsensus: Installed: (none) Candidate: 2.1.0-1 Version table: 2.1.0-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'policy', 'pbgenomicconsensus'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', '-y', 'install', 'pbgenomicconsensus'] 0m22.0s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates libaec0 libblas-common libblas3 libcurl3-gnutls libexpat1 libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libnettle6 libnghttp2-14 libp11-kit0 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 mime-support openssl python python-avro python-chardet python-h5py python-iso8601 python-minimal python-numpy python-pbcommand python-pbconsensuscore python-pbcore python-pbgenomicconsensus python-pkg-resources python-pysam python-requests python-six python-urllib3 python2.7 python2.7-minimal readline-common Suggested packages: gnutls-bin krb5-doc krb5-user python-doc python-tk python-h5py-doc gcc gfortran python-dev python-nose python-numpy-dbg python-numpy-doc python-pbcore-doc python-consensuscore2 python-setuptools python-cryptography python-idna python-openssl python-socks python-ntlm python2.7-doc binutils binfmt-support readline-doc Recommended packages: krb5-locales publicsuffix libsasl2-modules bzip2 file xz-utils python-consensuscore2 python-cryptography python-idna python-ipaddress python-openssl The following NEW packages will be installed: ca-certificates libaec0 libblas-common libblas3 libcurl3-gnutls libexpat1 libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libnettle6 libnghttp2-14 libp11-kit0 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 mime-support openssl pbgenomicconsensus python python-avro python-chardet python-h5py python-iso8601 python-minimal python-numpy python-pbcommand python-pbconsensuscore python-pbcore python-pbgenomicconsensus python-pkg-resources python-pysam python-requests python-six python-urllib3 python2.7 python2.7-minimal readline-common 0 upgraded, 63 newly installed, 0 to remove and 0 not upgraded. Need to get 29.8 MB of archives. After this operation, 90.3 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u3 [389 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u3 [1382 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u3 [83.7 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 python amd64 2.7.13-2 [154 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b2 [192 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b2 [136 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libtasn1-6 amd64 4.10-1.1+deb9u1 [50.6 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 libgnutls30 amd64 3.5.8-5+deb9u5 [896 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 libkrb5support0 amd64 1.15-1+deb9u1 [61.9 kB] Get:24 http://deb.debian.org/debian stretch/main amd64 libk5crypto3 amd64 1.15-1+deb9u1 [119 kB] Get:25 http://deb.debian.org/debian stretch/main amd64 libkrb5-3 amd64 1.15-1+deb9u1 [311 kB] Get:26 http://deb.debian.org/debian stretch/main amd64 libgssapi-krb5-2 amd64 1.15-1+deb9u1 [155 kB] Get:27 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [68.4 kB] Get:28 http://deb.debian.org/debian stretch/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [105 kB] Get:29 http://deb.debian.org/debian stretch/main amd64 libldap-common all 2.4.44+dfsg-5+deb9u4 [85.7 kB] Get:30 http://deb.debian.org/debian stretch/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u4 [219 kB] Get:31 http://deb.debian.org/debian stretch/main amd64 openssl amd64 1.1.0l-1~deb9u1 [749 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 ca-certificates all 20200601~deb9u1 [160 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 libaec0 amd64 0.3.2-1 [18.5 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 libblas-common amd64 3.7.0-2 [14.2 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 libblas3 amd64 3.7.0-2 [155 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:43 http://deb.debian.org/debian stretch/main amd64 libssh2-1 amd64 1.7.0-1+deb9u1 [139 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u10 [290 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 libsz2 amd64 0.3.2-1 [5730 B] Get:46 http://deb.debian.org/debian stretch/main amd64 libhdf5-100 amd64 1.10.0-patch1+docs-3+deb9u1 [1282 kB] Get:47 http://deb.debian.org/debian stretch/main amd64 libhts1 amd64 1.3.2-2 [257 kB] Get:48 http://deb.debian.org/debian stretch/main amd64 liblapack3 amd64 3.7.0-2 [2141 kB] Get:49 http://deb.debian.org/debian stretch/main amd64 python-pkg-resources all 33.1.1-1 [166 kB] Get:50 http://deb.debian.org/debian stretch/main amd64 python-numpy amd64 1:1.12.1-3 [1936 kB] Get:51 http://deb.debian.org/debian stretch/main amd64 python-six all 1.10.0-3 [14.4 kB] Get:52 http://deb.debian.org/debian stretch/main amd64 python-h5py amd64 2.7.0-1 [634 kB] Get:53 http://deb.debian.org/debian stretch/main amd64 python-avro all 1.8.1+dfsg-1 [58.1 kB] Get:54 http://deb.debian.org/debian stretch/main amd64 python-iso8601 all 0.1.11-1 [12.7 kB] Get:55 http://deb.debian.org/debian stretch/main amd64 python-urllib3 all 1.19.1-1 [77.5 kB] Get:56 http://deb.debian.org/debian stretch/main amd64 python-chardet all 2.3.0-2 [96.0 kB] Get:57 http://deb.debian.org/debian stretch/main amd64 python-requests all 2.12.4-1 [101 kB] Get:58 http://deb.debian.org/debian stretch/main amd64 python-pbcommand all 0.5.3-1 [79.6 kB] Get:59 http://deb.debian.org/debian stretch/main amd64 python-pbconsensuscore amd64 1.0.2-2 [651 kB] Get:60 http://deb.debian.org/debian stretch/main amd64 python-pysam amd64 0.10.0+ds-2 [1301 kB] Get:61 http://deb.debian.org/debian stretch/main amd64 python-pbcore all 1.2.11+dfsg-1 [9087 kB] Get:62 http://deb.debian.org/debian stretch/main amd64 python-pbgenomicconsensus all 2.1.0-1 [45.7 kB] Get:63 http://deb.debian.org/debian stretch/main amd64 pbgenomicconsensus all 2.1.0-1 [26.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 29.8 MB in 1s (27.8 MB/s) Selecting previously unselected package libpython2.7-minimal:amd64. (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 ... 4411 files and directories currently installed.) Preparing to unpack .../00-libpython2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../01-python2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking python2.7-minimal (2.7.13-2+deb9u3) ... Selecting previously unselected package python-minimal. 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Selecting previously unselected package python. (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 ... 5237 files and directories currently installed.) Preparing to unpack .../00-python_2.7.13-2_amd64.deb ... Unpacking python (2.7.13-2) ... Selecting previously unselected package libgmp10:amd64. Preparing to unpack .../01-libgmp10_2%3a6.1.2+dfsg-1_amd64.deb ... Unpacking libgmp10:amd64 (2:6.1.2+dfsg-1) ... Selecting previously unselected package libnettle6:amd64. 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Preparing to unpack .../47-python-pbcore_1.2.11+dfsg-1_all.deb ... Unpacking python-pbcore (1.2.11+dfsg-1) ... Selecting previously unselected package python-pbgenomicconsensus. Preparing to unpack .../48-python-pbgenomicconsensus_2.1.0-1_all.deb ... Unpacking python-pbgenomicconsensus (2.1.0-1) ... Selecting previously unselected package pbgenomicconsensus. Preparing to unpack .../49-pbgenomicconsensus_2.1.0-1_all.deb ... Unpacking pbgenomicconsensus (2.1.0-1) ... Setting up libquadmath0:amd64 (6.3.0-18+deb9u1) ... Setting up readline-common (7.0-3) ... Setting up libnettle6:amd64 (3.3-1+b2) ... Setting up libaec0:amd64 (0.3.2-1) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u3) ... Setting up libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Setting up mime-support (3.60) ... Setting up libldap-common (2.4.44+dfsg-5+deb9u4) ... Setting up libreadline7:amd64 (7.0-3) ... Setting up libblas-common (3.7.0-2) ... Setting up libgfortran3:amd64 (6.3.0-18+deb9u1) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-1) ... Setting up libblas3 (3.7.0-2) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libssh2-1:amd64 (1.7.0-1+deb9u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Setting up openssl (1.1.0l-1~deb9u1) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 126 added, 0 removed; done. Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up libidn11:amd64 (1.33-1+deb9u1) ... Setting up libsz2:amd64 (0.3.2-1) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up liblapack3 (3.7.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u1) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up python (2.7.13-2) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up python-avro (1.8.1+dfsg-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up python-pkg-resources (33.1.1-1) ... Setting up python-numpy (1:1.12.1-3) ... Setting up python-six (1.10.0-3) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Setting up python-iso8601 (0.1.11-1) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up python-pbconsensuscore (1.0.2-2) ... Setting up python-urllib3 (1.19.1-1) ... Setting up python-h5py (2.7.0-1) ... Setting up python-chardet (2.3.0-2) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up python-requests (2.12.4-1) ... Setting up python-pbcommand (0.5.3-1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Setting up libhts1:amd64 (1.3.2-2) ... Setting up python-pysam (0.10.0+ds-2) ... Setting up python-pbcore (1.2.11+dfsg-1) ... Setting up python-pbgenomicconsensus (2.1.0-1) ... Setting up pbgenomicconsensus (2.1.0-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Processing triggers for ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', '-y', 'install', 'pbgenomicconsensus'] 0m22.0s INFO: Running scripts post_install 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_install_exceptions'] 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_install_exceptions'] 0m22.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m22.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m22.4s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpuxl56u32 to stretch-lts 0m22.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main deb http://security.debian.org stretch/updates main 0m22.4s INFO: Running scripts pre_distupgrade 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_distupgrade_exceptions'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_distupgrade_exceptions'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', 'update'] 0m23.9s DUMP: Get:1 http://security.debian.org stretch/updates InRelease [59.1 kB] Ign:2 http://deb.debian.org/debian stretch InRelease Hit:3 http://deb.debian.org/debian stretch Release Get:4 http://security.debian.org stretch/updates/main amd64 Packages [782 kB] Get:5 http://security.debian.org stretch/updates/main Translation-en [368 kB] Fetched 1209 kB in 0s (2065 kB/s) Reading package lists... 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', 'update'] 0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', '-yf', 'dist-upgrade'] 0m40.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt ca-certificates debian-archive-keyring dpkg e2fslibs e2fsprogs gzip libapt-pkg5.0 libcomerr2 libcurl3-gnutls libexpat1 libgcrypt20 libgmp10 libgnutls30 libgssapi-krb5-2 libhogweed4 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblz4-1 liblzma5 libnettle6 libnghttp2-14 libp11-kit0 libpython2.7-minimal libpython2.7-stdlib libsasl2-2 libsasl2-modules-db libsqlite3-0 libss2 libssh2-1 libssl1.1 libsystemd0 libudev1 login openssl passwd python-urllib3 python2.7 python2.7-minimal tar zlib1g 44 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 19.8 MB of archives. After this operation, 96.3 kB of additional disk space will be used. Get:1 http://security.debian.org stretch/updates/main amd64 tar amd64 1.29b-1.1+deb9u1 [760 kB] Get:2 http://security.debian.org stretch/updates/main amd64 dpkg amd64 1.18.26 [2117 kB] Get:3 http://security.debian.org stretch/updates/main amd64 e2fslibs amd64 1.43.4-2+deb9u2 [208 kB] Get:4 http://security.debian.org stretch/updates/main amd64 e2fsprogs amd64 1.43.4-2+deb9u2 [948 kB] Get:5 http://security.debian.org stretch/updates/main amd64 gzip amd64 1.6-5+deb9u1 [114 kB] Get:6 http://security.debian.org stretch/updates/main amd64 login amd64 1:4.4-4.1+deb9u1 [790 kB] Get:7 http://security.debian.org stretch/updates/main amd64 debian-archive-keyring all 2017.5+deb9u2 [92.4 kB] Get:8 http://security.debian.org stretch/updates/main amd64 liblz4-1 amd64 0.0~r131-2+deb9u1 [33.2 kB] Get:9 http://security.debian.org stretch/updates/main amd64 liblzma5 amd64 5.2.2-1.2+deb9u1 [234 kB] Get:10 http://security.debian.org stretch/updates/main amd64 zlib1g amd64 1:1.2.8.dfsg-5+deb9u1 [87.8 kB] Get:11 http://security.debian.org stretch/updates/main amd64 libapt-pkg5.0 amd64 1.4.11 [917 kB] Get:12 http://security.debian.org stretch/updates/main amd64 apt amd64 1.4.11 [1232 kB] Get:13 http://security.debian.org stretch/updates/main amd64 libsystemd0 amd64 232-25+deb9u14 [282 kB] Get:14 http://security.debian.org stretch/updates/main amd64 python2.7 amd64 2.7.13-2+deb9u6 [286 kB] Get:15 http://security.debian.org stretch/updates/main amd64 libexpat1 amd64 2.2.0-2+deb9u5 [84.7 kB] Get:16 http://security.debian.org stretch/updates/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u3 [574 kB] Get:17 http://security.debian.org stretch/updates/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u6 [1360 kB] Get:18 http://security.debian.org stretch/updates/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u6 [1898 kB] Get:19 http://security.debian.org stretch/updates/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u6 [1382 kB] Get:20 http://security.debian.org stretch/updates/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u6 [390 kB] Get:21 http://security.debian.org stretch/updates/main amd64 libcomerr2 amd64 1.43.4-2+deb9u2 [63.8 kB] Get:22 http://security.debian.org stretch/updates/main amd64 libss2 amd64 1.43.4-2+deb9u2 [68.0 kB] Get:23 http://security.debian.org stretch/updates/main amd64 passwd amd64 1:4.4-4.1+deb9u1 [997 kB] Get:24 http://security.debian.org stretch/updates/main amd64 libudev1 amd64 232-25+deb9u14 [126 kB] Get:25 http://security.debian.org stretch/updates/main amd64 libgcrypt20 amd64 1.7.6-2+deb9u4 [523 kB] Get:26 http://security.debian.org stretch/updates/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1+deb9u1 [253 kB] Get:27 http://security.debian.org stretch/updates/main amd64 libhogweed4 amd64 3.3-1+deb9u1 [136 kB] Get:28 http://security.debian.org stretch/updates/main amd64 libnettle6 amd64 3.3-1+deb9u1 [192 kB] Get:29 http://security.debian.org stretch/updates/main amd64 libp11-kit0 amd64 0.23.3-2+deb9u1 [112 kB] Get:30 http://security.debian.org stretch/updates/main amd64 libgnutls30 amd64 3.5.8-5+deb9u6 [897 kB] Get:31 http://security.debian.org stretch/updates/main amd64 libgssapi-krb5-2 amd64 1.15-1+deb9u3 [155 kB] Get:32 http://security.debian.org stretch/updates/main amd64 libkrb5-3 amd64 1.15-1+deb9u3 [312 kB] Get:33 http://security.debian.org stretch/updates/main amd64 libkrb5support0 amd64 1.15-1+deb9u3 [62.3 kB] Get:34 http://security.debian.org stretch/updates/main amd64 libk5crypto3 amd64 1.15-1+deb9u3 [120 kB] Get:35 http://security.debian.org stretch/updates/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u2 [68.5 kB] Get:36 http://security.debian.org stretch/updates/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u2 [105 kB] Get:37 http://security.debian.org stretch/updates/main amd64 libldap-common all 2.4.44+dfsg-5+deb9u9 [86.3 kB] Get:38 http://security.debian.org stretch/updates/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u9 [220 kB] Get:39 http://security.debian.org stretch/updates/main amd64 openssl amd64 1.1.0l-1~deb9u6 [749 kB] Get:40 http://security.debian.org stretch/updates/main amd64 ca-certificates all 20200601~deb9u2 [168 kB] Get:41 http://security.debian.org stretch/updates/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u2 [79.4 kB] Get:42 http://security.debian.org stretch/updates/main amd64 libssh2-1 amd64 1.7.0-1+deb9u2 [139 kB] Get:43 http://security.debian.org stretch/updates/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u16 [296 kB] Get:44 http://security.debian.org stretch/updates/main amd64 python-urllib3 all 1.19.1-1+deb9u1 [78.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.8 MB in 0s (50.6 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 ... 6951 files and directories currently installed.) Preparing to unpack .../tar_1.29b-1.1+deb9u1_amd64.deb ... Unpacking tar (1.29b-1.1+deb9u1) over (1.29b-1.1) ... Setting up tar (1.29b-1.1+deb9u1) ... (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 ... 6952 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.7.6-2+deb9u4_amd64.deb ... Unpacking libgcrypt20:amd64 (1.7.6-2+deb9u4) over (1.7.6-2+deb9u3) ... Setting up libgcrypt20:amd64 (1.7.6-2+deb9u4) ... (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 ... 6952 files and directories currently installed.) Preparing to unpack .../00-libgmp10_2%3a6.1.2+dfsg-1+deb9u1_amd64.deb ... Unpacking libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) over (2:6.1.2+dfsg-1) ... Preparing to unpack .../01-libhogweed4_3.3-1+deb9u1_amd64.deb ... Unpacking libhogweed4:amd64 (3.3-1+deb9u1) over (3.3-1+b2) ... Preparing to unpack .../02-libnettle6_3.3-1+deb9u1_amd64.deb ... Unpacking libnettle6:amd64 (3.3-1+deb9u1) over (3.3-1+b2) ... 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Unpacking libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) over (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Preparing to unpack .../10-libsasl2-2_2.1.27~101-g0780600+dfsg-3+deb9u2_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) over (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Preparing to unpack .../11-libldap-common_2.4.44+dfsg-5+deb9u9_all.deb ... Unpacking libldap-common (2.4.44+dfsg-5+deb9u9) over (2.4.44+dfsg-5+deb9u4) ... Preparing to unpack .../12-libldap-2.4-2_2.4.44+dfsg-5+deb9u9_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u9) over (2.4.44+dfsg-5+deb9u4) ... Preparing to unpack .../13-openssl_1.1.0l-1~deb9u6_amd64.deb ... Unpacking openssl (1.1.0l-1~deb9u6) over (1.1.0l-1~deb9u1) ... Preparing to unpack .../14-ca-certificates_20200601~deb9u2_all.deb ... Unpacking ca-certificates (20200601~deb9u2) over (20200601~deb9u1) ... Preparing to unpack .../15-libnghttp2-14_1.18.1-1+deb9u2_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.18.1-1+deb9u2) over (1.18.1-1+deb9u1) ... Preparing to unpack .../16-libssh2-1_1.7.0-1+deb9u2_amd64.deb ... Unpacking libssh2-1:amd64 (1.7.0-1+deb9u2) over (1.7.0-1+deb9u1) ... Preparing to unpack .../17-libcurl3-gnutls_7.52.1-5+deb9u16_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.52.1-5+deb9u16) over (7.52.1-5+deb9u10) ... Preparing to unpack .../18-python-urllib3_1.19.1-1+deb9u1_all.deb ... Unpacking python-urllib3 (1.19.1-1+deb9u1) over (1.19.1-1) ... Setting up libnettle6:amd64 (3.3-1+deb9u1) ... Setting up python-urllib3 (1.19.1-1+deb9u1) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u5) ... Setting up libnghttp2-14:amd64 (1.18.1-1+deb9u2) ... Processing triggers for mime-support (3.60) ... Setting up libldap-common (2.4.44+dfsg-5+deb9u9) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u3) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) ... Setting up libssh2-1:amd64 (1.7.0-1+deb9u2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u6) ... Setting up libp11-kit0:amd64 (0.23.3-2+deb9u1) ... Setting up openssl (1.1.0l-1~deb9u6) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u3) ... Setting up libpython2.7-minimal:amd64 (2.7.13-2+deb9u6) ... Setting up ca-certificates (20200601~deb9u2) ... Updating certificates in /etc/ssl/certs... 11 added, 0 removed; done. Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u6) ... Setting up python2.7-minimal (2.7.13-2+deb9u6) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u3) ... Setting up python2.7 (2.7.13-2+deb9u6) ... Setting up libhogweed4:amd64 (3.3-1+deb9u1) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u3) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u6) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u9) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u16) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Processing triggers for ca-certificates (20200601~deb9u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', '-yf', 'dist-upgrade'] 0m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m40.3s DUMP: f0660a0a38f941b755664f52e8306b99 - 0m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m40.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'show', '--no-all-versions', 'pbgenomicconsensus'] 0m40.5s DUMP: Package: pbgenomicconsensus Version: 2.1.0-1 Installed-Size: 67 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any, python-pkg-resources, python-pbgenomicconsensus (= 2.1.0-1) Recommends: python-consensuscore2 Description-en: Pacific Biosciences variant and consensus caller The GenomicConsensus package provides Quiver, Pacific Biosciences' flagship consensus and variant caller. Quiver is an algorithm that finds the maximum likelihood template sequence given PacBio reads of the template. These reads are modeled using a conditional random field approach that prescribes a probability to a read given a template sequence. In addition to the base sequence of each read, Quiver uses several additional quality value covariates that the base caller provides. . This package is part of the SMRTAnalysis suite Description-md5: eb02e6be4887292eba0a2cc667e114d6 Homepage: https://github.com/PacificBiosciences/GenomicConsensus Section: science Priority: optional Filename: pool/main/p/pbgenomicconsensus/pbgenomicconsensus_2.1.0-1_all.deb Size: 26556 MD5sum: e310a37b7b32d8e2730cb690d99377f7 SHA256: 3b4e1676e11f5df9a439ae1302a89c20e173612e4f9062e95c67076188efab53 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'show', '--no-all-versions', 'pbgenomicconsensus'] 0m40.5s INFO: apt-cache knows about the following packages: pbgenomicconsensus 0m40.5s INFO: Running scripts pre_install 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_database-server'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_database-server'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_exceptions'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_exceptions'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_extras'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_extras'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_foreign_architecture'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_foreign_architecture'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'policy'] 0m40.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org stretch/updates/main amd64 Packages release v=9,o=Debian,a=oldoldstable,n=stretch,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m40.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'policy'] 0m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'policy', 'pbgenomicconsensus'] 0m40.7s DUMP: pbgenomicconsensus: Installed: 2.1.0-1 Candidate: 2.1.0-1 Version table: *** 2.1.0-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'policy', 'pbgenomicconsensus'] 0m40.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', '-y', 'install', 'pbgenomicconsensus'] 0m41.1s DUMP: Reading package lists... Building dependency tree... Reading state information... pbgenomicconsensus is already the newest version (2.1.0-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m41.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', '-y', 'install', 'pbgenomicconsensus'] 0m41.1s INFO: Running scripts post_install 0m41.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_install_exceptions'] 0m41.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_install_exceptions'] 0m41.1s INFO: Running scripts post_distupgrade 0m41.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m41.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m41.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_distupgrade_exceptions'] 0m41.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_distupgrade_exceptions'] 0m41.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_distupgrade_zz_backports'] 0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_distupgrade_zz_backports'] 0m41.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m41.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m41.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m41.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m41.9s INFO: Running scripts pre_install 0m41.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_database-server'] 0m41.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_database-server'] 0m41.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_exceptions'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_exceptions'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_extras'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_extras'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'policy'] 0m42.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org stretch/updates/main amd64 Packages release v=9,o=Debian,a=oldoldstable,n=stretch,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'policy'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'policy', 'pbgenomicconsensus'] 0m42.1s DUMP: pbgenomicconsensus: Installed: 2.1.0-1 Candidate: 2.1.0-1 Version table: *** 2.1.0-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-cache', 'policy', 'pbgenomicconsensus'] 0m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', '-y', 'install', 'pbgenomicconsensus=2.1.0-1'] 0m42.4s DUMP: Reading package lists... Building dependency tree... Reading state information... pbgenomicconsensus is already the newest version (2.1.0-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', '-y', 'install', 'pbgenomicconsensus=2.1.0-1'] 0m42.4s INFO: Running scripts post_install 0m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_install_exceptions'] 0m42.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_install_exceptions'] 0m42.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m42.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m43.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', '-ac', '--ignore-obsolete'] 0m44.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', '-ac', '--ignore-obsolete'] 0m44.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m44.0s DUMP: 0.15.6 0m44.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m44.0s INFO: Running adequate version 0.15.6 now. 0m44.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'pbgenomicconsensus'] 0m44.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'pbgenomicconsensus'] 0m44.2s INFO: Running scripts pre_remove 0m44.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m44.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m44.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m44.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m44.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m45.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m45.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_remove_exceptions'] 0m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/pre_remove_exceptions'] 0m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m45.4s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.11 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed ca-certificates ca-certificates 20200601~deb9u2 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u2 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.26 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u2 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u2 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+deb9u1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libaec0:amd64 libaec0 0.3.2-1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.11 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblas-common libblas-common 3.7.0-2 install ok installed libblas3 libblas3 3.7.0-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u2 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.52.1-5+deb9u16 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libexpat1:amd64 libexpat1 2.2.0-2+deb9u5 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libffi6:amd64 libffi6 3.2.1-6 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u4 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-1+deb9u1 install ok installed libgnutls30:amd64 libgnutls30 3.5.8-5+deb9u6 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.15-1+deb9u3 install ok installed libhdf5-100:amd64 libhdf5-100 1.10.0-patch1+docs-3+deb9u1 install ok installed libhogweed4:amd64 libhogweed4 3.3-1+deb9u1 install ok installed libhts1:amd64 libhts1 1.3.2-2 install ok installed libidn11:amd64 libidn11 1.33-1+deb9u1 install ok installed libidn2-0:amd64 libidn2-0 0.16-1+deb9u1 install ok installed libk5crypto3:amd64 libk5crypto3 1.15-1+deb9u3 install ok installed libkeyutils1:amd64 libkeyutils1 1.5.9-9 install ok installed libkrb5-3:amd64 libkrb5-3 1.15-1+deb9u3 install ok installed libkrb5support0:amd64 libkrb5support0 1.15-1+deb9u3 install ok installed liblapack3 liblapack3 3.7.0-2 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.44+dfsg-5+deb9u9 install ok installed libldap-common libldap-common 2.4.44+dfsg-5+deb9u9 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+deb9u1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+deb9u1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libnettle6:amd64 libnettle6 3.3-1+deb9u1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.18.1-1+deb9u2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.3-2+deb9u1 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libpsl5:amd64 libpsl5 0.17.0-3 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.13-2 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.13-2+deb9u6 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.13-2+deb9u6 install ok installed libquadmath0:amd64 libquadmath0 6.3.0-18+deb9u1 install ok installed libreadline7:amd64 libreadline7 7.0-3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-1+b1 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27~101-g0780600+dfsg-3+deb9u2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27~101-g0780600+dfsg-3+deb9u2 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.16.2-5+deb9u3 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u2 install ok installed libssh2-1:amd64 libssh2-1 1.7.0-1+deb9u2 install ok installed libssl1.1:amd64 libssl1.1 1.1.0l-1~deb9u6 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u14 install ok installed libsz2:amd64 libsz2 0.3.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.10-1.1+deb9u1 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u14 install ok installed libunistring0:amd64 libunistring0 0.9.6+really0.9.3-0.1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1+deb9u1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mime-support mime-support 3.60 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed openssl openssl 1.1.0l-1~deb9u6 install ok installed passwd passwd 1:4.4-4.1+deb9u1 install ok installed pbgenomicconsensus pbgenomicconsensus 2.1.0-1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed python python 2.7.13-2 install ok installed python-avro python-avro 1.8.1+dfsg-1 install ok installed python-chardet python-chardet 2.3.0-2 install ok installed python-h5py python-h5py 2.7.0-1 install ok installed python-iso8601 python-iso8601 0.1.11-1 install ok installed python-minimal python-minimal 2.7.13-2 install ok installed python-numpy python-numpy 1:1.12.1-3 install ok installed python-pbcommand python-pbcommand 0.5.3-1 install ok installed python-pbconsensuscore python-pbconsensuscore 1.0.2-2 install ok installed python-pbcore python-pbcore 1.2.11+dfsg-1 install ok installed python-pbgenomicconsensus python-pbgenomicconsensus 2.1.0-1 install ok installed python-pkg-resources python-pkg-resources 33.1.1-1 install ok installed python-pysam python-pysam 0.10.0+ds-2 install ok installed python-requests python-requests 2.12.4-1 install ok installed python-six python-six 1.10.0-3 install ok installed python-urllib3 python-urllib3 1.19.1-1+deb9u1 install ok installed python2.7 python2.7 2.7.13-2+deb9u6 install ok installed python2.7-minimal python2.7-minimal 2.7.13-2+deb9u6 install ok installed readline-common readline-common 7.0-3 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1+deb9u1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5+deb9u1 0m45.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m45.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', 'remove', 'ca-certificates', 'libaec0:amd64', 'libblas-common', 'libblas3', 'libcurl3-gnutls:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-100:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'mime-support', 'openssl', 'python', 'python-avro', 'python-chardet', 'python-h5py', 'python-iso8601', 'python-minimal', 'python-numpy', 'python-pbcommand', 'python-pbconsensuscore', 'python-pbcore', 'python-pbgenomicconsensus', 'python-pkg-resources', 'python-pysam', 'python-requests', 'python-six', 'python-urllib3', 'python2.7', 'python2.7-minimal', 'readline-common', 'pbgenomicconsensus'] 0m47.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates libaec0 libblas-common libblas3 libcurl3-gnutls libexpat1 libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libnettle6 libnghttp2-14 libp11-kit0 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 mime-support openssl pbgenomicconsensus python python-avro python-chardet python-h5py python-iso8601 python-minimal python-numpy python-pbcommand python-pbconsensuscore python-pbcore python-pbgenomicconsensus python-pkg-resources python-pysam python-requests python-six python-urllib3 python2.7 python2.7-minimal readline-common 0 upgraded, 0 newly installed, 63 to remove and 0 not upgraded. After this operation, 90.4 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 ... 6962 files and directories currently installed.) Removing pbgenomicconsensus (2.1.0-1) ... Removing python-pbgenomicconsensus (2.1.0-1) ... Removing python-pbcommand (0.5.3-1) ... Removing python-requests (2.12.4-1) ... Removing ca-certificates (20200601~deb9u2) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing python-pbcore (1.2.11+dfsg-1) ... Removing python-h5py (2.7.0-1) ... Removing libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Removing libsz2:amd64 (0.3.2-1) ... Removing libaec0:amd64 (0.3.2-1) ... Removing python-pbconsensuscore (1.0.2-2) ... Removing python-numpy (1:1.12.1-3) ... Removing liblapack3 (3.7.0-2) ... Removing libblas3 (3.7.0-2) ... Removing libblas-common (3.7.0-2) ... Removing python-pysam (0.10.0+ds-2) ... Removing libhts1:amd64 (1.3.2-2) ... Removing libcurl3-gnutls:amd64 (7.52.1-5+deb9u16) ... Removing python-urllib3 (1.19.1-1+deb9u1) ... Removing python-six (1.10.0-3) ... Removing libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u9) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Removing libgnutls30:amd64 (3.5.8-5+deb9u6) ... Removing libp11-kit0:amd64 (0.23.3-2+deb9u1) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libhogweed4:amd64 (3.3-1+deb9u1) ... Removing libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) ... Removing libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... Removing libidn11:amd64 (1.33-1+deb9u1) ... Removing libpsl5:amd64 (0.17.0-3) ... Removing libidn2-0:amd64 (0.16-1+deb9u1) ... Removing libkrb5-3:amd64 (1.15-1+deb9u3) ... Removing libk5crypto3:amd64 (1.15-1+deb9u3) ... Removing libkrb5support0:amd64 (1.15-1+deb9u3) ... Removing libkeyutils1:amd64 (1.5.9-9) ... Removing libldap-common (2.4.44+dfsg-5+deb9u9) ... Removing libnettle6:amd64 (3.3-1+deb9u1) ... Removing libnghttp2-14:amd64 (1.18.1-1+deb9u2) ... Removing libquadmath0:amd64 (6.3.0-18+deb9u1) ... Removing libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Removing libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Removing libssh2-1:amd64 (1.7.0-1+deb9u2) ... Removing openssl (1.1.0l-1~deb9u6) ... Removing libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing python-avro (1.8.1+dfsg-1) ... Removing python-chardet (2.3.0-2) ... Removing python-iso8601 (0.1.11-1) ... Removing python-pkg-resources (33.1.1-1) ... Removing python (2.7.13-2) ... Removing python2.7 (2.7.13-2+deb9u6) ... Removing libpython-stdlib:amd64 (2.7.13-2) ... Removing libpython2.7-stdlib:amd64 (2.7.13-2+deb9u6) ... Removing libexpat1:amd64 (2.2.0-2+deb9u5) ... Removing libffi6:amd64 (3.2.1-6) ... Removing python-minimal (2.7.13-2) ... Removing python2.7-minimal (2.7.13-2+deb9u6) ... Removing libpython2.7-minimal:amd64 (2.7.13-2+deb9u6) ... Removing libreadline7:amd64 (7.0-3) ... Removing libsqlite3-0:amd64 (3.16.2-5+deb9u3) ... Removing libssl1.1:amd64 (1.1.0l-1~deb9u6) ... Removing mime-support (3.60) ... Removing readline-common (7.0-3) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', 'remove', 'ca-certificates', 'libaec0:amd64', 'libblas-common', 'libblas3', 'libcurl3-gnutls:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-100:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'mime-support', 'openssl', 'python', 'python-avro', 'python-chardet', 'python-h5py', 'python-iso8601', 'python-minimal', 'python-numpy', 'python-pbcommand', 'python-pbconsensuscore', 'python-pbcore', 'python-pbgenomicconsensus', 'python-pkg-resources', 'python-pysam', 'python-requests', 'python-six', 'python-urllib3', 'python2.7', 'python2.7-minimal', 'readline-common', 'pbgenomicconsensus'] 0m47.3s INFO: Running scripts post_remove 0m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_remove_exceptions'] 0m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_remove_exceptions'] 0m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg', '--purge', 'ca-certificates', 'libaec0:amd64', 'libblas-common', 'libblas3', 'libcurl3-gnutls:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-100:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'mime-support', 'openssl', 'python', 'python-avro', 'python-chardet', 'python-h5py', 'python-iso8601', 'python-minimal', 'python-numpy', 'python-pbcommand', 'python-pbconsensuscore', 'python-pbcore', 'python-pbgenomicconsensus', 'python-pkg-resources', 'python-pysam', 'python-requests', 'python-six', 'python-urllib3', 'python2.7', 'python2.7-minimal', 'readline-common'] 0m47.6s DUMP: (Reading database ... 4423 files and directories currently installed.) Purging configuration files for ca-certificates (20200601~deb9u2) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libblas-common which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libffi6 which isn't installed dpkg: warning: ignoring request to remove libgfortran3 which isn't installed dpkg: warning: ignoring request to remove libgmp10 which isn't installed dpkg: warning: ignoring request to remove libgnutls30 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... dpkg: warning: ignoring request to remove libhdf5-100 which isn't installed dpkg: warning: ignoring request to remove libhogweed4 which isn't installed dpkg: warning: ignoring request to remove libhts1 which isn't installed dpkg: warning: ignoring request to remove libidn11 which isn't installed dpkg: warning: ignoring request to remove libidn2-0 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 libldap-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.44+dfsg-5+deb9u9) ... dpkg: warning: ignoring request to remove libnettle6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython-stdlib which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.13-2+deb9u6) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline7 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 (1.1.0l-1~deb9u6) ... dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libunistring0 which isn't installed Purging configuration files for mime-support (3.60) ... Purging configuration files for openssl (1.1.0l-1~deb9u6) ... Purging configuration files for python (2.7.13-2) ... dpkg: warning: ignoring request to remove python-avro which isn't installed dpkg: warning: ignoring request to remove python-chardet which isn't installed dpkg: warning: ignoring request to remove python-h5py which isn't installed dpkg: warning: ignoring request to remove python-iso8601 which isn't installed dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python-numpy which isn't installed dpkg: warning: ignoring request to remove python-pbcommand which isn't installed dpkg: warning: ignoring request to remove python-pbconsensuscore which isn't installed dpkg: warning: ignoring request to remove python-pbcore which isn't installed dpkg: warning: ignoring request to remove python-pbgenomicconsensus which isn't installed dpkg: warning: ignoring request to remove python-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python-pysam which isn't installed dpkg: warning: ignoring request to remove python-requests which isn't installed dpkg: warning: ignoring request to remove python-six which isn't installed dpkg: warning: ignoring request to remove python-urllib3 which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed Purging configuration files for python2.7-minimal (2.7.13-2+deb9u6) ... Purging configuration files for readline-common (7.0-3) ... 0m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg', '--purge', 'ca-certificates', 'libaec0:amd64', 'libblas-common', 'libblas3', 'libcurl3-gnutls:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-100:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'mime-support', 'openssl', 'python', 'python-avro', 'python-chardet', 'python-h5py', 'python-iso8601', 'python-minimal', 'python-numpy', 'python-pbcommand', 'python-pbconsensuscore', 'python-pbcore', 'python-pbgenomicconsensus', 'python-pkg-resources', 'python-pysam', 'python-requests', 'python-six', 'python-urllib3', 'python2.7', 'python2.7-minimal', 'readline-common'] 0m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg', '--purge', 'pbgenomicconsensus'] 0m47.6s DUMP: dpkg: warning: ignoring request to remove pbgenomicconsensus which isn't installed 0m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg', '--purge', 'pbgenomicconsensus'] 0m47.6s INFO: Running scripts post_purge 0m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_purge_exceptions'] 0m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_purge_exceptions'] 0m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg', '--purge', '--pending'] 0m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg', '--purge', '--pending'] 0m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg', '--remove', '--pending'] 0m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg', '--remove', '--pending'] 0m47.6s INFO: Running scripts post_test 0m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_test_exceptions'] 0m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'tmp/scripts/post_test_exceptions'] 0m47.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m47.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m47.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg-divert', '--list'] 0m47.9s 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 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'dpkg-divert', '--list'] 0m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', 'clean'] 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxl56u32', 'apt-get', 'clean'] 0m47.9s DEBUG: Recording chroot state 0m48.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/shm'] 0m48.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/shm'] 0m48.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/console'] 0m48.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/console'] 0m48.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/ptmx'] 0m48.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/ptmx'] 0m48.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/pts'] 0m48.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/dev/pts'] 0m48.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/proc'] 0m48.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxl56u32/proc'] 0m48.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m48.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpuxl56u32'] 0m48.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpuxl56u32 0m48.6s INFO: PASS: Upgrading between Debian distributions. 0m48.6s INFO: PASS: All tests. 0m48.6s INFO: piuparts run ends. ret=0 End: 2023-01-18 13:44:53 GMT