Start: 2023-01-01 13:38:44 GMT [stretch] Package: pbdagcon Version: 0.3+20161121+ds-1 Installed-Size: 1145 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.4), libhdf5-100, libhdf5-cpp-100 (>= 1.8.13), libhts1 (>= 1.0), libstdc++6 (>= 6), zlib1g (>= 1:1.1.4), libpbseq, libpbbam Suggests: blasr Description: sequence consensus using directed acyclic graphs Homepage: https://github.com/PacificBiosciences/pbdagcon Description-md5: 95465f5fc6fbaa2db477a48c78b7cd82 Section: science Priority: optional Filename: pool/main/p/pbdagcon/pbdagcon_0.3+20161121+ds-1_amd64.deb Size: 322426 MD5sum: fb5ecdb8914fd6ccd42f264509255d3d SHA256: 9308757881828c5c57e08d8a9bee767f6c91474e2555f185d450a7c4dab68b7e [stretch-lts] Package: pbdagcon Version: 0.3+20161121+ds-1 Installed-Size: 1145 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.4), libhdf5-100, libhdf5-cpp-100 (>= 1.8.13), libhts1 (>= 1.0), libstdc++6 (>= 6), zlib1g (>= 1:1.1.4), libpbseq, libpbbam Suggests: blasr Description: sequence consensus using directed acyclic graphs Homepage: https://github.com/PacificBiosciences/pbdagcon Description-md5: 95465f5fc6fbaa2db477a48c78b7cd82 Section: science Priority: optional Filename: pool/main/p/pbdagcon/pbdagcon_0.3+20161121+ds-1_amd64.deb Size: 322426 MD5sum: fb5ecdb8914fd6ccd42f264509255d3d SHA256: 9308757881828c5c57e08d8a9bee767f6c91474e2555f185d450a7c4dab68b7e 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 pbdagcon=0.3+20161121+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 pbdagcon=0.3+20161121+ds-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpixzvjfva 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpixzvjfva 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.9s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/proc'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/proc'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/pts'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/pts'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/ptmx'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/ptmx'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/console'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/console'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/shm'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/shm'] 0m2.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m2.0s DEBUG: Created policy-rc.d and chmodded it. 0m2.0s DEBUG: Created resolv.conf. 0m2.0s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpixzvjfva/tmp/scripts/ 0m2.0s INFO: Running scripts post_chroot_unpack 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', 'update'] 0m3.5s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', 'update'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', '-yf', 'dist-upgrade'] 0m3.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', '-yf', 'dist-upgrade'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.2s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.2s INFO: Running scripts post_setup 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_setup_dummy_users'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_setup_dummy_users'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_setup_forbid_home'] 0m5.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_setup_forbid_home'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.7s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_setup_minimize'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_setup_minimize'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_setup_zz_backports'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_setup_zz_backports'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.7s 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 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.7s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2next/reference-chroot-metadata.dat 0m5.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m5.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m5.9s INFO: Running scripts is_testable 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/is_testable_uninstallable'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/is_testable_uninstallable'] 0m5.9s INFO: Running scripts pre_test 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_test_exceptions'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_test_exceptions'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_test_root_password'] 0m6.0s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_test_root_password'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'show', '--no-all-versions', 'pbdagcon'] 0m6.2s DUMP: Package: pbdagcon Version: 0.3+20161121+ds-1 Installed-Size: 1145 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.4), libhdf5-100, libhdf5-cpp-100 (>= 1.8.13), libhts1 (>= 1.0), libstdc++6 (>= 6), zlib1g (>= 1:1.1.4), libpbseq, libpbbam Suggests: blasr Description-en: sequence consensus using directed acyclic graphs pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment. . It uses the alignment information from blasr to align sequence reads to a "backbone" sequence. Based on the underlying alignment directed acyclic graph (DAG), it will be able to use the new information from the reads to find the discrepancies between the reads and the "backbone" sequences. A dynamic programming process is then applied to the DAG to find the optimum sequence of bases as the consensus. The new consensus can be used as a new backbone sequence to iteratively improve the consensus quality. . While the code is developed for processing PacBio(TM) raw sequence data, the algorithm can be used for general consensus purpose. Currently, it only takes FASTA input. For shorter read sequences, one might need to adjust the blasr alignment parameters to get the alignment string properly. . The code and the underlying graphical data structure have been used for some algorithm development prototyping including phasing reads and pre-assembly. Description-md5: 95465f5fc6fbaa2db477a48c78b7cd82 Homepage: https://github.com/PacificBiosciences/pbdagcon Section: science Priority: optional Filename: pool/main/p/pbdagcon/pbdagcon_0.3+20161121+ds-1_amd64.deb Size: 322426 MD5sum: fb5ecdb8914fd6ccd42f264509255d3d SHA256: 9308757881828c5c57e08d8a9bee767f6c91474e2555f185d450a7c4dab68b7e 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'show', '--no-all-versions', 'pbdagcon'] 0m6.2s INFO: apt-cache knows about the following packages: pbdagcon 0m6.2s INFO: Running scripts pre_install 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_database-server'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_database-server'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_exceptions'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_exceptions'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_extras'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_extras'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'policy'] 0m6.3s 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: 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'policy'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'policy', 'pbdagcon'] 0m6.3s DUMP: pbdagcon: Installed: (none) Candidate: 0.3+20161121+ds-1 Version table: 0.3+20161121+ds-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'policy', 'pbdagcon'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', '-y', 'install', 'pbdagcon'] 0m10.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libaec0 libblasr libcurl3-gnutls libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libnettle6 libnghttp2-14 libp11-kit0 libpbbam libpbdata libpbihdf libpbseq libpsl5 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 Suggested packages: gnutls-bin krb5-doc krb5-user blasr Recommended packages: ca-certificates krb5-locales publicsuffix libsasl2-modules The following NEW packages will be installed: libaec0 libblasr libcurl3-gnutls libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libnettle6 libnghttp2-14 libp11-kit0 libpbbam libpbdata libpbihdf libpbseq libpsl5 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 pbdagcon 0 upgraded, 38 newly installed, 0 to remove and 0 not upgraded. Need to get 9278 kB of archives. After this operation, 27.6 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b2 [192 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b2 [136 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 libtasn1-6 amd64 4.10-1.1+deb9u1 [50.6 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 libgnutls30 amd64 3.5.8-5+deb9u5 [896 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 libkrb5support0 amd64 1.15-1+deb9u1 [61.9 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 libk5crypto3 amd64 1.15-1+deb9u1 [119 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libkrb5-3 amd64 1.15-1+deb9u1 [311 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 libgssapi-krb5-2 amd64 1.15-1+deb9u1 [155 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [68.4 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [105 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libldap-common all 2.4.44+dfsg-5+deb9u4 [85.7 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u4 [219 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 libaec0 amd64 0.3.2-1 [18.5 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB] Get:24 http://deb.debian.org/debian stretch/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:25 http://deb.debian.org/debian stretch/main amd64 libssh2-1 amd64 1.7.0-1+deb9u1 [139 kB] Get:26 http://deb.debian.org/debian stretch/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u10 [290 kB] Get:27 http://deb.debian.org/debian stretch/main amd64 libhts1 amd64 1.3.2-2 [257 kB] Get:28 http://deb.debian.org/debian stretch/main amd64 libpbbam amd64 0.7.4+ds-1 [478 kB] Get:29 http://deb.debian.org/debian stretch/main amd64 libpbdata amd64 0~20161219-1 [129 kB] Get:30 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:31 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libsz2 amd64 0.3.2-1 [5730 B] Get:33 http://deb.debian.org/debian stretch/main amd64 libhdf5-100 amd64 1.10.0-patch1+docs-3+deb9u1 [1282 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 libhdf5-cpp-100 amd64 1.10.0-patch1+docs-3+deb9u1 [130 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 libpbihdf amd64 0~20161219-1 [167 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 libblasr amd64 0~20161219-1 [867 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 libpbseq all 0~20161219-1 [3876 B] Get:38 http://deb.debian.org/debian stretch/main amd64 pbdagcon amd64 0.3+20161121+ds-1 [322 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9278 kB in 0s (15.9 MB/s) Selecting previously unselected package libssl1.1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4411 files and directories currently installed.) Preparing to unpack .../00-libssl1.1_1.1.0l-1~deb9u1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Selecting previously unselected package libgmp10:amd64. Preparing to unpack .../01-libgmp10_2%3a6.1.2+dfsg-1_amd64.deb ... Unpacking libgmp10:amd64 (2:6.1.2+dfsg-1) ... Selecting previously unselected package libnettle6:amd64. Preparing to unpack .../02-libnettle6_3.3-1+b2_amd64.deb ... Unpacking libnettle6:amd64 (3.3-1+b2) ... Selecting previously unselected package libhogweed4:amd64. Preparing to unpack .../03-libhogweed4_3.3-1+b2_amd64.deb ... Unpacking libhogweed4:amd64 (3.3-1+b2) ... Selecting previously unselected package libidn11:amd64. Preparing to unpack .../04-libidn11_1.33-1+deb9u1_amd64.deb ... Unpacking libidn11:amd64 (1.33-1+deb9u1) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../05-libffi6_3.2.1-6_amd64.deb ... Unpacking libffi6:amd64 (3.2.1-6) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../06-libp11-kit0_0.23.3-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.23.3-2) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../07-libtasn1-6_4.10-1.1+deb9u1_amd64.deb ... Unpacking libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Selecting previously unselected package libgnutls30:amd64. Preparing to unpack .../08-libgnutls30_3.5.8-5+deb9u5_amd64.deb ... Unpacking libgnutls30:amd64 (3.5.8-5+deb9u5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../09-libkeyutils1_1.5.9-9_amd64.deb ... Unpacking libkeyutils1:amd64 (1.5.9-9) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../10-libkrb5support0_1.15-1+deb9u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.15-1+deb9u1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../11-libk5crypto3_1.15-1+deb9u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.15-1+deb9u1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../12-libkrb5-3_1.15-1+deb9u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.15-1+deb9u1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../13-libgssapi-krb5-2_1.15-1+deb9u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../14-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3+deb9u1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../15-libsasl2-2_2.1.27~101-g0780600+dfsg-3+deb9u1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../16-libldap-common_2.4.44+dfsg-5+deb9u4_all.deb ... Unpacking libldap-common (2.4.44+dfsg-5+deb9u4) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../17-libldap-2.4-2_2.4.44+dfsg-5+deb9u4_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../18-libaec0_0.3.2-1_amd64.deb ... Unpacking libaec0:amd64 (0.3.2-1) ... Selecting previously unselected package libunistring0:amd64. Preparing to unpack .../19-libunistring0_0.9.6+really0.9.3-0.1_amd64.deb ... Unpacking libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../20-libidn2-0_0.16-1+deb9u1_amd64.deb ... Unpacking libidn2-0:amd64 (0.16-1+deb9u1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../21-libnghttp2-14_1.18.1-1+deb9u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../22-libpsl5_0.17.0-3_amd64.deb ... Unpacking libpsl5:amd64 (0.17.0-3) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../23-librtmp1_2.4+20151223.gitfa8646d.1-1+b1_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../24-libssh2-1_1.7.0-1+deb9u1_amd64.deb ... Unpacking libssh2-1:amd64 (1.7.0-1+deb9u1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../25-libcurl3-gnutls_7.52.1-5+deb9u10_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Selecting previously unselected package libhts1:amd64. Preparing to unpack .../26-libhts1_1.3.2-2_amd64.deb ... Unpacking libhts1:amd64 (1.3.2-2) ... Selecting previously unselected package libpbbam:amd64. Preparing to unpack .../27-libpbbam_0.7.4+ds-1_amd64.deb ... Unpacking libpbbam:amd64 (0.7.4+ds-1) ... Selecting previously unselected package libpbdata:amd64. Preparing to unpack .../28-libpbdata_0~20161219-1_amd64.deb ... Unpacking libpbdata:amd64 (0~20161219-1) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../29-libquadmath0_6.3.0-18+deb9u1_amd64.deb ... Unpacking libquadmath0:amd64 (6.3.0-18+deb9u1) ... Selecting previously unselected package libgfortran3:amd64. Preparing to unpack .../30-libgfortran3_6.3.0-18+deb9u1_amd64.deb ... Unpacking libgfortran3:amd64 (6.3.0-18+deb9u1) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../31-libsz2_0.3.2-1_amd64.deb ... Unpacking libsz2:amd64 (0.3.2-1) ... Selecting previously unselected package libhdf5-100:amd64. Preparing to unpack .../32-libhdf5-100_1.10.0-patch1+docs-3+deb9u1_amd64.deb ... Unpacking libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Selecting previously unselected package libhdf5-cpp-100:amd64. Preparing to unpack .../33-libhdf5-cpp-100_1.10.0-patch1+docs-3+deb9u1_amd64.deb ... Unpacking libhdf5-cpp-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Selecting previously unselected package libpbihdf:amd64. Preparing to unpack .../34-libpbihdf_0~20161219-1_amd64.deb ... Unpacking libpbihdf:amd64 (0~20161219-1) ... Selecting previously unselected package libblasr:amd64. Preparing to unpack .../35-libblasr_0~20161219-1_amd64.deb ... Unpacking libblasr:amd64 (0~20161219-1) ... Selecting previously unselected package libpbseq. Preparing to unpack .../36-libpbseq_0~20161219-1_all.deb ... Unpacking libpbseq (0~20161219-1) ... Selecting previously unselected package pbdagcon. Preparing to unpack .../37-pbdagcon_0.3+20161121+ds-1_amd64.deb ... Unpacking pbdagcon (0.3+20161121+ds-1) ... Setting up libquadmath0:amd64 (6.3.0-18+deb9u1) ... Setting up libnettle6:amd64 (3.3-1+b2) ... Setting up libaec0:amd64 (0.3.2-1) ... Setting up libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Setting up libldap-common (2.4.44+dfsg-5+deb9u4) ... Setting up libgfortran3:amd64 (6.3.0-18+deb9u1) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-1) ... Setting up libssh2-1:amd64 (1.7.0-1+deb9u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up libidn11:amd64 (1.33-1+deb9u1) ... Setting up libsz2:amd64 (0.3.2-1) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u1) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u1) ... Setting up libhdf5-cpp-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Setting up libhts1:amd64 (1.3.2-2) ... Setting up libpbbam:amd64 (0.7.4+ds-1) ... Setting up libpbdata:amd64 (0~20161219-1) ... Setting up libpbihdf:amd64 (0~20161219-1) ... Setting up libblasr:amd64 (0~20161219-1) ... Setting up libpbseq (0~20161219-1) ... Setting up pbdagcon (0.3+20161121+ds-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', '-y', 'install', 'pbdagcon'] 0m10.7s INFO: Running scripts post_install 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_install_exceptions'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_install_exceptions'] 0m10.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m11.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m11.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpixzvjfva to stretch-lts 0m11.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main deb http://security.debian.org stretch/updates main 0m11.0s INFO: Running scripts pre_distupgrade 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_distupgrade_exceptions'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_distupgrade_exceptions'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', 'update'] 0m13.0s 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 (1441 kB/s) Reading package lists... 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', 'update'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', '-yf', 'dist-upgrade'] 0m17.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt debian-archive-keyring dpkg e2fslibs e2fsprogs gzip libapt-pkg5.0 libcomerr2 libcurl3-gnutls libgcrypt20 libgmp10 libgnutls30 libgssapi-krb5-2 libhogweed4 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblz4-1 liblzma5 libnettle6 libnghttp2-14 libp11-kit0 libsasl2-2 libsasl2-modules-db libss2 libssh2-1 libssl1.1 libsystemd0 libudev1 login passwd tar zlib1g 35 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 14.2 MB of archives. After this operation, 74.8 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 libcomerr2 amd64 1.43.4-2+deb9u2 [63.8 kB] Get:15 http://security.debian.org stretch/updates/main amd64 libss2 amd64 1.43.4-2+deb9u2 [68.0 kB] Get:16 http://security.debian.org stretch/updates/main amd64 passwd amd64 1:4.4-4.1+deb9u1 [997 kB] Get:17 http://security.debian.org stretch/updates/main amd64 libudev1 amd64 232-25+deb9u14 [126 kB] Get:18 http://security.debian.org stretch/updates/main amd64 libgcrypt20 amd64 1.7.6-2+deb9u4 [523 kB] Get:19 http://security.debian.org stretch/updates/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u6 [1360 kB] Get:20 http://security.debian.org stretch/updates/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1+deb9u1 [253 kB] Get:21 http://security.debian.org stretch/updates/main amd64 libhogweed4 amd64 3.3-1+deb9u1 [136 kB] Get:22 http://security.debian.org stretch/updates/main amd64 libnettle6 amd64 3.3-1+deb9u1 [192 kB] Get:23 http://security.debian.org stretch/updates/main amd64 libp11-kit0 amd64 0.23.3-2+deb9u1 [112 kB] Get:24 http://security.debian.org stretch/updates/main amd64 libgnutls30 amd64 3.5.8-5+deb9u6 [897 kB] Get:25 http://security.debian.org stretch/updates/main amd64 libgssapi-krb5-2 amd64 1.15-1+deb9u3 [155 kB] Get:26 http://security.debian.org stretch/updates/main amd64 libkrb5-3 amd64 1.15-1+deb9u3 [312 kB] Get:27 http://security.debian.org stretch/updates/main amd64 libkrb5support0 amd64 1.15-1+deb9u3 [62.3 kB] Get:28 http://security.debian.org stretch/updates/main amd64 libk5crypto3 amd64 1.15-1+deb9u3 [120 kB] Get:29 http://security.debian.org stretch/updates/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u2 [68.5 kB] Get:30 http://security.debian.org stretch/updates/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u2 [105 kB] Get:31 http://security.debian.org stretch/updates/main amd64 libldap-common all 2.4.44+dfsg-5+deb9u9 [86.3 kB] Get:32 http://security.debian.org stretch/updates/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u9 [220 kB] Get:33 http://security.debian.org stretch/updates/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u2 [79.4 kB] Get:34 http://security.debian.org stretch/updates/main amd64 libssh2-1 amd64 1.7.0-1+deb9u2 [139 kB] Get:35 http://security.debian.org stretch/updates/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u16 [296 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.2 MB in 0s (56.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4710 files and directories currently installed.) Preparing to unpack .../tar_1.29b-1.1+deb9u1_amd64.deb ... Unpacking tar (1.29b-1.1+deb9u1) over (1.29b-1.1) ... Setting up tar (1.29b-1.1+deb9u1) ... (Reading database ... (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 ... 4710 files and directories currently installed.) Preparing to unpack .../dpkg_1.18.26_amd64.deb ... Unpacking dpkg (1.18.26) over (1.18.25) ... Setting up dpkg (1.18.26) ... (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 ... 4710 files and directories currently installed.) Preparing to unpack .../e2fslibs_1.43.4-2+deb9u2_amd64.deb ... Unpacking e2fslibs:amd64 (1.43.4-2+deb9u2) over (1.43.4-2+deb9u1) ... Setting up e2fslibs:amd64 (1.43.4-2+deb9u2) ... (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 ... 4710 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.43.4-2+deb9u2_amd64.deb ... Unpacking e2fsprogs (1.43.4-2+deb9u2) over (1.43.4-2+deb9u1) ... Setting up e2fsprogs (1.43.4-2+deb9u2) ... (Reading database ... (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 ... 4710 files and directories currently installed.) Preparing to unpack .../gzip_1.6-5+deb9u1_amd64.deb ... Unpacking gzip (1.6-5+deb9u1) over (1.6-5+b1) ... Setting up gzip (1.6-5+deb9u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4709 files and directories currently installed.) Preparing to unpack .../login_1%3a4.4-4.1+deb9u1_amd64.deb ... Unpacking login (1:4.4-4.1+deb9u1) over (1:4.4-4.1) ... Setting up login (1:4.4-4.1+deb9u1) ... Installing new version of config file /etc/securetty ... (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 ... 4709 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2017.5+deb9u2_all.deb ... Unpacking debian-archive-keyring (2017.5+deb9u2) over (2017.5+deb9u1) ... Setting up debian-archive-keyring (2017.5+deb9u2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4711 files and directories currently installed.) Preparing to unpack .../liblzma5_5.2.2-1.2+deb9u1_amd64.deb ... Unpacking liblzma5:amd64 (5.2.2-1.2+deb9u1) over (5.2.2-1.2+b1) ... Setting up liblzma5:amd64 (5.2.2-1.2+deb9u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4710 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.8.dfsg-5+deb9u1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.8.dfsg-5+deb9u1) over (1:1.2.8.dfsg-5) ... Setting up zlib1g:amd64 (1:1.2.8.dfsg-5+deb9u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4710 files and directories currently installed.) Preparing to unpack .../libapt-pkg5.0_1.4.11_amd64.deb ... Unpacking libapt-pkg5.0:amd64 (1.4.11) over (1.4.10) ... Setting up libapt-pkg5.0:amd64 (1.4.11) ... (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 ... 4710 files and directories currently installed.) Preparing to unpack .../archives/apt_1.4.11_amd64.deb ... Unpacking apt (1.4.11) over (1.4.10) ... Setting up apt (1.4.11) ... (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 ... 4710 files and directories currently installed.) Preparing to unpack .../libsystemd0_232-25+deb9u14_amd64.deb ... Unpacking libsystemd0:amd64 (232-25+deb9u14) over (232-25+deb9u12) ... Setting up libsystemd0:amd64 (232-25+deb9u14) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4710 files and directories currently installed.) Preparing to unpack .../libcomerr2_1.43.4-2+deb9u2_amd64.deb ... Unpacking libcomerr2:amd64 (1.43.4-2+deb9u2) over (1.43.4-2+deb9u1) ... Setting up libcomerr2:amd64 (1.43.4-2+deb9u2) ... (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 ... 4710 files and directories currently installed.) Preparing to unpack .../libss2_1.43.4-2+deb9u2_amd64.deb ... Unpacking libss2:amd64 (1.43.4-2+deb9u2) over (1.43.4-2+deb9u1) ... Setting up libss2:amd64 (1.43.4-2+deb9u2) ... (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 ... 4710 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.4-4.1+deb9u1_amd64.deb ... Unpacking passwd (1:4.4-4.1+deb9u1) over (1:4.4-4.1) ... Setting up passwd (1:4.4-4.1+deb9u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4710 files and directories currently installed.) Preparing to unpack .../libudev1_232-25+deb9u14_amd64.deb ... Unpacking libudev1:amd64 (232-25+deb9u14) over (232-25+deb9u12) ... Setting up libudev1:amd64 (232-25+deb9u14) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4710 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.7.6-2+deb9u4_amd64.deb ... Unpacking libgcrypt20:amd64 (1.7.6-2+deb9u4) over (1.7.6-2+deb9u3) ... Setting up libgcrypt20:amd64 (1.7.6-2+deb9u4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4710 files and directories currently installed.) Preparing to unpack .../00-libssl1.1_1.1.0l-1~deb9u6_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.0l-1~deb9u6) over (1.1.0l-1~deb9u1) ... Preparing to unpack .../01-libgmp10_2%3a6.1.2+dfsg-1+deb9u1_amd64.deb ... Unpacking libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) over (2:6.1.2+dfsg-1) ... Preparing to unpack .../02-libhogweed4_3.3-1+deb9u1_amd64.deb ... Unpacking libhogweed4:amd64 (3.3-1+deb9u1) over (3.3-1+b2) ... Preparing to unpack .../03-libnettle6_3.3-1+deb9u1_amd64.deb ... Unpacking libnettle6:amd64 (3.3-1+deb9u1) over (3.3-1+b2) ... Preparing to unpack .../04-libp11-kit0_0.23.3-2+deb9u1_amd64.deb ... Unpacking libp11-kit0:amd64 (0.23.3-2+deb9u1) over (0.23.3-2) ... Preparing to unpack .../05-libgnutls30_3.5.8-5+deb9u6_amd64.deb ... Unpacking libgnutls30:amd64 (3.5.8-5+deb9u6) over (3.5.8-5+deb9u5) ... Preparing to unpack .../06-libgssapi-krb5-2_1.15-1+deb9u3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.15-1+deb9u3) over (1.15-1+deb9u1) ... Preparing to unpack .../07-libkrb5-3_1.15-1+deb9u3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.15-1+deb9u3) over (1.15-1+deb9u1) ... Preparing to unpack .../08-libkrb5support0_1.15-1+deb9u3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.15-1+deb9u3) over (1.15-1+deb9u1) ... Preparing to unpack .../09-libk5crypto3_1.15-1+deb9u3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.15-1+deb9u3) over (1.15-1+deb9u1) ... Preparing to unpack .../10-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3+deb9u2_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) over (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Preparing to unpack .../11-libsasl2-2_2.1.27~101-g0780600+dfsg-3+deb9u2_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) over (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Preparing to unpack .../12-libldap-common_2.4.44+dfsg-5+deb9u9_all.deb ... Unpacking libldap-common (2.4.44+dfsg-5+deb9u9) over (2.4.44+dfsg-5+deb9u4) ... Preparing to unpack .../13-libldap-2.4-2_2.4.44+dfsg-5+deb9u9_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u9) over (2.4.44+dfsg-5+deb9u4) ... Preparing to unpack .../14-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 .../15-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 .../16-libcurl3-gnutls_7.52.1-5+deb9u16_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.52.1-5+deb9u16) over (7.52.1-5+deb9u10) ... Setting up libnettle6:amd64 (3.3-1+deb9u1) ... Setting up libnghttp2-14:amd64 (1.18.1-1+deb9u2) ... Setting up libldap-common (2.4.44+dfsg-5+deb9u9) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u3) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) ... Setting up libssh2-1:amd64 (1.7.0-1+deb9u2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u6) ... Setting up libp11-kit0:amd64 (0.23.3-2+deb9u1) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u3) ... Setting up libhogweed4:amd64 (3.3-1+deb9u1) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u3) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u6) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u9) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u16) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', '-yf', 'dist-upgrade'] 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.0s DUMP: f0660a0a38f941b755664f52e8306b99 - 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'show', '--no-all-versions', 'pbdagcon'] 0m18.3s DUMP: Package: pbdagcon Version: 0.3+20161121+ds-1 Installed-Size: 1145 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.4), libhdf5-100, libhdf5-cpp-100 (>= 1.8.13), libhts1 (>= 1.0), libstdc++6 (>= 6), zlib1g (>= 1:1.1.4), libpbseq, libpbbam Suggests: blasr Description-en: sequence consensus using directed acyclic graphs pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment. . It uses the alignment information from blasr to align sequence reads to a "backbone" sequence. Based on the underlying alignment directed acyclic graph (DAG), it will be able to use the new information from the reads to find the discrepancies between the reads and the "backbone" sequences. A dynamic programming process is then applied to the DAG to find the optimum sequence of bases as the consensus. The new consensus can be used as a new backbone sequence to iteratively improve the consensus quality. . While the code is developed for processing PacBio(TM) raw sequence data, the algorithm can be used for general consensus purpose. Currently, it only takes FASTA input. For shorter read sequences, one might need to adjust the blasr alignment parameters to get the alignment string properly. . The code and the underlying graphical data structure have been used for some algorithm development prototyping including phasing reads and pre-assembly. Description-md5: 95465f5fc6fbaa2db477a48c78b7cd82 Homepage: https://github.com/PacificBiosciences/pbdagcon Section: science Priority: optional Filename: pool/main/p/pbdagcon/pbdagcon_0.3+20161121+ds-1_amd64.deb Size: 322426 MD5sum: fb5ecdb8914fd6ccd42f264509255d3d SHA256: 9308757881828c5c57e08d8a9bee767f6c91474e2555f185d450a7c4dab68b7e 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'show', '--no-all-versions', 'pbdagcon'] 0m18.3s INFO: apt-cache knows about the following packages: pbdagcon 0m18.3s INFO: Running scripts pre_install 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_database-server'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_database-server'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_exceptions'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_exceptions'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_extras'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_extras'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'policy'] 0m18.5s 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: 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'policy'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'policy', 'pbdagcon'] 0m18.5s DUMP: pbdagcon: Installed: 0.3+20161121+ds-1 Candidate: 0.3+20161121+ds-1 Version table: *** 0.3+20161121+ds-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'policy', 'pbdagcon'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', '-y', 'install', 'pbdagcon'] 0m18.9s DUMP: Reading package lists... Building dependency tree... Reading state information... pbdagcon is already the newest version (0.3+20161121+ds-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', '-y', 'install', 'pbdagcon'] 0m18.9s INFO: Running scripts post_install 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_install_exceptions'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_install_exceptions'] 0m18.9s INFO: Running scripts post_distupgrade 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_distupgrade_exceptions'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_distupgrade_exceptions'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m19.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m19.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m19.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m19.4s INFO: Running scripts pre_install 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_database-server'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_database-server'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_exceptions'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_exceptions'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_extras'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_extras'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'policy'] 0m19.5s 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: 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'policy'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'policy', 'pbdagcon'] 0m19.6s DUMP: pbdagcon: Installed: 0.3+20161121+ds-1 Candidate: 0.3+20161121+ds-1 Version table: *** 0.3+20161121+ds-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-cache', 'policy', 'pbdagcon'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', '-y', 'install', 'pbdagcon=0.3+20161121+ds-1'] 0m19.9s DUMP: Reading package lists... Building dependency tree... Reading state information... pbdagcon is already the newest version (0.3+20161121+ds-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', '-y', 'install', 'pbdagcon=0.3+20161121+ds-1'] 0m19.9s INFO: Running scripts post_install 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_install_exceptions'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_install_exceptions'] 0m19.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m20.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m20.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', '-ac', '--ignore-obsolete'] 0m21.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', '-ac', '--ignore-obsolete'] 0m21.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.0s DUMP: 0.15.6 0m21.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.0s INFO: Running adequate version 0.15.6 now. 0m21.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'pbdagcon'] 0m21.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'pbdagcon'] 0m21.2s INFO: Running scripts pre_remove 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_remove_exceptions'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/pre_remove_exceptions'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m22.7s 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 coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u2 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.26 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u2 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u2 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+deb9u1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libaec0:amd64 libaec0 0.3.2-1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.11 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblasr:amd64 libblasr 0~20161219-1 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u2 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.52.1-5+deb9u16 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libffi6:amd64 libffi6 3.2.1-6 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u4 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-1+deb9u1 install ok installed libgnutls30:amd64 libgnutls30 3.5.8-5+deb9u6 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.15-1+deb9u3 install ok installed libhdf5-100:amd64 libhdf5-100 1.10.0-patch1+docs-3+deb9u1 install ok installed libhdf5-cpp-100:amd64 libhdf5-cpp-100 1.10.0-patch1+docs-3+deb9u1 install ok installed libhogweed4:amd64 libhogweed4 3.3-1+deb9u1 install ok installed libhts1:amd64 libhts1 1.3.2-2 install ok installed libidn11:amd64 libidn11 1.33-1+deb9u1 install ok installed libidn2-0:amd64 libidn2-0 0.16-1+deb9u1 install ok installed libk5crypto3:amd64 libk5crypto3 1.15-1+deb9u3 install ok installed libkeyutils1:amd64 libkeyutils1 1.5.9-9 install ok installed libkrb5-3:amd64 libkrb5-3 1.15-1+deb9u3 install ok installed libkrb5support0:amd64 libkrb5support0 1.15-1+deb9u3 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.44+dfsg-5+deb9u9 install ok installed libldap-common libldap-common 2.4.44+dfsg-5+deb9u9 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+deb9u1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+deb9u1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libnettle6:amd64 libnettle6 3.3-1+deb9u1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.18.1-1+deb9u2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.3-2+deb9u1 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpbbam:amd64 libpbbam 0.7.4+ds-1 install ok installed libpbdata:amd64 libpbdata 0~20161219-1 install ok installed libpbihdf:amd64 libpbihdf 0~20161219-1 install ok installed libpbseq libpbseq 0~20161219-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libpsl5:amd64 libpsl5 0.17.0-3 install ok installed libquadmath0:amd64 libquadmath0 6.3.0-18+deb9u1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-1+b1 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27~101-g0780600+dfsg-3+deb9u2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27~101-g0780600+dfsg-3+deb9u2 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u2 install ok installed libssh2-1:amd64 libssh2-1 1.7.0-1+deb9u2 install ok installed libssl1.1:amd64 libssl1.1 1.1.0l-1~deb9u6 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u14 install ok installed libsz2:amd64 libsz2 0.3.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.10-1.1+deb9u1 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u14 install ok installed libunistring0:amd64 libunistring0 0.9.6+really0.9.3-0.1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1+deb9u1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1+deb9u1 install ok installed pbdagcon pbdagcon 0.3+20161121+ds-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+deb9u1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5+deb9u1 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', 'remove', 'libaec0:amd64', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-100:amd64', 'libhdf5-cpp-100:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpbbam:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpsl5:amd64', 'libquadmath0:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'pbdagcon'] 0m23.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libaec0 libblasr libcurl3-gnutls libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libnettle6 libnghttp2-14 libp11-kit0 libpbbam libpbdata libpbihdf libpbseq libpsl5 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 pbdagcon 0 upgraded, 0 newly installed, 38 to remove and 0 not upgraded. After this operation, 27.6 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 ... 4709 files and directories currently installed.) Removing pbdagcon (0.3+20161121+ds-1) ... Removing libpbseq (0~20161219-1) ... Removing libblasr:amd64 (0~20161219-1) ... Removing libpbihdf:amd64 (0~20161219-1) ... Removing libhdf5-cpp-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Removing libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Removing libsz2:amd64 (0.3.2-1) ... Removing libaec0:amd64 (0.3.2-1) ... Removing libpbdata:amd64 (0~20161219-1) ... Removing libpbbam:amd64 (0.7.4+ds-1) ... 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 libgnutls30:amd64 (3.5.8-5+deb9u6) ... Removing libp11-kit0:amd64 (0.23.3-2+deb9u1) ... Removing libffi6:amd64 (3.2.1-6) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libhogweed4:amd64 (3.3-1+deb9u1) ... Removing libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) ... Removing libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... Removing libidn11:amd64 (1.33-1+deb9u1) ... Removing libpsl5:amd64 (0.17.0-3) ... Removing libidn2-0:amd64 (0.16-1+deb9u1) ... Removing libkrb5-3:amd64 (1.15-1+deb9u3) ... Removing libk5crypto3:amd64 (1.15-1+deb9u3) ... Removing libkrb5support0:amd64 (1.15-1+deb9u3) ... Removing libkeyutils1:amd64 (1.5.9-9) ... Removing libldap-common (2.4.44+dfsg-5+deb9u9) ... Removing libnettle6:amd64 (3.3-1+deb9u1) ... Removing libnghttp2-14:amd64 (1.18.1-1+deb9u2) ... Removing libquadmath0:amd64 (6.3.0-18+deb9u1) ... Removing libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Removing libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Removing libssh2-1:amd64 (1.7.0-1+deb9u2) ... Removing libssl1.1:amd64 (1.1.0l-1~deb9u6) ... Removing libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', 'remove', 'libaec0:amd64', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-100:amd64', 'libhdf5-cpp-100:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpbbam:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpsl5:amd64', 'libquadmath0:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'pbdagcon'] 0m23.5s INFO: Running scripts post_remove 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_remove_exceptions'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_remove_exceptions'] 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg', '--purge', 'libaec0:amd64', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-100:amd64', 'libhdf5-cpp-100:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpbbam:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpsl5:amd64', 'libquadmath0:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64'] 0m23.6s DUMP: dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libblasr which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libffi6 which isn't installed dpkg: warning: ignoring request to remove libgfortran3 which isn't installed dpkg: warning: ignoring request to remove libgmp10 which isn't installed dpkg: warning: ignoring request to remove libgnutls30 which isn't installed (Reading database ... 4416 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... dpkg: warning: ignoring request to remove libhdf5-100 which isn't installed dpkg: warning: ignoring request to remove libhdf5-cpp-100 which isn't installed dpkg: warning: ignoring request to remove libhogweed4 which isn't installed dpkg: warning: ignoring request to remove libhts1 which isn't installed dpkg: warning: ignoring request to remove libidn11 which isn't installed dpkg: warning: ignoring request to remove libidn2-0 which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.44+dfsg-5+deb9u9) ... dpkg: warning: ignoring request to remove libnettle6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libpbbam which isn't installed dpkg: warning: ignoring request to remove libpbdata which isn't installed dpkg: warning: ignoring request to remove libpbihdf which isn't installed dpkg: warning: ignoring request to remove libpbseq which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 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 libssh2-1 which isn't installed Purging configuration files for libssl1.1:amd64 (1.1.0l-1~deb9u6) ... dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libunistring0 which isn't installed 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg', '--purge', 'libaec0:amd64', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-100:amd64', 'libhdf5-cpp-100:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpbbam:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpsl5:amd64', 'libquadmath0:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg', '--purge', 'pbdagcon'] 0m23.6s DUMP: dpkg: warning: ignoring request to remove pbdagcon which isn't installed 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg', '--purge', 'pbdagcon'] 0m23.6s INFO: Running scripts post_purge 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_purge_exceptions'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_purge_exceptions'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg', '--purge', '--pending'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg', '--purge', '--pending'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg', '--remove', '--pending'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg', '--remove', '--pending'] 0m23.6s INFO: Running scripts post_test 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_test_exceptions'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'tmp/scripts/post_test_exceptions'] 0m23.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m23.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg-divert', '--list'] 0m23.8s 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 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'dpkg-divert', '--list'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', 'clean'] 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpixzvjfva', 'apt-get', 'clean'] 0m23.9s DEBUG: Recording chroot state 0m24.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/shm'] 0m24.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/shm'] 0m24.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/console'] 0m24.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/console'] 0m24.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/ptmx'] 0m24.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/ptmx'] 0m24.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/pts'] 0m24.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/dev/pts'] 0m24.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/proc'] 0m24.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpixzvjfva/proc'] 0m24.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m24.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpixzvjfva'] 0m24.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpixzvjfva 0m24.8s INFO: PASS: Upgrading between Debian distributions. 0m24.8s INFO: PASS: All tests. 0m24.8s INFO: piuparts run ends. ret=0 End: 2023-01-01 13:39:10 GMT