Start: 2023-01-25 12:57:53 GMT [stretch] Package: spades Version: 3.9.1+dfsg-1 Installed-Size: 17258 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.15), libgcc1 (>= 1:4.0), libgomp1 (>= 4.9), libhat-trie0, libjemalloc1 (>= 2.1.1), libnlopt0 (>= 2.2.4), libssw0, libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3), python, python-joblib, python-yaml, bwa, bamtools, samtools Description: genome assembler for single-cell and isolates data sets Homepage: http://bioinf.spbau.ru/en/spades Description-md5: a8af60ccfdd2e159193efb52065bef14 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, implemented-in::python, interface::commandline, role::program, scope::utility, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/s/spades/spades_3.9.1+dfsg-1_amd64.deb Size: 3449736 MD5sum: 7babab4f83d9622eb2503fb257104b32 SHA256: b2212137f2175a8d7e623d9a5d4b94c14c3f88046a91a53e2d34b095d6e3d92f [stretch-lts] Package: spades Version: 3.9.1+dfsg-1 Installed-Size: 17258 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.15), libgcc1 (>= 1:4.0), libgomp1 (>= 4.9), libhat-trie0, libjemalloc1 (>= 2.1.1), libnlopt0 (>= 2.2.4), libssw0, libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3), python, python-joblib, python-yaml, bwa, bamtools, samtools Description: genome assembler for single-cell and isolates data sets Homepage: http://bioinf.spbau.ru/en/spades Description-md5: a8af60ccfdd2e159193efb52065bef14 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, implemented-in::python, interface::commandline, role::program, scope::utility, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/s/spades/spades_3.9.1+dfsg-1_amd64.deb Size: 3449736 MD5sum: 7babab4f83d9622eb2503fb257104b32 SHA256: b2212137f2175a8d7e623d9a5d4b94c14c3f88046a91a53e2d34b095d6e3d92f 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 spades=3.9.1+dfsg-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 spades=3.9.1+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp1qq2481e 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp1qq2481e 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/proc'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/proc'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/pts'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/pts'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/ptmx'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/ptmx'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/console'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/console'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/shm'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/shm'] 0m1.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.3s DEBUG: Created policy-rc.d and chmodded it. 0m1.3s DEBUG: Created resolv.conf. 0m1.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp1qq2481e/tmp/scripts/ 0m1.3s INFO: Running scripts post_chroot_unpack 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', 'update'] 0m1.9s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', 'update'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.6s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.6s INFO: Running scripts post_setup 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_setup_dummy_users'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_setup_dummy_users'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_setup_forbid_home'] 0m3.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_setup_forbid_home'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.3s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_setup_minimize'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_setup_minimize'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_setup_zz_backports'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_setup_zz_backports'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.3s 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 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2next/reference-chroot-metadata.dat 0m3.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m3.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m3.5s INFO: Running scripts is_testable 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s INFO: Running scripts pre_test 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_test_exceptions'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_test_exceptions'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_test_root_password'] 0m3.6s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_test_root_password'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'show', '--no-all-versions', 'spades'] 0m3.7s DUMP: Package: spades Version: 3.9.1+dfsg-1 Installed-Size: 17258 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.15), libgcc1 (>= 1:4.0), libgomp1 (>= 4.9), libhat-trie0, libjemalloc1 (>= 2.1.1), libnlopt0 (>= 2.2.4), libssw0, libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3), python, python-joblib, python-yaml, bwa, bamtools, samtools Description-en: genome assembler for single-cell and isolates data sets The SPAdes ?? St. Petersburg genome assembler is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio and Sanger reads. You can also provide additional contigs that will be used as long reads. Description-md5: a8af60ccfdd2e159193efb52065bef14 Homepage: http://bioinf.spbau.ru/en/spades Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, implemented-in::python, interface::commandline, role::program, scope::utility, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/s/spades/spades_3.9.1+dfsg-1_amd64.deb Size: 3449736 MD5sum: 7babab4f83d9622eb2503fb257104b32 SHA256: b2212137f2175a8d7e623d9a5d4b94c14c3f88046a91a53e2d34b095d6e3d92f 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'show', '--no-all-versions', 'spades'] 0m3.7s INFO: apt-cache knows about the following packages: spades 0m3.7s INFO: Running scripts pre_install 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'policy'] 0m3.8s 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: 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'policy'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'policy', 'spades'] 0m3.8s DUMP: spades: Installed: (none) Candidate: 3.9.1+dfsg-1 Version table: 3.9.1+dfsg-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'policy', 'spades'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', '-y', 'install', 'spades'] 0m9.8s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bamtools bwa libbamtools2.4.0 libcurl3-gnutls libexpat1 libffi6 libgmp10 libgnutls30 libgomp1 libgssapi-krb5-2 libhat-trie0 libhogweed4 libhts1 libidn11 libidn2-0 libjemalloc1 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libncurses5 libnettle6 libnghttp2-14 libnlopt0 libp11-kit0 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libssw0 libtasn1-6 libunistring0 libyaml-0-2 mime-support python python-joblib python-minimal python-yaml python2.7 python2.7-minimal readline-common samtools Suggested packages: gnutls-bin krb5-doc krb5-user python-doc python-tk python2.7-doc binutils binfmt-support readline-doc Recommended packages: ca-certificates krb5-locales libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils python-numpy python-pytest python-simplejson The following NEW packages will be installed: bamtools bwa libbamtools2.4.0 libcurl3-gnutls libexpat1 libffi6 libgmp10 libgnutls30 libgomp1 libgssapi-krb5-2 libhat-trie0 libhogweed4 libhts1 libidn11 libidn2-0 libjemalloc1 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libncurses5 libnettle6 libnghttp2-14 libnlopt0 libp11-kit0 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libssw0 libtasn1-6 libunistring0 libyaml-0-2 mime-support python python-joblib python-minimal python-yaml python2.7 python2.7-minimal readline-common samtools spades 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 15.7 MB of archives. After this operation, 56.2 MB of additional disk space will be used. 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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 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amd64 2.4.1+dfsg-1 [190 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 bamtools amd64 2.4.1+dfsg-1 [214 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 bwa amd64 0.7.15-2+deb9u1 [194 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 libssh2-1 amd64 1.7.0-1+deb9u1 [139 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u10 [290 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:43 http://deb.debian.org/debian stretch/main amd64 libhat-trie0 amd64 0.0~git25f9e946-2 [10.7 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 libhts1 amd64 1.3.2-2 [257 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 libncurses5 amd64 6.0+20161126-1+deb9u2 [93.4 kB] Get:46 http://deb.debian.org/debian stretch/main amd64 libnlopt0 amd64 2.4.2+dfsg-2+b2 [162 kB] Get:47 http://deb.debian.org/debian stretch/main amd64 libssw0 amd64 1.1-1+b1 [16.5 kB] Get:48 http://deb.debian.org/debian stretch/main amd64 libyaml-0-2 amd64 0.1.7-2 [47.6 kB] Get:49 http://deb.debian.org/debian stretch/main amd64 python-joblib all 0.10.3+git55-g660fe5d-1 [115 kB] Get:50 http://deb.debian.org/debian stretch/main amd64 python-yaml amd64 3.12-1 [119 kB] Get:51 http://deb.debian.org/debian stretch/main amd64 samtools amd64 1.3.1-3 [254 kB] Get:52 http://deb.debian.org/debian stretch/main amd64 libjemalloc1 amd64 3.6.0-9.1 [89.8 kB] Get:53 http://deb.debian.org/debian stretch/main amd64 spades amd64 3.9.1+dfsg-1 [3450 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.7 MB in 1s (12.4 MB/s) Selecting previously unselected package libpython2.7-minimal:amd64. 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Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up libidn11:amd64 (1.33-1+deb9u1) ... Setting up libhat-trie0:amd64 (0.0~git25f9e946-2) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up bamtools (2.4.1+dfsg-1) ... 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 python-yaml (3.12-1) ... Setting up python-joblib (0.10.3+git55-g660fe5d-1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Setting up libhts1:amd64 (1.3.2-2) ... Setting up samtools (1.3.1-3) ... Setting up spades (3.9.1+dfsg-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', '-y', 'install', 'spades'] 0m9.8s INFO: Running scripts post_install 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_install_exceptions'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_install_exceptions'] 0m9.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m10.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m10.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp1qq2481e to stretch-lts 0m10.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main deb http://security.debian.org stretch/updates main 0m10.2s INFO: Running scripts pre_distupgrade 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', 'update'] 0m11.4s 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 (3187 kB/s) Reading package lists... 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', 'update'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', '-yf', 'dist-upgrade'] 0m15.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt 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 passwd python2.7 python2.7-minimal tar zlib1g 41 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 18.8 MB of archives. After this operation, 72.7 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 libnghttp2-14 amd64 1.18.1-1+deb9u2 [79.4 kB] Get:40 http://security.debian.org stretch/updates/main amd64 libssh2-1 amd64 1.7.0-1+deb9u2 [139 kB] Get:41 http://security.debian.org stretch/updates/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u16 [296 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.8 MB in 0s (94.0 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 ... 5883 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 ... 5883 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.43.4-2+deb9u2_amd64.deb ... Unpacking e2fsprogs (1.43.4-2+deb9u2) over (1.43.4-2+deb9u1) ... Setting up e2fsprogs (1.43.4-2+deb9u2) ... (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 ... 5884 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.4-4.1+deb9u1_amd64.deb ... Unpacking passwd (1:4.4-4.1+deb9u1) over (1:4.4-4.1) ... Setting up passwd (1:4.4-4.1+deb9u1) ... (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 ... 5884 files and directories currently installed.) Preparing to unpack .../libudev1_232-25+deb9u14_amd64.deb ... Unpacking libudev1:amd64 (232-25+deb9u14) over (232-25+deb9u12) ... Setting up libudev1:amd64 (232-25+deb9u14) ... (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 ... 5884 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 ... 5884 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) ... Preparing to unpack .../03-libp11-kit0_0.23.3-2+deb9u1_amd64.deb ... Unpacking libp11-kit0:amd64 (0.23.3-2+deb9u1) over (0.23.3-2) ... Preparing to unpack .../04-libgnutls30_3.5.8-5+deb9u6_amd64.deb ... Unpacking libgnutls30:amd64 (3.5.8-5+deb9u6) over (3.5.8-5+deb9u5) ... Preparing to unpack .../05-libgssapi-krb5-2_1.15-1+deb9u3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.15-1+deb9u3) over (1.15-1+deb9u1) ... Preparing to unpack .../06-libkrb5-3_1.15-1+deb9u3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.15-1+deb9u3) over (1.15-1+deb9u1) ... Preparing to unpack .../07-libkrb5support0_1.15-1+deb9u3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.15-1+deb9u3) over (1.15-1+deb9u1) ... Preparing to unpack .../08-libk5crypto3_1.15-1+deb9u3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.15-1+deb9u3) over (1.15-1+deb9u1) ... Preparing to unpack .../09-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3+deb9u2_amd64.deb ... 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-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 .../14-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 .../15-libcurl3-gnutls_7.52.1-5+deb9u16_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.52.1-5+deb9u16) over (7.52.1-5+deb9u10) ... Setting up libnettle6:amd64 (3.3-1+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 libsqlite3-0:amd64 (3.16.2-5+deb9u3) ... Setting up libpython2.7-minimal:amd64 (2.7.13-2+deb9u6) ... 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) ... 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', '-yf', 'dist-upgrade'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m16.1s DUMP: f0660a0a38f941b755664f52e8306b99 - 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'show', '--no-all-versions', 'spades'] 0m16.3s DUMP: Package: spades Version: 3.9.1+dfsg-1 Installed-Size: 17258 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.15), libgcc1 (>= 1:4.0), libgomp1 (>= 4.9), libhat-trie0, libjemalloc1 (>= 2.1.1), libnlopt0 (>= 2.2.4), libssw0, libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3), python, python-joblib, python-yaml, bwa, bamtools, samtools Description-en: genome assembler for single-cell and isolates data sets The SPAdes ?? St. Petersburg genome assembler is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio and Sanger reads. You can also provide additional contigs that will be used as long reads. Description-md5: a8af60ccfdd2e159193efb52065bef14 Homepage: http://bioinf.spbau.ru/en/spades Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, implemented-in::python, interface::commandline, role::program, scope::utility, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/s/spades/spades_3.9.1+dfsg-1_amd64.deb Size: 3449736 MD5sum: 7babab4f83d9622eb2503fb257104b32 SHA256: b2212137f2175a8d7e623d9a5d4b94c14c3f88046a91a53e2d34b095d6e3d92f 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'show', '--no-all-versions', 'spades'] 0m16.3s INFO: apt-cache knows about the following packages: spades 0m16.3s INFO: Running scripts pre_install 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_database-server'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_database-server'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_exceptions'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_exceptions'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_extras'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_extras'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_foreign_architecture'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_foreign_architecture'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'policy'] 0m16.4s 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: 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'policy'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'policy', 'spades'] 0m16.5s DUMP: spades: Installed: 3.9.1+dfsg-1 Candidate: 3.9.1+dfsg-1 Version table: *** 3.9.1+dfsg-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'policy', 'spades'] 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', '-y', 'install', 'spades'] 0m16.7s DUMP: Reading package lists... Building dependency tree... Reading state information... spades is already the newest version (3.9.1+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', '-y', 'install', 'spades'] 0m16.7s INFO: Running scripts post_install 0m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_install_exceptions'] 0m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_install_exceptions'] 0m16.7s INFO: Running scripts post_distupgrade 0m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m17.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m17.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m17.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m17.3s INFO: Running scripts pre_install 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_database-server'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_database-server'] 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_exceptions'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_exceptions'] 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_extras'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_extras'] 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'policy'] 0m17.4s 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: 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'policy'] 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'policy', 'spades'] 0m17.5s DUMP: spades: Installed: 3.9.1+dfsg-1 Candidate: 3.9.1+dfsg-1 Version table: *** 3.9.1+dfsg-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-cache', 'policy', 'spades'] 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', '-y', 'install', 'spades=3.9.1+dfsg-1'] 0m17.7s DUMP: Reading package lists... Building dependency tree... Reading state information... spades is already the newest version (3.9.1+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', '-y', 'install', 'spades=3.9.1+dfsg-1'] 0m17.7s INFO: Running scripts post_install 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_install_exceptions'] 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_install_exceptions'] 0m17.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m18.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m18.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', '-ac', '--ignore-obsolete'] 0m19.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', '-ac', '--ignore-obsolete'] 0m19.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m19.2s DUMP: 0.15.6 0m19.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m19.2s INFO: Running adequate version 0.15.6 now. 0m19.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'spades'] 0m19.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'spades'] 0m19.3s INFO: Running scripts pre_remove 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_remove_exceptions'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/pre_remove_exceptions'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m20.2s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.11 install ok installed bamtools bamtools 2.4.1+dfsg-1 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 bwa bwa 0.7.15-2+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+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 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 libbamtools2.4.0 libbamtools2.4.0 2.4.1+dfsg-1 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 libgmp10:amd64 libgmp10 2:6.1.2+dfsg-1+deb9u1 install ok installed libgnutls30:amd64 libgnutls30 3.5.8-5+deb9u6 install ok installed libgomp1:amd64 libgomp1 6.3.0-18+deb9u1 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 libhat-trie0:amd64 libhat-trie0 0.0~git25f9e946-2 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 libjemalloc1 libjemalloc1 3.6.0-9.1 install ok installed libjsoncpp1:amd64 libjsoncpp1 1.7.4-3 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 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 libncurses5:amd64 libncurses5 6.0+20161126-1+deb9u2 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 libnlopt0:amd64 libnlopt0 2.4.2+dfsg-2+b2 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 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 libssw0:amd64 libssw0 1.1-1+b1 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 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 libyaml-0-2:amd64 libyaml-0-2 0.1.7-2 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 passwd passwd 1:4.4-4.1+deb9u1 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-joblib python-joblib 0.10.3+git55-g660fe5d-1 install ok installed python-minimal python-minimal 2.7.13-2 install ok installed python-yaml python-yaml 3.12-1 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 samtools samtools 1.3.1-3 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed spades spades 3.9.1+dfsg-1 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 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', 'remove', 'bamtools', 'bwa', 'libbamtools2.4.0', 'libcurl3-gnutls:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhat-trie0:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libjemalloc1', 'libjsoncpp1:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libncurses5:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libp11-kit0:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libssw0:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'libyaml-0-2:amd64', 'mime-support', 'python', 'python-joblib', 'python-minimal', 'python-yaml', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools', 'spades'] 0m20.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bamtools bwa libbamtools2.4.0 libcurl3-gnutls libexpat1 libffi6 libgmp10 libgnutls30 libgomp1 libgssapi-krb5-2 libhat-trie0 libhogweed4 libhts1 libidn11 libidn2-0 libjemalloc1 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libncurses5 libnettle6 libnghttp2-14 libnlopt0 libp11-kit0 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libssw0 libtasn1-6 libunistring0 libyaml-0-2 mime-support python python-joblib python-minimal python-yaml python2.7 python2.7-minimal readline-common samtools spades 0 upgraded, 0 newly installed, 53 to remove and 0 not upgraded. After this operation, 56.3 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 ... 5883 files and directories currently installed.) Removing spades (3.9.1+dfsg-1) ... Removing bamtools (2.4.1+dfsg-1) ... Removing bwa (0.7.15-2+deb9u1) ... Removing libbamtools2.4.0 (2.4.1+dfsg-1) ... Removing samtools (1.3.1-3) ... Removing libhts1:amd64 (1.3.2-2) ... Removing libcurl3-gnutls:amd64 (7.52.1-5+deb9u16) ... Removing python-yaml (3.12-1) ... Removing python-joblib (0.10.3+git55-g660fe5d-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 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 libffi6:amd64 (3.2.1-6) ... Removing libhogweed4:amd64 (3.3-1+deb9u1) ... Removing libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) ... Removing libgomp1:amd64 (6.3.0-18+deb9u1) ... Removing libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... Removing libhat-trie0:amd64 (0.0~git25f9e946-2) ... Removing libidn11:amd64 (1.33-1+deb9u1) ... Removing libpsl5:amd64 (0.17.0-3) ... Removing libidn2-0:amd64 (0.16-1+deb9u1) ... Removing libjemalloc1 (3.6.0-9.1) ... Removing libjsoncpp1:amd64 (1.7.4-3) ... 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 libncurses5:amd64 (6.0+20161126-1+deb9u2) ... Removing libnettle6:amd64 (3.3-1+deb9u1) ... Removing libnghttp2-14:amd64 (1.18.1-1+deb9u2) ... Removing libnlopt0:amd64 (2.4.2+dfsg-2+b2) ... 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 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 libsqlite3-0:amd64 (3.16.2-5+deb9u3) ... Removing libssh2-1:amd64 (1.7.0-1+deb9u2) ... Removing libssl1.1:amd64 (1.1.0l-1~deb9u6) ... Removing libssw0:amd64 (1.1-1+b1) ... Removing libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing libyaml-0-2:amd64 (0.1.7-2) ... Removing mime-support (3.60) ... Removing readline-common (7.0-3) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', 'remove', 'bamtools', 'bwa', 'libbamtools2.4.0', 'libcurl3-gnutls:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhat-trie0:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libjemalloc1', 'libjsoncpp1:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libncurses5:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libp11-kit0:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libssw0:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'libyaml-0-2:amd64', 'mime-support', 'python', 'python-joblib', 'python-minimal', 'python-yaml', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools', 'spades'] 0m20.9s INFO: Running scripts post_remove 0m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_remove_exceptions'] 0m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_remove_exceptions'] 0m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg', '--purge', 'bamtools', 'bwa', 'libbamtools2.4.0', 'libcurl3-gnutls:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhat-trie0:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libjemalloc1', 'libjsoncpp1:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libncurses5:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libp11-kit0:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libssw0:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'libyaml-0-2:amd64', 'mime-support', 'python', 'python-joblib', 'python-minimal', 'python-yaml', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools'] 0m21.0s DUMP: dpkg: warning: ignoring request to remove bamtools which isn't installed dpkg: warning: ignoring request to remove bwa which isn't installed dpkg: warning: ignoring request to remove libbamtools2.4.0 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 libgmp10 which isn't installed dpkg: warning: ignoring request to remove libgnutls30 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed (Reading database ... 4420 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... dpkg: warning: ignoring request to remove libhat-trie0 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 libjemalloc1 which isn't installed dpkg: warning: ignoring request to remove libjsoncpp1 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 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 libncurses5 which isn't installed 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 libnlopt0 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 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 libssw0 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 dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed Purging configuration files for mime-support (3.60) ... Purging configuration files for python (2.7.13-2) ... dpkg: warning: ignoring request to remove python-joblib which isn't installed dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python-yaml 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) ... dpkg: warning: ignoring request to remove samtools which isn't installed 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg', '--purge', 'bamtools', 'bwa', 'libbamtools2.4.0', 'libcurl3-gnutls:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhat-trie0:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libjemalloc1', 'libjsoncpp1:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libncurses5:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libp11-kit0:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libssw0:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'libyaml-0-2:amd64', 'mime-support', 'python', 'python-joblib', 'python-minimal', 'python-yaml', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg', '--purge', 'spades'] 0m21.0s DUMP: dpkg: warning: ignoring request to remove spades which isn't installed 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg', '--purge', 'spades'] 0m21.0s INFO: Running scripts post_purge 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_purge_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_purge_exceptions'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg', '--purge', '--pending'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg', '--purge', '--pending'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg', '--remove', '--pending'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg', '--remove', '--pending'] 0m21.0s INFO: Running scripts post_test 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_test_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'tmp/scripts/post_test_exceptions'] 0m21.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m21.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg-divert', '--list'] 0m21.2s 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 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'dpkg-divert', '--list'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', 'clean'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qq2481e', 'apt-get', 'clean'] 0m21.3s DEBUG: Recording chroot state 0m21.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/shm'] 0m21.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/shm'] 0m21.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/console'] 0m21.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/console'] 0m21.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/ptmx'] 0m21.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/ptmx'] 0m21.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/pts'] 0m21.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/dev/pts'] 0m21.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/proc'] 0m22.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qq2481e/proc'] 0m22.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m22.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp1qq2481e'] 0m22.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp1qq2481e 0m22.0s INFO: PASS: Upgrading between Debian distributions. 0m22.0s INFO: PASS: All tests. 0m22.0s INFO: piuparts run ends. ret=0 End: 2023-01-25 12:58:16 GMT