Start: 2023-01-25 12:58:16 GMT [stretch] Package: pbhoney Source: pbsuite Version: 15.8.24+dfsg-2 Installed-Size: 2356 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any (<< 2.8), python:any (>= 2.7.5-5~), python-pbsuite-utils (= 15.8.24+dfsg-2), python-pbbanana (= 15.8.24+dfsg-2), python-pysam (>= 0.8.0), python-networkx, python-h5py (>= 2.0.1), python-numpy, python-intervaltree-bio, blasr (>= 5.3), samtools Recommends: pbdagcon Description: genomic structural variation discovery Homepage: http://sourceforge.net/projects/pb-jelly Description-md5: 10f81042bd82750e013162caaa443ce8 Section: science Priority: optional Filename: pool/main/p/pbsuite/pbhoney_15.8.24+dfsg-2_all.deb Size: 1311344 MD5sum: a3405188905b51e06693337e30ff319c SHA256: 90b80cb0e864dcba7f32584ed58df06aa92d46ef792a62a1b46ee512bdb132f9 [stretch-lts] Package: pbhoney Source: pbsuite Version: 15.8.24+dfsg-2 Installed-Size: 2356 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any (<< 2.8), python:any (>= 2.7.5-5~), python-pbsuite-utils (= 15.8.24+dfsg-2), python-pbbanana (= 15.8.24+dfsg-2), python-pysam (>= 0.8.0), python-networkx, python-h5py (>= 2.0.1), python-numpy, python-intervaltree-bio, blasr (>= 5.3), samtools Recommends: pbdagcon Description: genomic structural variation discovery Homepage: http://sourceforge.net/projects/pb-jelly Description-md5: 10f81042bd82750e013162caaa443ce8 Section: science Priority: optional Filename: pool/main/p/pbsuite/pbhoney_15.8.24+dfsg-2_all.deb Size: 1311344 MD5sum: a3405188905b51e06693337e30ff319c SHA256: 90b80cb0e864dcba7f32584ed58df06aa92d46ef792a62a1b46ee512bdb132f9 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 pbhoney=15.8.24+dfsg-2 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 pbhoney=15.8.24+dfsg-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmppo2t8zby 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmppo2t8zby 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/proc'] 0m1.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/proc'] 0m1.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/pts'] 0m1.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/pts'] 0m1.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/ptmx'] 0m1.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/ptmx'] 0m1.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/console'] 0m1.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/console'] 0m1.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/shm'] 0m1.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/shm'] 0m1.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.3s DEBUG: Created policy-rc.d and chmodded it. 0m1.3s DEBUG: Created resolv.conf. 0m1.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmppo2t8zby/tmp/scripts/ 0m1.3s INFO: Running scripts post_chroot_unpack 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', 'update'] 0m2.1s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', 'update'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s INFO: Running scripts post_setup 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2next/reference-chroot-metadata.dat 0m3.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m3.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m3.8s INFO: Running scripts is_testable 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/is_testable_uninstallable'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/is_testable_uninstallable'] 0m3.8s INFO: Running scripts pre_test 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_test_exceptions'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_test_exceptions'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_test_root_password'] 0m3.8s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_test_root_password'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'show', '--no-all-versions', 'pbhoney'] 0m3.9s DUMP: Package: pbhoney Source: pbsuite Version: 15.8.24+dfsg-2 Installed-Size: 2356 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any (<< 2.8), python:any (>= 2.7.5-5~), python-pbsuite-utils (= 15.8.24+dfsg-2), python-pbbanana (= 15.8.24+dfsg-2), python-pysam (>= 0.8.0), python-networkx, python-h5py (>= 2.0.1), python-numpy, python-intervaltree-bio, blasr (>= 5.3), samtools Recommends: pbdagcon Description-en: genomic structural variation discovery PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants. . PBHoney is part of the PBSuite. Description-md5: 10f81042bd82750e013162caaa443ce8 Homepage: http://sourceforge.net/projects/pb-jelly Section: science Priority: optional Filename: pool/main/p/pbsuite/pbhoney_15.8.24+dfsg-2_all.deb Size: 1311344 MD5sum: a3405188905b51e06693337e30ff319c SHA256: 90b80cb0e864dcba7f32584ed58df06aa92d46ef792a62a1b46ee512bdb132f9 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'show', '--no-all-versions', 'pbhoney'] 0m3.9s INFO: apt-cache knows about the following packages: pbhoney 0m3.9s INFO: Running scripts pre_install 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_database-server'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_database-server'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_exceptions'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_exceptions'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_extras'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_extras'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'policy'] 0m4.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'policy'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'policy', 'pbhoney'] 0m4.1s DUMP: pbhoney: Installed: (none) Candidate: 15.8.24+dfsg-2 Version table: 15.8.24+dfsg-2 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'policy', 'pbhoney'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', '-y', 'install', 'pbhoney'] 0m11.0s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: blasr libaec0 libblas-common libblas3 libblasr libcurl3-gnutls libexpat1 libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libncurses5 libnettle6 libnghttp2-14 libp11-kit0 libpbbam libpbdata libpbihdf libpbseq libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 mime-support pbjelly python python-decorator python-h5py python-intervaltree python-intervaltree-bio python-minimal python-networkx python-numpy python-pbbanana python-pbsuite-utils python-pysam python-six python-sortedcontainers python2.7 python2.7-minimal readline-common samtools Suggested packages: gnutls-bin krb5-doc krb5-user python-doc python-tk python-h5py-doc python-networkx-doc gcc gfortran python-dev python-nose python-numpy-dbg python-numpy-doc python-sortedcontainers-doc python2.7-doc binutils binfmt-support readline-doc Recommended packages: ca-certificates krb5-locales libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils pbdagcon python-matplotlib python-pkg-resources python-pygraphviz | python-pydot python-scipy python-yaml The following NEW packages will be installed: blasr libaec0 libblas-common libblas3 libblasr libcurl3-gnutls libexpat1 libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libncurses5 libnettle6 libnghttp2-14 libp11-kit0 libpbbam libpbdata libpbihdf libpbseq libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 mime-support pbhoney pbjelly python python-decorator python-h5py python-intervaltree python-intervaltree-bio python-minimal python-networkx python-numpy python-pbbanana python-pbsuite-utils python-pysam python-six python-sortedcontainers python2.7 python2.7-minimal readline-common samtools 0 upgraded, 68 newly installed, 0 to remove and 0 not upgraded. Need to get 25.2 MB of archives. After this operation, 89.9 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u3 [389 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u3 [1382 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u3 [83.7 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 python amd64 2.7.13-2 [154 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b2 [192 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b2 [136 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libtasn1-6 amd64 4.10-1.1+deb9u1 [50.6 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 libgnutls30 amd64 3.5.8-5+deb9u5 [896 kB] Get:22 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amd64 6.3.0-18+deb9u1 [131 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 libaec0 amd64 0.3.2-1 [18.5 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 libsz2 amd64 0.3.2-1 [5730 B] Get:35 http://deb.debian.org/debian stretch/main amd64 libhdf5-100 amd64 1.10.0-patch1+docs-3+deb9u1 [1282 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 libhdf5-cpp-100 amd64 1.10.0-patch1+docs-3+deb9u1 [130 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 libssh2-1 amd64 1.7.0-1+deb9u1 [139 kB] Get:43 http://deb.debian.org/debian stretch/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u10 [290 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 libhts1 amd64 1.3.2-2 [257 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 libpbbam amd64 0.7.4+ds-1 [478 kB] Get:46 http://deb.debian.org/debian stretch/main amd64 libpbdata amd64 0~20161219-1 [129 kB] Get:47 http://deb.debian.org/debian stretch/main amd64 libpbihdf amd64 0~20161219-1 [167 kB] Get:48 http://deb.debian.org/debian stretch/main amd64 libblasr amd64 0~20161219-1 [867 kB] Get:49 http://deb.debian.org/debian stretch/main amd64 libpbseq all 0~20161219-1 [3876 B] Get:50 http://deb.debian.org/debian stretch/main amd64 blasr amd64 5.3+0-1 [691 kB] Get:51 http://deb.debian.org/debian stretch/main amd64 libblas-common amd64 3.7.0-2 [14.2 kB] Get:52 http://deb.debian.org/debian stretch/main amd64 libblas3 amd64 3.7.0-2 [155 kB] Get:53 http://deb.debian.org/debian stretch/main amd64 liblapack3 amd64 3.7.0-2 [2141 kB] Get:54 http://deb.debian.org/debian stretch/main amd64 libncurses5 amd64 6.0+20161126-1+deb9u2 [93.4 kB] Get:55 http://deb.debian.org/debian stretch/main amd64 python-pysam amd64 0.10.0+ds-2 [1301 kB] Get:56 http://deb.debian.org/debian stretch/main amd64 python-pbsuite-utils all 15.8.24+dfsg-2 [508 kB] Get:57 http://deb.debian.org/debian stretch/main amd64 python-decorator all 4.0.11-1 [13.3 kB] Get:58 http://deb.debian.org/debian stretch/main amd64 python-networkx all 1.11-2 [822 kB] Get:59 http://deb.debian.org/debian stretch/main amd64 pbjelly all 15.8.24+dfsg-2 [1210 kB] Get:60 http://deb.debian.org/debian stretch/main amd64 python-pbbanana all 15.8.24+dfsg-2 [19.3 kB] Get:61 http://deb.debian.org/debian stretch/main amd64 python-numpy amd64 1:1.12.1-3 [1936 kB] Get:62 http://deb.debian.org/debian stretch/main amd64 python-six all 1.10.0-3 [14.4 kB] Get:63 http://deb.debian.org/debian stretch/main amd64 python-h5py amd64 2.7.0-1 [634 kB] Get:64 http://deb.debian.org/debian stretch/main amd64 python-sortedcontainers all 1.5.7-1 [26.2 kB] Get:65 http://deb.debian.org/debian stretch/main amd64 python-intervaltree all 2.1.0-2 [32.0 kB] Get:66 http://deb.debian.org/debian stretch/main amd64 python-intervaltree-bio all 1.0.1-1 [7818 B] Get:67 http://deb.debian.org/debian stretch/main amd64 samtools amd64 1.3.1-3 [254 kB] Get:68 http://deb.debian.org/debian stretch/main amd64 pbhoney all 15.8.24+dfsg-2 [1311 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.2 MB in 0s (77.6 MB/s) Selecting previously unselected package libpython2.7-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4411 files and directories currently installed.) Preparing to unpack .../00-libpython2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../01-python2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking python2.7-minimal (2.7.13-2+deb9u3) ... Selecting previously unselected package python-minimal. 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Unpacking samtools (1.3.1-3) ... Selecting previously unselected package pbhoney. Preparing to unpack .../54-pbhoney_15.8.24+dfsg-2_all.deb ... Unpacking pbhoney (15.8.24+dfsg-2) ... Setting up libquadmath0:amd64 (6.3.0-18+deb9u1) ... Setting up libncurses5:amd64 (6.0+20161126-1+deb9u2) ... Setting up readline-common (7.0-3) ... Setting up libnettle6:amd64 (3.3-1+b2) ... Setting up libaec0:amd64 (0.3.2-1) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u3) ... Setting up libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Setting up mime-support (3.60) ... Setting up libldap-common (2.4.44+dfsg-5+deb9u4) ... Setting up libreadline7:amd64 (7.0-3) ... Setting up libblas-common (3.7.0-2) ... Setting up libgfortran3:amd64 (6.3.0-18+deb9u1) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-1) ... Setting up libblas3 (3.7.0-2) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libssh2-1:amd64 (1.7.0-1+deb9u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up libidn11:amd64 (1.33-1+deb9u1) ... Setting up libsz2:amd64 (0.3.2-1) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up liblapack3 (3.7.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u1) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up python (2.7.13-2) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u1) ... Setting up 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 python-numpy (1:1.12.1-3) ... Setting up python-six (1.10.0-3) ... Setting up python-sortedcontainers (1.5.7-1) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up python-decorator (4.0.11-1) ... Setting up python-h5py (2.7.0-1) ... Setting up python-networkx (1.11-2) ... Setting up python-intervaltree (2.1.0-2) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up python-intervaltree-bio (1.0.1-1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Setting up libhts1:amd64 (1.3.2-2) ... Setting up python-pysam (0.10.0+ds-2) ... Setting up libpbbam:amd64 (0.7.4+ds-1) ... Setting up samtools (1.3.1-3) ... Setting up python-pbsuite-utils (15.8.24+dfsg-2) ... 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 blasr (5.3+0-1) ... Setting up pbjelly (15.8.24+dfsg-2) ... Setting up python-pbbanana (15.8.24+dfsg-2) ... Setting up pbhoney (15.8.24+dfsg-2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', '-y', 'install', 'pbhoney'] 0m11.0s INFO: Running scripts post_install 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_install_exceptions'] 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_install_exceptions'] 0m11.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m11.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m11.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmppo2t8zby to stretch-lts 0m11.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main deb http://security.debian.org stretch/updates main 0m11.5s INFO: Running scripts pre_distupgrade 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_distupgrade_exceptions'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_distupgrade_exceptions'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', 'update'] 0m13.1s 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 (2373 kB/s) Reading package lists... 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', 'update'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', '-yf', 'dist-upgrade'] 0m17.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt debian-archive-keyring dpkg e2fslibs e2fsprogs gzip libapt-pkg5.0 libcomerr2 libcurl3-gnutls libexpat1 libgcrypt20 libgmp10 libgnutls30 libgssapi-krb5-2 libhogweed4 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblz4-1 liblzma5 libnettle6 libnghttp2-14 libp11-kit0 libpython2.7-minimal libpython2.7-stdlib libsasl2-2 libsasl2-modules-db libsqlite3-0 libss2 libssh2-1 libssl1.1 libsystemd0 libudev1 login passwd python2.7 python2.7-minimal tar zlib1g 41 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 18.8 MB of archives. After this operation, 72.7 kB of additional disk space will be used. Get:1 http://security.debian.org stretch/updates/main amd64 tar amd64 1.29b-1.1+deb9u1 [760 kB] Get:2 http://security.debian.org stretch/updates/main amd64 dpkg amd64 1.18.26 [2117 kB] Get:3 http://security.debian.org stretch/updates/main amd64 e2fslibs amd64 1.43.4-2+deb9u2 [208 kB] Get:4 http://security.debian.org stretch/updates/main amd64 e2fsprogs amd64 1.43.4-2+deb9u2 [948 kB] Get:5 http://security.debian.org stretch/updates/main amd64 gzip amd64 1.6-5+deb9u1 [114 kB] Get:6 http://security.debian.org stretch/updates/main amd64 login amd64 1:4.4-4.1+deb9u1 [790 kB] Get:7 http://security.debian.org stretch/updates/main amd64 debian-archive-keyring all 2017.5+deb9u2 [92.4 kB] Get:8 http://security.debian.org stretch/updates/main amd64 liblz4-1 amd64 0.0~r131-2+deb9u1 [33.2 kB] Get:9 http://security.debian.org stretch/updates/main amd64 liblzma5 amd64 5.2.2-1.2+deb9u1 [234 kB] Get:10 http://security.debian.org stretch/updates/main amd64 zlib1g amd64 1:1.2.8.dfsg-5+deb9u1 [87.8 kB] Get:11 http://security.debian.org stretch/updates/main amd64 libapt-pkg5.0 amd64 1.4.11 [917 kB] Get:12 http://security.debian.org stretch/updates/main amd64 apt amd64 1.4.11 [1232 kB] Get:13 http://security.debian.org stretch/updates/main amd64 libsystemd0 amd64 232-25+deb9u14 [282 kB] Get:14 http://security.debian.org stretch/updates/main amd64 python2.7 amd64 2.7.13-2+deb9u6 [286 kB] Get:15 http://security.debian.org stretch/updates/main amd64 libexpat1 amd64 2.2.0-2+deb9u5 [84.7 kB] Get:16 http://security.debian.org stretch/updates/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u3 [574 kB] Get:17 http://security.debian.org stretch/updates/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u6 [1360 kB] Get:18 http://security.debian.org stretch/updates/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u6 [1898 kB] Get:19 http://security.debian.org stretch/updates/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u6 [1382 kB] Get:20 http://security.debian.org stretch/updates/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u6 [390 kB] Get:21 http://security.debian.org stretch/updates/main amd64 libcomerr2 amd64 1.43.4-2+deb9u2 [63.8 kB] Get:22 http://security.debian.org stretch/updates/main amd64 libss2 amd64 1.43.4-2+deb9u2 [68.0 kB] Get:23 http://security.debian.org stretch/updates/main amd64 passwd amd64 1:4.4-4.1+deb9u1 [997 kB] Get:24 http://security.debian.org stretch/updates/main amd64 libudev1 amd64 232-25+deb9u14 [126 kB] Get:25 http://security.debian.org stretch/updates/main amd64 libgcrypt20 amd64 1.7.6-2+deb9u4 [523 kB] Get:26 http://security.debian.org stretch/updates/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1+deb9u1 [253 kB] Get:27 http://security.debian.org stretch/updates/main amd64 libhogweed4 amd64 3.3-1+deb9u1 [136 kB] Get:28 http://security.debian.org stretch/updates/main amd64 libnettle6 amd64 3.3-1+deb9u1 [192 kB] Get:29 http://security.debian.org stretch/updates/main amd64 libp11-kit0 amd64 0.23.3-2+deb9u1 [112 kB] Get:30 http://security.debian.org stretch/updates/main amd64 libgnutls30 amd64 3.5.8-5+deb9u6 [897 kB] Get:31 http://security.debian.org stretch/updates/main amd64 libgssapi-krb5-2 amd64 1.15-1+deb9u3 [155 kB] Get:32 http://security.debian.org stretch/updates/main amd64 libkrb5-3 amd64 1.15-1+deb9u3 [312 kB] Get:33 http://security.debian.org stretch/updates/main amd64 libkrb5support0 amd64 1.15-1+deb9u3 [62.3 kB] Get:34 http://security.debian.org stretch/updates/main amd64 libk5crypto3 amd64 1.15-1+deb9u3 [120 kB] Get:35 http://security.debian.org stretch/updates/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u2 [68.5 kB] Get:36 http://security.debian.org stretch/updates/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u2 [105 kB] Get:37 http://security.debian.org stretch/updates/main amd64 libldap-common all 2.4.44+dfsg-5+deb9u9 [86.3 kB] Get:38 http://security.debian.org stretch/updates/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u9 [220 kB] Get:39 http://security.debian.org stretch/updates/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u2 [79.4 kB] Get:40 http://security.debian.org stretch/updates/main amd64 libssh2-1 amd64 1.7.0-1+deb9u2 [139 kB] Get:41 http://security.debian.org stretch/updates/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u16 [296 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.8 MB in 0s (94.2 MB/s) (Reading database ... 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Unpacking libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) over (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Preparing to unpack .../10-libsasl2-2_2.1.27~101-g0780600+dfsg-3+deb9u2_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) over (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Preparing to unpack .../11-libldap-common_2.4.44+dfsg-5+deb9u9_all.deb ... Unpacking libldap-common (2.4.44+dfsg-5+deb9u9) over (2.4.44+dfsg-5+deb9u4) ... Preparing to unpack .../12-libldap-2.4-2_2.4.44+dfsg-5+deb9u9_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u9) over (2.4.44+dfsg-5+deb9u4) ... Preparing to unpack .../13-libnghttp2-14_1.18.1-1+deb9u2_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.18.1-1+deb9u2) over (1.18.1-1+deb9u1) ... Preparing to unpack .../14-libssh2-1_1.7.0-1+deb9u2_amd64.deb ... Unpacking libssh2-1:amd64 (1.7.0-1+deb9u2) over (1.7.0-1+deb9u1) ... Preparing to unpack .../15-libcurl3-gnutls_7.52.1-5+deb9u16_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.52.1-5+deb9u16) over (7.52.1-5+deb9u10) ... Setting up libnettle6:amd64 (3.3-1+deb9u1) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u5) ... Setting up libnghttp2-14:amd64 (1.18.1-1+deb9u2) ... Processing triggers for mime-support (3.60) ... Setting up libldap-common (2.4.44+dfsg-5+deb9u9) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u3) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) ... Setting up libssh2-1:amd64 (1.7.0-1+deb9u2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u6) ... Setting up libp11-kit0:amd64 (0.23.3-2+deb9u1) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u3) ... Setting up libpython2.7-minimal:amd64 (2.7.13-2+deb9u6) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u6) ... Setting up python2.7-minimal (2.7.13-2+deb9u6) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u3) ... Setting up python2.7 (2.7.13-2+deb9u6) ... Setting up libhogweed4:amd64 (3.3-1+deb9u1) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u3) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u6) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u9) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u16) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', '-yf', 'dist-upgrade'] 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.1s DUMP: f0660a0a38f941b755664f52e8306b99 - 0m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'show', '--no-all-versions', 'pbhoney'] 0m18.2s DUMP: Package: pbhoney Source: pbsuite Version: 15.8.24+dfsg-2 Installed-Size: 2356 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any (<< 2.8), python:any (>= 2.7.5-5~), python-pbsuite-utils (= 15.8.24+dfsg-2), python-pbbanana (= 15.8.24+dfsg-2), python-pysam (>= 0.8.0), python-networkx, python-h5py (>= 2.0.1), python-numpy, python-intervaltree-bio, blasr (>= 5.3), samtools Recommends: pbdagcon Description-en: genomic structural variation discovery PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants. . PBHoney is part of the PBSuite. Description-md5: 10f81042bd82750e013162caaa443ce8 Homepage: http://sourceforge.net/projects/pb-jelly Section: science Priority: optional Filename: pool/main/p/pbsuite/pbhoney_15.8.24+dfsg-2_all.deb Size: 1311344 MD5sum: a3405188905b51e06693337e30ff319c SHA256: 90b80cb0e864dcba7f32584ed58df06aa92d46ef792a62a1b46ee512bdb132f9 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'show', '--no-all-versions', 'pbhoney'] 0m18.2s INFO: apt-cache knows about the following packages: pbhoney 0m18.2s INFO: Running scripts pre_install 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_database-server'] 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_database-server'] 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_exceptions'] 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_exceptions'] 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_extras'] 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_extras'] 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'policy'] 0m18.3s 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: 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'policy'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'policy', 'pbhoney'] 0m18.4s DUMP: pbhoney: Installed: 15.8.24+dfsg-2 Candidate: 15.8.24+dfsg-2 Version table: *** 15.8.24+dfsg-2 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'policy', 'pbhoney'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', '-y', 'install', 'pbhoney'] 0m18.7s DUMP: Reading package lists... Building dependency tree... Reading state information... pbhoney is already the newest version (15.8.24+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', '-y', 'install', 'pbhoney'] 0m18.7s INFO: Running scripts post_install 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_install_exceptions'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_install_exceptions'] 0m18.7s INFO: Running scripts post_distupgrade 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_distupgrade_exceptions'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_distupgrade_exceptions'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_distupgrade_zz_backports'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_distupgrade_zz_backports'] 0m18.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m19.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m19.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m19.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m19.6s INFO: Running scripts pre_install 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_database-server'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_database-server'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_exceptions'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_exceptions'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_extras'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_extras'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'policy'] 0m19.7s 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: 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'policy'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'policy', 'pbhoney'] 0m19.8s DUMP: pbhoney: Installed: 15.8.24+dfsg-2 Candidate: 15.8.24+dfsg-2 Version table: *** 15.8.24+dfsg-2 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-cache', 'policy', 'pbhoney'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', '-y', 'install', 'pbhoney=15.8.24+dfsg-2'] 0m20.0s DUMP: Reading package lists... Building dependency tree... Reading state information... pbhoney is already the newest version (15.8.24+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', '-y', 'install', 'pbhoney=15.8.24+dfsg-2'] 0m20.0s INFO: Running scripts post_install 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_install_exceptions'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_install_exceptions'] 0m20.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m20.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m20.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', '-ac', '--ignore-obsolete'] 0m21.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', '-ac', '--ignore-obsolete'] 0m21.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.4s DUMP: 0.15.6 0m21.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.4s INFO: Running adequate version 0.15.6 now. 0m21.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'pbhoney'] 0m21.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'pbhoney'] 0m21.5s INFO: Running scripts pre_remove 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_remove_exceptions'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/pre_remove_exceptions'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m22.5s 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 blasr blasr 5.3+0-1 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 libblas-common libblas-common 3.7.0-2 install ok installed libblas3 libblas3 3.7.0-2 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 libexpat1:amd64 libexpat1 2.2.0-2+deb9u5 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libffi6:amd64 libffi6 3.2.1-6 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u4 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-1+deb9u1 install ok installed libgnutls30:amd64 libgnutls30 3.5.8-5+deb9u6 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.15-1+deb9u3 install ok installed libhdf5-100:amd64 libhdf5-100 1.10.0-patch1+docs-3+deb9u1 install ok installed 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 liblapack3 liblapack3 3.7.0-2 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.44+dfsg-5+deb9u9 install ok installed libldap-common libldap-common 2.4.44+dfsg-5+deb9u9 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+deb9u1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+deb9u1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncurses5:amd64 libncurses5 6.0+20161126-1+deb9u2 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libnettle6:amd64 libnettle6 3.3-1+deb9u1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.18.1-1+deb9u2 install ok installed 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 libpython-stdlib:amd64 libpython-stdlib 2.7.13-2 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.13-2+deb9u6 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.13-2+deb9u6 install ok installed libquadmath0:amd64 libquadmath0 6.3.0-18+deb9u1 install ok installed libreadline7:amd64 libreadline7 7.0-3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-1+b1 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27~101-g0780600+dfsg-3+deb9u2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27~101-g0780600+dfsg-3+deb9u2 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.16.2-5+deb9u3 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u2 install ok installed libssh2-1:amd64 libssh2-1 1.7.0-1+deb9u2 install ok installed libssl1.1:amd64 libssl1.1 1.1.0l-1~deb9u6 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u14 install ok installed libsz2:amd64 libsz2 0.3.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.10-1.1+deb9u1 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u14 install ok installed libunistring0:amd64 libunistring0 0.9.6+really0.9.3-0.1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1+deb9u1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mime-support mime-support 3.60 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1+deb9u1 install ok installed pbhoney pbhoney 15.8.24+dfsg-2 install ok installed pbjelly pbjelly 15.8.24+dfsg-2 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed python python 2.7.13-2 install ok installed python-decorator python-decorator 4.0.11-1 install ok installed python-h5py python-h5py 2.7.0-1 install ok installed python-intervaltree python-intervaltree 2.1.0-2 install ok installed python-intervaltree-bio python-intervaltree-bio 1.0.1-1 install ok installed python-minimal python-minimal 2.7.13-2 install ok installed python-networkx python-networkx 1.11-2 install ok installed python-numpy python-numpy 1:1.12.1-3 install ok installed python-pbbanana python-pbbanana 15.8.24+dfsg-2 install ok installed python-pbsuite-utils python-pbsuite-utils 15.8.24+dfsg-2 install ok installed python-pysam python-pysam 0.10.0+ds-2 install ok installed python-six python-six 1.10.0-3 install ok installed python-sortedcontainers python-sortedcontainers 1.5.7-1 install ok installed python2.7 python2.7 2.7.13-2+deb9u6 install ok installed python2.7-minimal python2.7-minimal 2.7.13-2+deb9u6 install ok installed readline-common readline-common 7.0-3 install ok installed samtools samtools 1.3.1-3 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed 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 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', 'remove', 'blasr', 'libaec0:amd64', 'libblas-common', 'libblas3', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libexpat1: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', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libncurses5:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpbbam:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'mime-support', 'pbjelly', 'python', 'python-decorator', 'python-h5py', 'python-intervaltree', 'python-intervaltree-bio', 'python-minimal', 'python-networkx', 'python-numpy', 'python-pbbanana', 'python-pbsuite-utils', 'python-pysam', 'python-six', 'python-sortedcontainers', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools', 'pbhoney'] 0m23.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blasr libaec0 libblas-common libblas3 libblasr libcurl3-gnutls libexpat1 libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libncurses5 libnettle6 libnghttp2-14 libp11-kit0 libpbbam libpbdata libpbihdf libpbseq libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 mime-support pbhoney pbjelly python python-decorator python-h5py python-intervaltree python-intervaltree-bio python-minimal python-networkx python-numpy python-pbbanana python-pbsuite-utils python-pysam python-six python-sortedcontainers python2.7 python2.7-minimal readline-common samtools 0 upgraded, 0 newly installed, 68 to remove and 0 not upgraded. After this operation, 89.9 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 ... 6921 files and directories currently installed.) Removing pbhoney (15.8.24+dfsg-2) ... Removing python-pbbanana (15.8.24+dfsg-2) ... Removing pbjelly (15.8.24+dfsg-2) ... Removing blasr (5.3+0-1) ... 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 python-h5py (2.7.0-1) ... Removing libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Removing libsz2:amd64 (0.3.2-1) ... Removing libaec0:amd64 (0.3.2-1) ... Removing python-numpy (1:1.12.1-3) ... Removing liblapack3 (3.7.0-2) ... Removing libblas3 (3.7.0-2) ... Removing libblas-common (3.7.0-2) ... Removing samtools (1.3.1-3) ... Removing python-pbsuite-utils (15.8.24+dfsg-2) ... Removing python-pysam (0.10.0+ds-2) ... Removing python-intervaltree-bio (1.0.1-1) ... Removing python-intervaltree (2.1.0-2) ... Removing python-sortedcontainers (1.5.7-1) ... Removing python-six (1.10.0-3) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libncurses5:amd64 (6.0+20161126-1+deb9u2) ... Removing libpbdata:amd64 (0~20161219-1) ... Removing libpbbam:amd64 (0.7.4+ds-1) ... Removing libquadmath0:amd64 (6.3.0-18+deb9u1) ... Removing python-networkx (1.11-2) ... Removing python-decorator (4.0.11-1) ... Removing libhts1:amd64 (1.3.2-2) ... Removing libcurl3-gnutls:amd64 (7.52.1-5+deb9u16) ... Removing python (2.7.13-2) ... Removing python2.7 (2.7.13-2+deb9u6) ... Removing libpython-stdlib:amd64 (2.7.13-2) ... Removing libpython2.7-stdlib:amd64 (2.7.13-2+deb9u6) ... Removing libexpat1:amd64 (2.2.0-2+deb9u5) ... Removing libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u9) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Removing libgnutls30:amd64 (3.5.8-5+deb9u6) ... Removing libp11-kit0:amd64 (0.23.3-2+deb9u1) ... Removing libffi6:amd64 (3.2.1-6) ... Removing libhogweed4:amd64 (3.3-1+deb9u1) ... Removing libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) ... Removing 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 python-minimal (2.7.13-2) ... Removing python2.7-minimal (2.7.13-2+deb9u6) ... Removing libpython2.7-minimal:amd64 (2.7.13-2+deb9u6) ... Removing libreadline7:amd64 (7.0-3) ... Removing libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Removing libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u2) ... Removing libsqlite3-0:amd64 (3.16.2-5+deb9u3) ... Removing libssh2-1:amd64 (1.7.0-1+deb9u2) ... Removing libssl1.1:amd64 (1.1.0l-1~deb9u6) ... Removing libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing mime-support (3.60) ... Removing readline-common (7.0-3) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', 'remove', 'blasr', 'libaec0:amd64', 'libblas-common', 'libblas3', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libexpat1: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', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libncurses5:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpbbam:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'mime-support', 'pbjelly', 'python', 'python-decorator', 'python-h5py', 'python-intervaltree', 'python-intervaltree-bio', 'python-minimal', 'python-networkx', 'python-numpy', 'python-pbbanana', 'python-pbsuite-utils', 'python-pysam', 'python-six', 'python-sortedcontainers', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools', 'pbhoney'] 0m23.8s INFO: Running scripts post_remove 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_remove_exceptions'] 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_remove_exceptions'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg', '--purge', 'blasr', 'libaec0:amd64', 'libblas-common', 'libblas3', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libexpat1: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', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libncurses5:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpbbam:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'mime-support', 'pbjelly', 'python', 'python-decorator', 'python-h5py', 'python-intervaltree', 'python-intervaltree-bio', 'python-minimal', 'python-networkx', 'python-numpy', 'python-pbbanana', 'python-pbsuite-utils', 'python-pysam', 'python-six', 'python-sortedcontainers', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools'] 0m23.9s DUMP: dpkg: warning: ignoring request to remove blasr which isn't installed dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libblas-common which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libblasr which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libffi6 which isn't installed dpkg: warning: ignoring request to remove libgfortran3 which isn't installed dpkg: warning: ignoring request to remove libgmp10 which isn't installed dpkg: warning: ignoring request to remove libgnutls30 which isn't installed (Reading database ... 4420 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.15-1+deb9u3) ... dpkg: warning: ignoring request to remove 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 liblapack3 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.44+dfsg-5+deb9u9) ... dpkg: warning: ignoring request to remove libncurses5 which isn't installed dpkg: warning: ignoring request to remove libnettle6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove 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 libpython-stdlib which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.13-2+deb9u6) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline7 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed Purging configuration files for libssl1.1:amd64 (1.1.0l-1~deb9u6) ... dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libunistring0 which isn't installed Purging configuration files for mime-support (3.60) ... dpkg: warning: ignoring request to remove pbjelly which isn't installed Purging configuration files for python (2.7.13-2) ... dpkg: warning: ignoring request to remove python-decorator which isn't installed dpkg: warning: ignoring request to remove python-h5py which isn't installed dpkg: warning: ignoring request to remove python-intervaltree which isn't installed dpkg: warning: ignoring request to remove python-intervaltree-bio which isn't installed dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python-networkx which isn't installed dpkg: warning: ignoring request to remove python-numpy which isn't installed dpkg: warning: ignoring request to remove python-pbbanana which isn't installed dpkg: warning: ignoring request to remove python-pbsuite-utils which isn't installed dpkg: warning: ignoring request to remove python-pysam which isn't installed dpkg: warning: ignoring request to remove python-six which isn't installed dpkg: warning: ignoring request to remove python-sortedcontainers which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed Purging configuration files for python2.7-minimal (2.7.13-2+deb9u6) ... Purging configuration files for readline-common (7.0-3) ... dpkg: warning: ignoring request to remove samtools which isn't installed 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg', '--purge', 'blasr', 'libaec0:amd64', 'libblas-common', 'libblas3', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libexpat1: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', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libncurses5:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpbbam:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'mime-support', 'pbjelly', 'python', 'python-decorator', 'python-h5py', 'python-intervaltree', 'python-intervaltree-bio', 'python-minimal', 'python-networkx', 'python-numpy', 'python-pbbanana', 'python-pbsuite-utils', 'python-pysam', 'python-six', 'python-sortedcontainers', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools'] 0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg', '--purge', 'pbhoney'] 0m23.9s DUMP: dpkg: warning: ignoring request to remove pbhoney which isn't installed 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg', '--purge', 'pbhoney'] 0m23.9s INFO: Running scripts post_purge 0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_purge_exceptions'] 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_purge_exceptions'] 0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg', '--purge', '--pending'] 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg', '--purge', '--pending'] 0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg', '--remove', '--pending'] 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg', '--remove', '--pending'] 0m23.9s INFO: Running scripts post_test 0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_test_exceptions'] 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'tmp/scripts/post_test_exceptions'] 0m23.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m24.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg-divert', '--list'] 0m24.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'dpkg-divert', '--list'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', 'clean'] 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppo2t8zby', 'apt-get', 'clean'] 0m24.3s DEBUG: Recording chroot state 0m24.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/shm'] 0m24.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/shm'] 0m24.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/console'] 0m24.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/console'] 0m24.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/ptmx'] 0m25.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/ptmx'] 0m25.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/pts'] 0m25.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/dev/pts'] 0m25.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/proc'] 0m25.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppo2t8zby/proc'] 0m25.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m25.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmppo2t8zby'] 0m25.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmppo2t8zby 0m25.1s INFO: PASS: Upgrading between Debian distributions. 0m25.1s INFO: PASS: All tests. 0m25.1s INFO: piuparts run ends. ret=0 End: 2023-01-25 12:58:41 GMT