Start: 2023-03-22 05:44:22 GMT [stretch] Package: iva Version: 1.0.8+ds-1 Installed-Size: 8766 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 1.6), python3-networkx, python3-pysam, python3:any (>= 3.3.2-2~), kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description: iterative virus sequence assembler Homepage: https://github.com/sanger-pathogens/iva Description-md5: 698e26411c0dbe5917f816e7b7229be9 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.8+ds-1_amd64.deb Size: 8577338 MD5sum: 750623e5fa9d5205e0df4fb2e7ee1f3e SHA256: f7c8b70fcdc13f4921f03f11035ff4925f51cb93e2b5782b2d1a0e2919b5319e [stretch-lts] Package: iva Version: 1.0.8+ds-1 Installed-Size: 8766 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 1.6), python3-networkx, python3-pysam, python3:any (>= 3.3.2-2~), kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description: iterative virus sequence assembler Homepage: https://github.com/sanger-pathogens/iva Description-md5: 698e26411c0dbe5917f816e7b7229be9 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.8+ds-1_amd64.deb Size: 8577338 MD5sum: 750623e5fa9d5205e0df4fb2e7ee1f3e SHA256: f7c8b70fcdc13f4921f03f11035ff4925f51cb93e2b5782b2d1a0e2919b5319e 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 iva=1.0.8+ds-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 iva=1.0.8+ds-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/tmppl12n6yp 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmppl12n6yp 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', '-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/tmppl12n6yp/proc'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/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/tmppl12n6yp/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/tmppl12n6yp/dev/pts'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/ptmx'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/ptmx'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/console'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/console'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/shm'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/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/tmppl12n6yp/tmp/scripts/ 0m1.3s INFO: Running scripts post_chroot_unpack 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', 'update'] 0m2.2s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', 'update'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s INFO: Running scripts post_setup 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_setup_minimize'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_setup_minimize'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_setup_zz_backports'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_setup_zz_backports'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.7s 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 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.7s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2next/reference-chroot-metadata.dat 0m3.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 0m4.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 0m4.0s INFO: Running scripts is_testable 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/is_testable_uninstallable'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/is_testable_uninstallable'] 0m4.0s INFO: Running scripts pre_test 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_test_exceptions'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_test_exceptions'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_test_root_password'] 0m4.0s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_test_root_password'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m4.2s DUMP: Package: iva Version: 1.0.8+ds-1 Installed-Size: 8766 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 1.6), python3-networkx, python3-pysam, python3:any (>= 3.3.2-2~), kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description-en: iterative virus sequence assembler IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth. . IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence. Description-md5: 698e26411c0dbe5917f816e7b7229be9 Homepage: https://github.com/sanger-pathogens/iva Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.8+ds-1_amd64.deb Size: 8577338 MD5sum: 750623e5fa9d5205e0df4fb2e7ee1f3e SHA256: f7c8b70fcdc13f4921f03f11035ff4925f51cb93e2b5782b2d1a0e2919b5319e 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m4.2s INFO: apt-cache knows about the following packages: iva 0m4.2s INFO: Running scripts pre_install 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_database-server'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_database-server'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_exceptions'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_exceptions'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_extras'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_extras'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'policy'] 0m4.3s 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: 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'policy'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'policy', 'iva'] 0m4.4s DUMP: iva: Installed: (none) Candidate: 1.0.8+ds-1 Version table: 1.0.8+ds-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'policy', 'iva'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', '-y', 'install', 'iva'] 0m27.0s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates ca-certificates-java default-jre-headless dh-python fastaq fontconfig-config fonts-dejavu-core gawk java-common kmc libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libblas-common libblas3 libbsd0 libcups2 libcurl3-gnutls libdbus-1-3 libexpat1 libffi6 libfontconfig1 libfreetype6 libgdbm3 libgfortran3 libgmp10 libgnutls30 libgomp1 libgssapi-krb5-2 libhogweed4 libhts1 libidn11 libidn2-0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmpdec2 libmpfr4 libncurses5 libnettle6 libnghttp2-14 libnspr4 libnss3 libp11-kit0 libpcsclite1 libperl5.24 libpng16-16 libpsl5 libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 libtasn1-6 libunistring0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxrender1 libxtst6 lsb-base mime-support mummer openjdk-8-jre-headless openssl perl perl-modules-5.24 python3 python3-decorator python3-minimal python3-networkx python3-numpy python3-pkg-resources python3-pysam python3.5 python3.5-minimal readline-common samtools smalt ucf x11-common Suggested packages: default-jre libdpkg-perl gawk-doc cups-common gnutls-bin krb5-doc krb5-user liblcms2-utils pcscd libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei fonts-wqy-zenhei fonts-indic perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make python3-doc python3-tk python3-venv python-networkx-doc gcc gfortran python-numpy-doc python3-dev python3-nose python3-numpy-dbg python3-setuptools python3.5-venv python3.5-doc binutils binfmt-support readline-doc Recommended packages: r-base-core bioperl trimmomatic dbus krb5-locales libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils netbase rename python3-scipy python3-yaml python The following NEW packages will be installed: ca-certificates ca-certificates-java default-jre-headless dh-python fastaq fontconfig-config fonts-dejavu-core gawk iva java-common kmc libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libblas-common libblas3 libbsd0 libcups2 libcurl3-gnutls libdbus-1-3 libexpat1 libffi6 libfontconfig1 libfreetype6 libgdbm3 libgfortran3 libgmp10 libgnutls30 libgomp1 libgssapi-krb5-2 libhogweed4 libhts1 libidn11 libidn2-0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmpdec2 libmpfr4 libncurses5 libnettle6 libnghttp2-14 libnspr4 libnss3 libp11-kit0 libpcsclite1 libperl5.24 libpng16-16 libpsl5 libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 libtasn1-6 libunistring0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxrender1 libxtst6 lsb-base mime-support mummer openjdk-8-jre-headless openssl perl perl-modules-5.24 python3 python3-decorator python3-minimal python3-networkx python3-numpy python3-pkg-resources python3-pysam python3.5 python3.5-minimal readline-common samtools smalt ucf x11-common 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. Need to get 71.1 MB of archives. After this operation, 248 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 perl-modules-5.24 all 5.24.1-3+deb9u7 [2723 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 libgdbm3 amd64 1.8.3-14 [30.0 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 libperl5.24 amd64 5.24.1-3+deb9u7 [3527 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 perl amd64 5.24.1-3+deb9u7 [218 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 libmpfr4 amd64 3.1.5-1 [556 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 libsigsegv2 amd64 2.10-5 [28.9 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 gawk amd64 1:4.1.4+dfsg-1 [571 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libpython3.5-minimal amd64 3.5.3-1+deb9u1 [573 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u3 [83.7 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 python3.5-minimal amd64 3.5.3-1+deb9u1 [1691 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 python3-minimal amd64 3.5.3-1 [35.3 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 libmpdec2 amd64 2.4.2-1 [85.2 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libpython3.5-stdlib amd64 3.5.3-1+deb9u1 [2167 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 python3.5 amd64 3.5.3-1+deb9u1 [229 kB] Get:22 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http://deb.debian.org/debian stretch/main amd64 samtools amd64 1.3.1-3 [254 kB] Get:85 http://deb.debian.org/debian stretch/main amd64 fastaq all 3.14.0-1 [46.6 kB] Get:86 http://deb.debian.org/debian stretch/main amd64 python3-decorator all 4.0.11-1 [13.3 kB] Get:87 http://deb.debian.org/debian stretch/main amd64 python3-networkx all 1.11-2 [624 kB] Get:88 http://deb.debian.org/debian stretch/main amd64 python3-pysam amd64 0.10.0+ds-2 [1299 kB] Get:89 http://deb.debian.org/debian stretch/main amd64 libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:90 http://deb.debian.org/debian stretch/main amd64 kmc amd64 2.3+dfsg-5 [467 kB] Get:91 http://deb.debian.org/debian stretch/main amd64 mummer amd64 3.23+dfsg-2 [809 kB] Get:92 http://deb.debian.org/debian stretch/main amd64 libbambamc0 amd64 0.0.50-1 [35.4 kB] Get:93 http://deb.debian.org/debian stretch/main amd64 smalt amd64 0.7.6-6 [112 kB] Get:94 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:95 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:96 http://deb.debian.org/debian stretch/main amd64 libblas-common amd64 3.7.0-2 [14.2 kB] Get:97 http://deb.debian.org/debian stretch/main amd64 libblas3 amd64 3.7.0-2 [155 kB] Get:98 http://deb.debian.org/debian stretch/main amd64 liblapack3 amd64 3.7.0-2 [2141 kB] Get:99 http://deb.debian.org/debian stretch/main amd64 python3-numpy amd64 1:1.12.1-3 [1934 kB] Get:100 http://deb.debian.org/debian stretch/main amd64 iva amd64 1.0.8+ds-1 [8577 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 71.1 MB in 0s (72.0 MB/s) Selecting previously unselected package perl-modules-5.24. 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Setting up kmc (2.3+dfsg-5) ... Setting up gawk (1:4.1.4+dfsg-1) ... Setting up libbsd0:amd64 (0.8.3-1) ... Setting up libnspr4:amd64 (2:4.12-6) ... Setting up ucf (3.0036) ... Setting up libfreetype6:amd64 (2.6.3-3.2+deb9u1) ... Setting up libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up lsb-base (9.20161125) ... Setting up perl (5.24.1-3+deb9u7) ... update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode 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 openssl (1.1.0l-1~deb9u1) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up libbambamc0 (0.0.50-1) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 126 added, 0 removed; done. Setting up libx11-data (2:1.6.4-3+deb9u1) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up libidn11:amd64 (1.33-1+deb9u1) ... Setting up libmpdec2:amd64 (2.4.2-1) ... Setting up libdbus-1-3:amd64 (1.10.32-0+deb9u1) ... Setting up libavahi-common-data:amd64 (0.6.32-2) ... Setting up fontconfig-config (2.11.0-6.7) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up mummer (3.23+dfsg-2) ... 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 libpython3.5-stdlib:amd64 (3.5.3-1+deb9u1) ... Setting up libnss3:amd64 (2:3.26.2-1.1+deb9u1) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u1) ... Setting up smalt (0.7.6-6) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up libavahi-common3:amd64 (0.6.32-2) ... Setting up libxcb1:amd64 (1.12-1) ... Setting up python3.5 (3.5.3-1+deb9u1) ... Setting up libpython3-stdlib:amd64 (3.5.3-1) ... Setting up libfontconfig1:amd64 (2.11.0-6.7+b1) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up libx11-6:amd64 (2:1.6.4-3+deb9u1) ... 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 libxrender1:amd64 (1:0.9.10-1) ... Setting up libavahi-client3:amd64 (0.6.32-2) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up libcups2:amd64 (2.2.1-8+deb9u6) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up libhts1:amd64 (1.3.2-2) ... Setting up samtools (1.3.1-3) ... Setting up openjdk-8-jre-headless:amd64 (8u252-b09-1~deb9u1) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ca-certificates-java (20170929~deb9u3) ... Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Taiwan_GRCA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Setting up python3 (3.5.3-1) ... Setting up python3-numpy (1:1.12.1-3) ... Setting up python3-pkg-resources (33.1.1-1) ... Setting up fastaq (3.14.0-1) ... Setting up python3-pysam (0.10.0+ds-2) ... Setting up dh-python (2.20170125) ... Setting up python3-decorator (4.0.11-1) ... Setting up default-jre-headless (2:1.8-58+deb9u1) ... Setting up python3-networkx (1.11-2) ... Setting up iva (1.0.8+ds-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. done. 0m27.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', '-y', 'install', 'iva'] 0m27.0s INFO: Running scripts post_install 0m27.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_install_exceptions'] 0m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_install_exceptions'] 0m27.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 0m27.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 0m27.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmppl12n6yp to stretch-lts 0m27.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main deb http://security.debian.org stretch/updates main 0m27.7s INFO: Running scripts pre_distupgrade 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m27.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', 'update'] 0m29.4s 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 (2297 kB/s) Reading package lists... 0m29.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', 'update'] 0m29.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', '-yf', 'dist-upgrade'] 0m48.7s 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 libavahi-client3 libavahi-common-data libavahi-common3 libbsd0 libcomerr2 libcups2 libcurl3-gnutls libexpat1 libfreetype6 libgcrypt20 libgmp10 libgnutls30 libgssapi-krb5-2 libhogweed4 libjpeg62-turbo libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblz4-1 liblzma5 libnettle6 libnghttp2-14 libnss3 libp11-kit0 libpython3.5-minimal libpython3.5-stdlib libsasl2-2 libsasl2-modules-db libsqlite3-0 libss2 libssh2-1 libssl1.1 libsystemd0 libudev1 libx11-6 libx11-data login openjdk-8-jre-headless openssl passwd python3.5 python3.5-minimal tar zlib1g 54 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 52.0 MB of archives. After this operation, 3370 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 libssl1.1 amd64 1.1.0l-1~deb9u6 [1360 kB] Get:15 http://security.debian.org stretch/updates/main amd64 python3.5 amd64 3.5.3-1+deb9u5 [231 kB] Get:16 http://security.debian.org stretch/updates/main amd64 libpython3.5-stdlib amd64 3.5.3-1+deb9u5 [2167 kB] Get:17 http://security.debian.org stretch/updates/main amd64 python3.5-minimal amd64 3.5.3-1+deb9u5 [1692 kB] Get:18 http://security.debian.org stretch/updates/main amd64 libpython3.5-minimal amd64 3.5.3-1+deb9u5 [574 kB] Get:19 http://security.debian.org stretch/updates/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u3 [574 kB] Get:20 http://security.debian.org stretch/updates/main amd64 libexpat1 amd64 2.2.0-2+deb9u5 [84.7 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 libavahi-common-data amd64 0.6.32-2+deb9u1 [118 kB] Get:42 http://security.debian.org stretch/updates/main amd64 libavahi-common3 amd64 0.6.32-2+deb9u1 [52.3 kB] Get:43 http://security.debian.org stretch/updates/main amd64 libavahi-client3 amd64 0.6.32-2+deb9u1 [55.6 kB] Get:44 http://security.debian.org stretch/updates/main amd64 libbsd0 amd64 0.8.3-1+deb9u1 [82.9 kB] Get:45 http://security.debian.org stretch/updates/main amd64 libcups2 amd64 2.2.1-8+deb9u8 [307 kB] Get:46 http://security.debian.org stretch/updates/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u2 [79.4 kB] Get:47 http://security.debian.org stretch/updates/main amd64 libssh2-1 amd64 1.7.0-1+deb9u2 [139 kB] Get:48 http://security.debian.org stretch/updates/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u16 [296 kB] Get:49 http://security.debian.org stretch/updates/main amd64 libfreetype6 amd64 2.6.3-3.2+deb9u2 [438 kB] Get:50 http://security.debian.org stretch/updates/main amd64 libjpeg62-turbo amd64 1:1.5.1-2+deb9u2 [134 kB] Get:51 http://security.debian.org stretch/updates/main amd64 libnss3 amd64 2:3.26.2-1.1+deb9u5 [1244 kB] Get:52 http://security.debian.org stretch/updates/main amd64 libx11-data all 2:1.6.4-3+deb9u4 [291 kB] Get:53 http://security.debian.org stretch/updates/main amd64 libx11-6 amd64 2:1.6.4-3+deb9u4 [748 kB] Get:54 http://security.debian.org stretch/updates/main amd64 openjdk-8-jre-headless amd64 8u332-ga-1~deb9u1 [28.1 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 52.0 MB in 0s (101 MB/s) (Reading database ... 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Unpacking libavahi-common-data:amd64 (0.6.32-2+deb9u1) over (0.6.32-2) ... Preparing to unpack .../16-libavahi-common3_0.6.32-2+deb9u1_amd64.deb ... Unpacking libavahi-common3:amd64 (0.6.32-2+deb9u1) over (0.6.32-2) ... Preparing to unpack .../17-libavahi-client3_0.6.32-2+deb9u1_amd64.deb ... Unpacking libavahi-client3:amd64 (0.6.32-2+deb9u1) over (0.6.32-2) ... Preparing to unpack .../18-libbsd0_0.8.3-1+deb9u1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.3-1+deb9u1) over (0.8.3-1) ... Preparing to unpack .../19-libcups2_2.2.1-8+deb9u8_amd64.deb ... Unpacking libcups2:amd64 (2.2.1-8+deb9u8) over (2.2.1-8+deb9u6) ... Preparing to unpack .../20-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 .../21-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 .../22-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 .../23-libfreetype6_2.6.3-3.2+deb9u2_amd64.deb ... Unpacking libfreetype6:amd64 (2.6.3-3.2+deb9u2) over (2.6.3-3.2+deb9u1) ... Preparing to unpack .../24-libjpeg62-turbo_1%3a1.5.1-2+deb9u2_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:1.5.1-2+deb9u2) over (1:1.5.1-2) ... Preparing to unpack .../25-libnss3_2%3a3.26.2-1.1+deb9u5_amd64.deb ... Unpacking libnss3:amd64 (2:3.26.2-1.1+deb9u5) over (2:3.26.2-1.1+deb9u1) ... Preparing to unpack .../26-libx11-data_2%3a1.6.4-3+deb9u4_all.deb ... Unpacking libx11-data (2:1.6.4-3+deb9u4) over (2:1.6.4-3+deb9u1) ... Preparing to unpack .../27-libx11-6_2%3a1.6.4-3+deb9u4_amd64.deb ... Unpacking libx11-6:amd64 (2:1.6.4-3+deb9u4) over (2:1.6.4-3+deb9u1) ... Preparing to unpack .../28-openjdk-8-jre-headless_8u332-ga-1~deb9u1_amd64.deb ... Unpacking openjdk-8-jre-headless:amd64 (8u332-ga-1~deb9u1) over (8u252-b09-1~deb9u1) ... Setting up libnettle6:amd64 (3.3-1+deb9u1) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u5) ... Setting up libjpeg62-turbo:amd64 (1:1.5.1-2+deb9u2) ... 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 libbsd0:amd64 (0.8.3-1+deb9u1) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u3) ... Setting up libfreetype6:amd64 (2.6.3-3.2+deb9u2) ... 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 ca-certificates (20200601~deb9u2) ... Updating certificates in /etc/ssl/certs... 11 added, 0 removed; done. Setting up libx11-data (2:1.6.4-3+deb9u4) ... Setting up libavahi-common-data:amd64 (0.6.32-2+deb9u1) ... Setting up libpython3.5-minimal:amd64 (3.5.3-1+deb9u5) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u3) ... Setting up libpython3.5-stdlib:amd64 (3.5.3-1+deb9u5) ... Setting up libx11-6:amd64 (2:1.6.4-3+deb9u4) ... Setting up libnss3:amd64 (2:3.26.2-1.1+deb9u5) ... Setting up libhogweed4:amd64 (3.3-1+deb9u1) ... Setting up python3.5-minimal (3.5.3-1+deb9u5) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u3) ... Setting up libavahi-common3:amd64 (0.6.32-2+deb9u1) ... Setting up python3.5 (3.5.3-1+deb9u5) ... 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 libavahi-client3:amd64 (0.6.32-2+deb9u1) ... Setting up libcups2:amd64 (2.2.1-8+deb9u8) ... Setting up openjdk-8-jre-headless:amd64 (8u332-ga-1~deb9u1) ... Installing new version of config file /etc/java-8-openjdk/accessibility.properties ... Installing new version of config file /etc/java-8-openjdk/security/blacklisted.certs ... Installing new version of config file /etc/java-8-openjdk/security/java.security ... 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. done. 0m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', '-yf', 'dist-upgrade'] 0m48.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m49.1s DUMP: f0660a0a38f941b755664f52e8306b99 - 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m49.3s DUMP: Package: iva Version: 1.0.8+ds-1 Installed-Size: 8766 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 1.6), python3-networkx, python3-pysam, python3:any (>= 3.3.2-2~), kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description-en: iterative virus sequence assembler IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth. . IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence. Description-md5: 698e26411c0dbe5917f816e7b7229be9 Homepage: https://github.com/sanger-pathogens/iva Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.8+ds-1_amd64.deb Size: 8577338 MD5sum: 750623e5fa9d5205e0df4fb2e7ee1f3e SHA256: f7c8b70fcdc13f4921f03f11035ff4925f51cb93e2b5782b2d1a0e2919b5319e 0m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m49.3s INFO: apt-cache knows about the following packages: iva 0m49.3s INFO: Running scripts pre_install 0m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_database-server'] 0m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_database-server'] 0m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_exceptions'] 0m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_exceptions'] 0m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_extras'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_extras'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_foreign_architecture'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_foreign_architecture'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'policy'] 0m49.5s 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: 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'policy'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'policy', 'iva'] 0m49.5s DUMP: iva: Installed: 1.0.8+ds-1 Candidate: 1.0.8+ds-1 Version table: *** 1.0.8+ds-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'policy', 'iva'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', '-y', 'install', 'iva'] 0m49.8s DUMP: Reading package lists... Building dependency tree... Reading state information... iva is already the newest version (1.0.8+ds-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', '-y', 'install', 'iva'] 0m49.8s INFO: Running scripts post_install 0m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_install_exceptions'] 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_install_exceptions'] 0m49.8s INFO: Running scripts post_distupgrade 0m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_distupgrade_exceptions'] 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_distupgrade_exceptions'] 0m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m49.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m49.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_distupgrade_zz_backports'] 0m49.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_distupgrade_zz_backports'] 0m49.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 0m50.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 0m50.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 0m50.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 0m50.9s INFO: Running scripts pre_install 0m50.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_database-server'] 0m50.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_database-server'] 0m50.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_exceptions'] 0m50.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_exceptions'] 0m50.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_extras'] 0m50.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_extras'] 0m50.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_foreign_architecture'] 0m50.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_foreign_architecture'] 0m50.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m51.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m51.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'policy'] 0m51.0s 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: 0m51.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'policy'] 0m51.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'policy', 'iva'] 0m51.1s DUMP: iva: Installed: 1.0.8+ds-1 Candidate: 1.0.8+ds-1 Version table: *** 1.0.8+ds-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m51.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-cache', 'policy', 'iva'] 0m51.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', '-y', 'install', 'iva=1.0.8+ds-1'] 0m51.3s DUMP: Reading package lists... Building dependency tree... Reading state information... iva is already the newest version (1.0.8+ds-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m51.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', '-y', 'install', 'iva=1.0.8+ds-1'] 0m51.3s INFO: Running scripts post_install 0m51.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_install_exceptions'] 0m51.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_install_exceptions'] 0m51.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 0m52.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 0m52.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', '-ac', '--ignore-obsolete'] 0m53.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', '-ac', '--ignore-obsolete'] 0m53.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m53.7s DUMP: 0.15.6 0m53.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m53.7s INFO: Running adequate version 0.15.6 now. 0m53.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'iva'] 0m53.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'iva'] 0m53.8s INFO: Running scripts pre_remove 0m53.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m56.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m56.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_remove_exceptions'] 0m56.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/pre_remove_exceptions'] 0m56.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m56.3s 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 ca-certificates-java ca-certificates-java 20170929~deb9u3 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 default-jre-headless default-jre-headless 2:1.8-58+deb9u1 install ok installed dh-python dh-python 2.20170125 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 fastaq fastaq 3.14.0-1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed fontconfig-config fontconfig-config 2.11.0-6.7 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-1 install ok installed gawk gawk 1:4.1.4+dfsg-1 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 iva iva 1.0.8+ds-1 install ok installed java-common java-common 0.58+deb9u1 install ok installed kmc kmc 2.3+dfsg-5 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 libavahi-client3:amd64 libavahi-client3 0.6.32-2+deb9u1 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.6.32-2+deb9u1 install ok installed libavahi-common3:amd64 libavahi-common3 0.6.32-2+deb9u1 install ok installed libbambamc0 libbambamc0 0.0.50-1 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 libbsd0:amd64 libbsd0 0.8.3-1+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 libcups2:amd64 libcups2 2.2.1-8+deb9u8 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 libdbus-1-3:amd64 libdbus-1-3 1.10.32-0+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 libfontconfig1:amd64 libfontconfig1 2.11.0-6.7+b1 install ok installed libfreetype6:amd64 libfreetype6 2.6.3-3.2+deb9u2 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 libgdbm3:amd64 libgdbm3 1.8.3-14 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 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 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 libjpeg62-turbo:amd64 libjpeg62-turbo 1:1.5.1-2+deb9u2 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 liblcms2-2:amd64 liblcms2-2 2.8-4+deb9u1 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 libmpdec2:amd64 libmpdec2 2.4.2-1 install ok installed libmpfr4:amd64 libmpfr4 3.1.5-1 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 libnspr4:amd64 libnspr4 2:4.12-6 install ok installed libnss3:amd64 libnss3 2:3.26.2-1.1+deb9u5 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 libpcsclite1:amd64 libpcsclite1 1.8.20-1 install ok installed libperl5.24:amd64 libperl5.24 5.24.1-3+deb9u7 install ok installed libpng16-16:amd64 libpng16-16 1.6.28-1+deb9u1 install ok installed libpsl5:amd64 libpsl5 0.17.0-3 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.5.3-1 install ok installed libpython3.5-minimal:amd64 libpython3.5-minimal 3.5.3-1+deb9u5 install ok installed libpython3.5-stdlib:amd64 libpython3.5-stdlib 3.5.3-1+deb9u5 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 libsigsegv2:amd64 libsigsegv2 2.10-5 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 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 libx11-6:amd64 libx11-6 2:1.6.4-3+deb9u4 install ok installed libx11-data libx11-data 2:1.6.4-3+deb9u4 install ok installed libxau6:amd64 libxau6 1:1.0.8-1 install ok installed libxcb1:amd64 libxcb1 1.12-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.3-1+b2 install ok installed libxi6:amd64 libxi6 2:1.7.9-1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1 install ok installed libxtst6:amd64 libxtst6 2:1.2.3-1 install ok installed login login 1:4.4-4.1+deb9u1 install ok installed lsb-base lsb-base 9.20161125 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 mummer mummer 3.23+dfsg-2 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 openjdk-8-jre-headless:amd64 openjdk-8-jre-headless 8u332-ga-1~deb9u1 install ok installed openssl openssl 1.1.0l-1~deb9u6 install ok installed passwd passwd 1:4.4-4.1+deb9u1 install ok installed perl perl 5.24.1-3+deb9u7 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed perl-modules-5.24 perl-modules-5.24 5.24.1-3+deb9u7 install ok installed python3 python3 3.5.3-1 install ok installed python3-decorator python3-decorator 4.0.11-1 install ok installed python3-minimal python3-minimal 3.5.3-1 install ok installed python3-networkx python3-networkx 1.11-2 install ok installed python3-numpy python3-numpy 1:1.12.1-3 install ok installed python3-pkg-resources python3-pkg-resources 33.1.1-1 install ok installed python3-pysam python3-pysam 0.10.0+ds-2 install ok installed python3.5 python3.5 3.5.3-1+deb9u5 install ok installed python3.5-minimal python3.5-minimal 3.5.3-1+deb9u5 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 smalt smalt 0.7.6-6 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1+deb9u1 install ok installed ucf ucf 3.0036 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed x11-common x11-common 1:7.7+19 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5+deb9u1 0m56.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m56.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', 'remove', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'dh-python', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'gawk', 'java-common', 'kmc', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbambamc0', 'libblas-common', 'libblas3', 'libbsd0:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdbus-1-3:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdbm3:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libmpfr4:amd64', 'libncurses5:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libp11-kit0:amd64', 'libpcsclite1:amd64', 'libperl5.24:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.5-minimal:amd64', 'libpython3.5-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxi6:amd64', 'libxrender1:amd64', 'libxtst6:amd64', 'lsb-base', 'mime-support', 'mummer', 'openjdk-8-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.24', 'python3', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-pkg-resources', 'python3-pysam', 'python3.5', 'python3.5-minimal', 'readline-common', 'samtools', 'smalt', 'ucf', 'x11-common', 'iva'] 1m0.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates ca-certificates-java default-jre-headless dh-python fastaq fontconfig-config fonts-dejavu-core gawk iva java-common kmc libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libblas-common libblas3 libbsd0 libcups2 libcurl3-gnutls libdbus-1-3 libexpat1 libffi6 libfontconfig1 libfreetype6 libgdbm3 libgfortran3 libgmp10 libgnutls30 libgomp1 libgssapi-krb5-2 libhogweed4 libhts1 libidn11 libidn2-0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmpdec2 libmpfr4 libncurses5 libnettle6 libnghttp2-14 libnspr4 libnss3 libp11-kit0 libpcsclite1 libperl5.24 libpng16-16 libpsl5 libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 libtasn1-6 libunistring0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxrender1 libxtst6 lsb-base mime-support mummer openjdk-8-jre-headless openssl perl perl-modules-5.24 python3 python3-decorator python3-minimal python3-networkx python3-numpy python3-pkg-resources python3-pysam python3.5 python3.5-minimal readline-common samtools smalt ucf x11-common 0 upgraded, 0 newly installed, 100 to remove and 0 not upgraded. After this operation, 252 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 ... 10164 files and directories currently installed.) Removing iva (1.0.8+ds-1) ... Removing default-jre-headless (2:1.8-58+deb9u1) ... Removing python3-pysam (0.10.0+ds-2) ... Removing fastaq (3.14.0-1) ... Removing python3-pkg-resources (33.1.1-1) ... Removing python3-numpy (1:1.12.1-3) ... Removing python3-networkx (1.11-2) ... Removing mummer (3.23+dfsg-2) ... Removing gawk (1:4.1.4+dfsg-1) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing kmc (2.3+dfsg-5) ... Removing smalt (0.7.6-6) ... Removing libbambamc0 (0.0.50-1) ... Removing liblapack3 (3.7.0-2) ... Removing libblas3 (3.7.0-2) ... Removing libblas-common (3.7.0-2) ... Removing samtools (1.3.1-3) ... Removing libhts1:amd64 (1.3.2-2) ... Removing libcurl3-gnutls:amd64 (7.52.1-5+deb9u16) ... Removing libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u9) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Removing perl (5.24.1-3+deb9u7) ... Removing libperl5.24:amd64 (5.24.1-3+deb9u7) ... Removing libgdbm3:amd64 (1.8.3-14) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libmpfr4:amd64 (3.1.5-1) ... Removing libgomp1:amd64 (6.3.0-18+deb9u1) ... Removing libpsl5:amd64 (0.17.0-3) ... Removing libidn2-0:amd64 (0.16-1+deb9u1) ... Removing libldap-common (2.4.44+dfsg-5+deb9u9) ... Removing libncurses5:amd64 (6.0+20161126-1+deb9u2) ... 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 libsigsegv2:amd64 (2.10-5) ... Removing libssh2-1:amd64 (1.7.0-1+deb9u2) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing perl-modules-5.24 (5.24.1-3+deb9u7) ... Removing python3-decorator (4.0.11-1) ... Removing ca-certificates-java (20170929~deb9u3) ... Removing ca-certificates (20200601~deb9u2) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing dh-python (2.20170125) ... Removing openssl (1.1.0l-1~deb9u6) ... Removing openjdk-8-jre-headless:amd64 (8u332-ga-1~deb9u1) ... Removing python3 (3.5.3-1) ... Removing libfontconfig1:amd64 (2.11.0-6.7+b1) ... Removing fontconfig-config (2.11.0-6.7) ... Removing fonts-dejavu-core (2.37-1) ... Removing java-common (0.58+deb9u1) ... Removing libcups2:amd64 (2.2.1-8+deb9u8) ... Removing libavahi-client3:amd64 (0.6.32-2+deb9u1) ... Removing libavahi-common3:amd64 (0.6.32-2+deb9u1) ... Removing libavahi-common-data:amd64 (0.6.32-2+deb9u1) ... Removing libxtst6:amd64 (2:1.2.3-1) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing libdbus-1-3:amd64 (1.10.32-0+deb9u1) ... Removing python3.5 (3.5.3-1+deb9u5) ... Removing python3-minimal (3.5.3-1) ... Removing python3.5-minimal (3.5.3-1+deb9u5) ... Removing libexpat1:amd64 (2.2.0-2+deb9u5) ... 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 libfreetype6:amd64 (2.6.3-3.2+deb9u2) ... 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 libjpeg62-turbo:amd64 (1:1.5.1-2+deb9u2) ... 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 liblcms2-2:amd64 (2.8-4+deb9u1) ... Removing libpython3-stdlib:amd64 (3.5.3-1) ... Removing libpython3.5-stdlib:amd64 (3.5.3-1+deb9u5) ... Removing libmpdec2:amd64 (2.4.2-1) ... Removing libnettle6:amd64 (3.3-1+deb9u1) ... Removing libnss3:amd64 (2:3.26.2-1.1+deb9u5) ... Removing libnspr4:amd64 (2:4.12-6) ... Removing libpcsclite1:amd64 (1.8.20-1) ... Removing libpng16-16:amd64 (1.6.28-1+deb9u1) ... Removing libpython3.5-minimal:amd64 (3.5.3-1+deb9u5) ... 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 libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Removing libxi6:amd64 (2:1.7.9-1) ... Removing libxext6:amd64 (2:1.3.3-1+b2) ... Removing x11-common (1:7.7+19) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing lsb-base (9.20161125) ... Removing mime-support (3.60) ... Removing readline-common (7.0-3) ... Removing ucf (3.0036) ... Removing libx11-6:amd64 (2:1.6.4-3+deb9u4) ... Removing libxcb1:amd64 (1.12-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.8.3-1+deb9u1) ... Removing libx11-data (2:1.6.4-3+deb9u4) ... Removing libxau6:amd64 (1:1.0.8-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 1m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', 'remove', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'dh-python', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'gawk', 'java-common', 'kmc', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbambamc0', 'libblas-common', 'libblas3', 'libbsd0:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdbus-1-3:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdbm3:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libmpfr4:amd64', 'libncurses5:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libp11-kit0:amd64', 'libpcsclite1:amd64', 'libperl5.24:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.5-minimal:amd64', 'libpython3.5-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxi6:amd64', 'libxrender1:amd64', 'libxtst6:amd64', 'lsb-base', 'mime-support', 'mummer', 'openjdk-8-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.24', 'python3', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-pkg-resources', 'python3-pysam', 'python3.5', 'python3.5-minimal', 'readline-common', 'samtools', 'smalt', 'ucf', 'x11-common', 'iva'] 1m0.6s INFO: Running scripts post_remove 1m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_remove_exceptions'] 1m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_remove_exceptions'] 1m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg', '--purge', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'dh-python', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'gawk', 'java-common', 'kmc', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbambamc0', 'libblas-common', 'libblas3', 'libbsd0:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdbus-1-3:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdbm3:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libmpfr4:amd64', 'libncurses5:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libp11-kit0:amd64', 'libpcsclite1:amd64', 'libperl5.24:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.5-minimal:amd64', 'libpython3.5-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxi6:amd64', 'libxrender1:amd64', 'libxtst6:amd64', 'lsb-base', 'mime-support', 'mummer', 'openjdk-8-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.24', 'python3', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-pkg-resources', 'python3-pysam', 'python3.5', 'python3.5-minimal', 'readline-common', 'samtools', 'smalt', 'ucf', 'x11-common'] 1m1.6s DUMP: (Reading database ... 4494 files and directories currently installed.) Purging configuration files for ca-certificates (20200601~deb9u2) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20170929~deb9u3) ... dpkg: warning: ignoring request to remove default-jre-headless which isn't installed dpkg: warning: ignoring request to remove dh-python which isn't installed dpkg: warning: ignoring request to remove fastaq which isn't installed Purging configuration files for fontconfig-config (2.11.0-6.7) ... Purging configuration files for fonts-dejavu-core (2.37-1) ... dpkg: warning: ignoring request to remove gawk which isn't installed Purging configuration files for java-common (0.58+deb9u1) ... dpkg: warning: ignoring request to remove kmc which isn't installed dpkg: warning: ignoring request to remove libavahi-client3 which isn't installed dpkg: warning: ignoring request to remove libavahi-common-data which isn't installed dpkg: warning: ignoring request to remove libavahi-common3 which isn't installed Purging configuration files for libbambamc0 (0.0.50-1) ... 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 libbsd0 which isn't installed dpkg: warning: ignoring request to remove libcups2 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libdbus-1-3 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 libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libgdbm3 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 dpkg: warning: ignoring request to remove libgomp1 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... 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 libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.44+dfsg-5+deb9u9) ... dpkg: warning: ignoring request to remove libmpdec2 which isn't installed dpkg: warning: ignoring request to remove libmpfr4 which isn't installed 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 libnspr4 which isn't installed dpkg: warning: ignoring request to remove libnss3 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libpcsclite1 which isn't installed dpkg: warning: ignoring request to remove libperl5.24 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.5-minimal:amd64 (3.5.3-1+deb9u5) ... dpkg: warning: ignoring request to remove libpython3.5-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 libsigsegv2 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 libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libunistring0 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed Purging configuration files for libxau6:amd64 (1:1.0.8-1) ... dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxi6 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxtst6 which isn't installed dpkg: warning: ignoring request to remove lsb-base which isn't installed Purging configuration files for mime-support (3.60) ... dpkg: warning: ignoring request to remove mummer which isn't installed Purging configuration files for openjdk-8-jre-headless:amd64 (8u332-ga-1~deb9u1) ... Purging configuration files for openssl (1.1.0l-1~deb9u6) ... Purging configuration files for perl (5.24.1-3+deb9u7) ... dpkg: warning: ignoring request to remove perl-modules-5.24 which isn't installed Purging configuration files for python3 (3.5.3-1) ... dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-networkx which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3.5 which isn't installed Purging configuration files for python3.5-minimal (3.5.3-1+deb9u5) ... Purging configuration files for readline-common (7.0-3) ... dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove smalt which isn't installed Purging configuration files for ucf (3.0036) ... Purging configuration files for x11-common (1:7.7+19) ... 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg', '--purge', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'dh-python', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'gawk', 'java-common', 'kmc', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbambamc0', 'libblas-common', 'libblas3', 'libbsd0:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdbus-1-3:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdbm3:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libmpfr4:amd64', 'libncurses5:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libp11-kit0:amd64', 'libpcsclite1:amd64', 'libperl5.24:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.5-minimal:amd64', 'libpython3.5-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxi6:amd64', 'libxrender1:amd64', 'libxtst6:amd64', 'lsb-base', 'mime-support', 'mummer', 'openjdk-8-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.24', 'python3', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-pkg-resources', 'python3-pysam', 'python3.5', 'python3.5-minimal', 'readline-common', 'samtools', 'smalt', 'ucf', 'x11-common'] 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg', '--purge', 'iva'] 1m1.6s DUMP: dpkg: warning: ignoring request to remove iva which isn't installed 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg', '--purge', 'iva'] 1m1.6s INFO: Running scripts post_purge 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_purge_exceptions'] 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_purge_exceptions'] 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg', '--purge', '--pending'] 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg', '--purge', '--pending'] 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg', '--remove', '--pending'] 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg', '--remove', '--pending'] 1m1.6s INFO: Running scripts post_test 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_test_exceptions'] 1m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'tmp/scripts/post_test_exceptions'] 1m1.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 1m1.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 1m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg-divert', '--list'] 1m1.9s 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 1m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'dpkg-divert', '--list'] 1m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', 'clean'] 1m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppl12n6yp', 'apt-get', 'clean'] 1m2.0s DEBUG: Recording chroot state 1m2.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/shm'] 1m2.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/shm'] 1m2.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/console'] 1m2.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/console'] 1m2.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/ptmx'] 1m2.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/ptmx'] 1m2.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/pts'] 1m2.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/dev/pts'] 1m2.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/proc'] 1m2.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppl12n6yp/proc'] 1m2.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 1m2.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmppl12n6yp'] 1m2.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmppl12n6yp 1m2.8s INFO: PASS: Upgrading between Debian distributions. 1m2.8s INFO: PASS: All tests. 1m2.8s INFO: piuparts run ends. ret=0 End: 2023-03-22 05:45:25 GMT