Start: 2022-11-13 02:24:16 GMT [jessie] Package: gasic Version: 0.0.r18-2 Installed-Size: 103 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python:any (>= 2.6.6-7~), python-scipy, python-numpy, python-biopython, python-pysam, bowtie, bowtie2, bwa, seqan-apps Description: genome abundance similarity correction Homepage: http://sourceforge.net/projects/gasic/ Description-md5: bdb1fbe60cfde219955bdb0d4f72e27c Section: science Priority: optional Filename: pool/main/g/gasic/gasic_0.0.r18-2_amd64.deb Size: 19882 MD5sum: f0423f38927183f83ec9f8ff271e706b SHA1: e3f4f0e438c7dd911a528b4226212d52c67632e1 SHA256: f42bec5be51a7738c1373b96b39cdbe059fa8e3aa5a8fb0af351e8e7874772ff [stretch] Package: gasic Version: 0.0.r19-1 Installed-Size: 74 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python:any (>= 2.6.6-7~), python-scipy, python-numpy, python-biopython, python-pysam, python-matplotlib, bowtie, bowtie2, bwa, seqan-apps Description: genome abundance similarity correction Homepage: http://sourceforge.net/projects/gasic/ Description-md5: bdb1fbe60cfde219955bdb0d4f72e27c Section: science Priority: optional Filename: pool/main/g/gasic/gasic_0.0.r19-1_amd64.deb Size: 19922 MD5sum: 72c96ac61c52ec65dab1caeee027c422 SHA256: cf8500919e647641eba13e8fc31d18a0d74640eb895016f01ce0e83316b16bc1 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --upgrade-before-dist-upgrade --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/jessie_amd64.tar.gz -d jessie -d stretch -B /srv/piuparts.debian.org/slave/refchroot/jessie2Xstretch/reference-chroot-metadata.dat --apt gasic=0.0.r19-1 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 --upgrade-before-dist-upgrade --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/jessie_amd64.tar.gz -d jessie -d stretch -B /srv/piuparts.debian.org/slave/refchroot/jessie2Xstretch/reference-chroot-metadata.dat --apt gasic=0.0.r19-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-19-amd64 #1 SMP Debian 5.10.149-2 (2022-10-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpwf4utdmp 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpwf4utdmp 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz'] 0m1.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/proc'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/proc'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/pts'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/pts'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/ptmx'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/ptmx'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/console'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/console'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/shm'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/shm'] 0m1.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ jessie 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/tmpwf4utdmp/tmp/scripts/ 0m1.4s INFO: Running scripts post_chroot_unpack 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', 'update'] 0m2.9s DUMP: Ign http://deb.debian.org jessie InRelease Hit http://deb.debian.org jessie Release.gpg Hit http://deb.debian.org jessie Release Hit http://deb.debian.org jessie/main amd64 Packages Hit http://deb.debian.org jessie/main Translation-en Reading package lists... 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', 'update'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', '-yf', 'dist-upgrade'] 0m3.1s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', '-yf', 'dist-upgrade'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s DUMP: c58dd1ad19dd97acb5ff8b7cd65de431 - 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s INFO: Running scripts post_setup 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_setup_dummy_users'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_setup_dummy_users'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_setup_forbid_home'] 0m4.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_setup_forbid_home'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.4s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_setup_minimize'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_setup_minimize'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s DUMP: install ok installed acl acl 2.2.52-2 install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 1.0.9.8.4 install ok installed base-files base-files 8+deb8u11 install ok installed base-passwd base-passwd 3.5.37 install ok installed bash bash 4.3-11+deb8u1 install ok installed bsdutils bsdutils 1:2.25.2-6 install ok installed coreutils coreutils 8.23-4 install ok installed dash dash 0.5.7-4+b1 install ok installed debconf debconf 1.5.56+deb8u1 install ok installed debconf-i18n debconf-i18n 1.5.56+deb8u1 install ok installed debian-archive-keyring debian-archive-keyring 2017.5~deb8u1 install ok installed debianutils debianutils 4.4+b1 install ok installed diffutils diffutils 1:3.3-1+b1 install ok installed dmsetup dmsetup 2:1.02.90-2.2+deb8u1 install ok installed dpkg dpkg 1.17.27 install ok installed e2fslibs:amd64 e2fslibs 1.42.12-2+b1 install ok installed e2fsprogs e2fsprogs 1.42.12-2+b1 install ok installed findutils findutils 4.4.2-9+b1 install ok installed gcc-4.9-base:amd64 gcc-4.9-base 4.9.2-10+deb8u1 install ok installed gnupg gnupg 1.4.18-7+deb8u5 install ok installed gpgv gpgv 1.4.18-7+deb8u5 install ok installed grep grep 2.20-4.1 install ok installed gzip gzip 1.6-4 install ok installed hostname hostname 3.15 install ok installed init init 1.22 install ok installed initscripts initscripts 2.88dsf-59 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.52-2 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 1.0.9.8.4 install ok installed libattr1:amd64 libattr1 1:2.4.47-2 install ok installed libaudit-common libaudit-common 1:2.4-1 install ok installed libaudit1:amd64 libaudit1 1:2.4-1+b1 install ok installed libblkid1:amd64 libblkid1 2.25.2-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-7+b3 install ok installed libc-bin libc-bin 2.19-18+deb8u10 install ok installed libc6:amd64 libc6 2.19-18+deb8u10 install ok installed libcap2:amd64 libcap2 1:2.24-8 install ok installed libcap2-bin libcap2-bin 1:2.24-8 install ok installed libcomerr2:amd64 libcomerr2 1.42.12-2+b1 install ok installed libcryptsetup4:amd64 libcryptsetup4 2:1.6.6-5 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-9+deb8u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.192 install ok installed libdevmapper1.02.1:amd64 libdevmapper1.02.1 2:1.02.90-2.2+deb8u1 install ok installed libgcc1:amd64 libgcc1 1:4.9.2-10+deb8u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.6.3-2+deb8u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.17-3 install ok installed libkmod2:amd64 libkmod2 18-3 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-8+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2+b3 install ok installed libmount1:amd64 libmount1 2.25.2-6 install ok installed libncurses5:amd64 libncurses5 5.9+20140913-1+deb8u3 install ok installed libncursesw5:amd64 libncursesw5 5.9+20140913-1+deb8u3 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.1+deb8u2+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.1+deb8u2+b1 install ok installed libpam-runtime libpam-runtime 1.1.8-3.1+deb8u2 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.1+deb8u2+b1 install ok installed libpcre3:amd64 libpcre3 2:8.35-3.3+deb8u4 install ok installed libprocps3:amd64 libprocps3 2:3.3.9-9+deb8u1 install ok installed libreadline6:amd64 libreadline6 6.3-8+b3 install ok installed libselinux1:amd64 libselinux1 2.3-2 install ok installed libsemanage-common libsemanage-common 2.3-1 install ok installed libsemanage1:amd64 libsemanage1 2.3-1+b1 install ok installed libsepol1:amd64 libsepol1 2.3-2 install ok installed libslang2:amd64 libslang2 2.3.0-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.25.2-6 install ok installed libss2:amd64 libss2 1.42.12-2+b1 install ok installed libstdc++6:amd64 libstdc++6 4.9.2-10+deb8u1 install ok installed libsystemd0:amd64 libsystemd0 215-17+deb8u7 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b3 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5+b2 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9+20140913-1+deb8u3 install ok installed libudev1:amd64 libudev1 215-17+deb8u7 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-25 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3+b2 install ok installed libuuid1:amd64 libuuid1 2.25.2-6 install ok installed login login 1:4.2-3+deb8u4 install ok installed lsb-base lsb-base 4.1+Debian13+nmu1 install ok installed mawk mawk 1.3.3-17 install ok installed mount mount 2.25.2-6 install ok installed multiarch-support multiarch-support 2.19-18+deb8u10 install ok installed ncurses-base ncurses-base 5.9+20140913-1+deb8u3 install ok installed ncurses-bin ncurses-bin 5.9+20140913-1+deb8u3 install ok installed passwd passwd 1:4.2-3+deb8u4 install ok installed perl-base perl-base 5.20.2-3+deb8u11 install ok installed procps procps 2:3.3.9-9+deb8u1 install ok installed readline-common readline-common 6.3-8 install ok installed sed sed 4.2.2-4+deb8u1 install ok installed sensible-utils sensible-utils 0.0.9+deb8u1 install ok installed startpar startpar 0.59-3 install ok installed systemd systemd 215-17+deb8u7 install ok installed systemd-sysv systemd-sysv 215-17+deb8u7 install ok installed sysv-rc sysv-rc 2.88dsf-59 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59 install ok installed tar tar 1.27.1-2+deb8u1 install ok installed tzdata tzdata 2018e-0+deb8u1 install ok installed udev udev 215-17+deb8u7 install ok installed util-linux util-linux 2.25.2-6 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-2+b1 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/jessie2Xstretch/reference-chroot-metadata.dat 0m4.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 0m5.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 0m5.1s INFO: Running scripts is_testable 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/is_testable_uninstallable'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/is_testable_uninstallable'] 0m5.1s INFO: Running scripts pre_test 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_test_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_test_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_test_root_password'] 0m5.2s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_test_root_password'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'show', '--no-all-versions', 'gasic'] 0m5.2s DUMP: Package: gasic Version: 0.0.r18-2 Installed-Size: 103 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python:any (>= 2.6.6-7~), python-scipy, python-numpy, python-biopython, python-pysam, bowtie, bowtie2, bwa, seqan-apps Description-en: genome abundance similarity correction One goal of sequencing based metagenomic analysis is the quantitative taxonomic assessment of microbial community compositions. However, the majority of approaches either quantify at low resolution (e.g. at phylum level) or have severe problems discerning highly similar species. Yet, accurate quantification on species level is desirable in applications such as metagenomic diagnostics or community comparison. GASiC is a method to correct read alignment results for the ambiguities imposed by similarities of genomes. It has superior performance over existing methods. Description-md5: bdb1fbe60cfde219955bdb0d4f72e27c Homepage: http://sourceforge.net/projects/gasic/ Section: science Priority: optional Filename: pool/main/g/gasic/gasic_0.0.r18-2_amd64.deb Size: 19882 MD5sum: f0423f38927183f83ec9f8ff271e706b SHA1: e3f4f0e438c7dd911a528b4226212d52c67632e1 SHA256: f42bec5be51a7738c1373b96b39cdbe059fa8e3aa5a8fb0af351e8e7874772ff 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'show', '--no-all-versions', 'gasic'] 0m5.2s INFO: apt-cache knows about the following packages: gasic 0m5.2s INFO: Running scripts pre_install 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'policy'] 0m5.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian/ jessie/main Translation-en 500 http://deb.debian.org/debian/ jessie/main amd64 Packages release v=8.11,o=Debian,a=oldoldstable,n=jessie,l=Debian,c=main origin deb.debian.org Pinned packages: 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'policy'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'policy', 'gasic'] 0m5.3s DUMP: gasic: Installed: (none) Candidate: 0.0.r18-2 Version table: 0.0.r18-2 0 500 http://deb.debian.org/debian/ jessie/main amd64 Packages 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'policy', 'gasic'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', '-y', 'install', 'gasic'] 0m15.4s DUMP: Reading package lists... Building dependency tree... The following extra packages will be installed: bowtie bowtie2 bwa cython libblas-common libblas3 libexpat1 libffi6 libgfortran3 libgomp1 liblapack3 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libsqlite3-0 libssl1.0.0 mime-support python python-biopython python-decorator python-minimal python-numpy python-pyrex python-pysam python-reportlab python-reportlab-accel python-scipy python2.7 python2.7-minimal seqan-apps Suggested packages: bowtie-examples bowtie2-examples samtools python-doc python-tk clustalo clustalw dialign dssp emboss fasttree mafft muscle phyml prank probcons python-mysqldb python-matplotlib python-pil python-rdflib python-renderpm python-psycopg2 raxml t-coffee wise gfortran python-nose python-numpy-dbg python-numpy-doc pdf-viewer python-egenix-mxtexttools python-reportlab-doc python2.7-doc binutils binfmt-support Recommended packages: python-dev gcc file python-biopython-doc ncbi-blast+ python-all-dev g++ c++-compiler python-imaging The following NEW packages will be installed: bowtie bowtie2 bwa cython gasic libblas-common libblas3 libexpat1 libffi6 libgfortran3 libgomp1 liblapack3 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libsqlite3-0 libssl1.0.0 mime-support python python-biopython python-decorator python-minimal python-numpy python-pyrex python-pysam python-reportlab python-reportlab-accel python-scipy python2.7 python2.7-minimal seqan-apps 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 32.1 MB of archives. After this operation, 163 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian/ jessie/main libssl1.0.0 amd64 1.0.1t-1+deb8u8 [1044 kB] Get:2 http://deb.debian.org/debian/ jessie/main libsqlite3-0 amd64 3.8.7.1-1+deb8u2 [438 kB] Get:3 http://deb.debian.org/debian/ jessie/main libpython2.7-minimal amd64 2.7.9-2+deb8u1 [378 kB] Get:4 http://deb.debian.org/debian/ jessie/main python2.7-minimal amd64 2.7.9-2+deb8u1 [1401 kB] Get:5 http://deb.debian.org/debian/ jessie/main python-minimal amd64 2.7.9-1 [40.3 kB] Get:6 http://deb.debian.org/debian/ jessie/main mime-support all 3.58 [36.0 kB] Get:7 http://deb.debian.org/debian/ jessie/main libexpat1 amd64 2.1.0-6+deb8u4 [80.2 kB] Get:8 http://deb.debian.org/debian/ jessie/main libffi6 amd64 3.1-2+deb8u1 [20.2 kB] Get:9 http://deb.debian.org/debian/ jessie/main libpython2.7-stdlib amd64 2.7.9-2+deb8u1 [1847 kB] Get:10 http://deb.debian.org/debian/ jessie/main python2.7 amd64 2.7.9-2+deb8u1 [252 kB] Get:11 http://deb.debian.org/debian/ jessie/main libpython-stdlib amd64 2.7.9-1 [19.5 kB] Get:12 http://deb.debian.org/debian/ jessie/main python amd64 2.7.9-1 [151 kB] Get:13 http://deb.debian.org/debian/ jessie/main libquadmath0 amd64 4.9.2-10+deb8u1 [129 kB] Get:14 http://deb.debian.org/debian/ jessie/main libgfortran3 amd64 4.9.2-10+deb8u1 [254 kB] Get:15 http://deb.debian.org/debian/ jessie/main libgomp1 amd64 4.9.2-10+deb8u1 [37.8 kB] Get:16 http://deb.debian.org/debian/ jessie/main bwa amd64 0.7.10-1 [169 kB] Get:17 http://deb.debian.org/debian/ jessie/main cython amd64 0.21.1-1 [1518 kB] Get:18 http://deb.debian.org/debian/ jessie/main python-decorator all 3.4.0-2 [22.3 kB] Get:19 http://deb.debian.org/debian/ jessie/main libblas-common amd64 1.2.20110419-10 [8496 B] Get:20 http://deb.debian.org/debian/ jessie/main libblas3 amd64 1.2.20110419-10 [167 kB] Get:21 http://deb.debian.org/debian/ jessie/main liblapack3 amd64 3.5.0-4 [1852 kB] Get:22 http://deb.debian.org/debian/ jessie/main python-numpy amd64 1:1.8.2-2 [1630 kB] Get:23 http://deb.debian.org/debian/ jessie/main python-scipy amd64 0.14.0-2 [8144 kB] Get:24 http://deb.debian.org/debian/ jessie/main python-reportlab-accel amd64 3.1.8-3+deb8u1 [25.7 kB] Get:25 http://deb.debian.org/debian/ jessie/main python-reportlab all 3.1.8-3+deb8u1 [453 kB] Get:26 http://deb.debian.org/debian/ jessie/main python-biopython amd64 1.64+dfsg-5 [1165 kB] Get:27 http://deb.debian.org/debian/ jessie/main python-pyrex all 0.9.8.5-2.1 [222 kB] Get:28 http://deb.debian.org/debian/ jessie/main python-pysam amd64 0.7.7-1 [596 kB] Get:29 http://deb.debian.org/debian/ jessie/main bowtie amd64 1.1.1-2 [1369 kB] Get:30 http://deb.debian.org/debian/ jessie/main bowtie2 amd64 2.2.4-1 [1086 kB] Get:31 http://deb.debian.org/debian/ jessie/main seqan-apps amd64 1.4.1+dfsg-2 [7487 kB] Get:32 http://deb.debian.org/debian/ jessie/main gasic amd64 0.0.r18-2 [19.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 32.1 MB in 1s (16.8 MB/s) Selecting previously unselected package libssl1.0.0: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 ... 7449 files and directories currently installed.) Preparing to unpack .../libssl1.0.0_1.0.1t-1+deb8u8_amd64.deb ... Unpacking libssl1.0.0:amd64 (1.0.1t-1+deb8u8) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../libsqlite3-0_3.8.7.1-1+deb8u2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.8.7.1-1+deb8u2) ... Selecting previously unselected package libpython2.7-minimal:amd64. Preparing to unpack .../libpython2.7-minimal_2.7.9-2+deb8u1_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.9-2+deb8u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../python2.7-minimal_2.7.9-2+deb8u1_amd64.deb ... Unpacking python2.7-minimal (2.7.9-2+deb8u1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../python-minimal_2.7.9-1_amd64.deb ... Unpacking python-minimal (2.7.9-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../mime-support_3.58_all.deb ... Unpacking mime-support (3.58) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.1.0-6+deb8u4_amd64.deb ... Unpacking libexpat1:amd64 (2.1.0-6+deb8u4) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../libffi6_3.1-2+deb8u1_amd64.deb ... Unpacking libffi6:amd64 (3.1-2+deb8u1) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Preparing to unpack .../libpython2.7-stdlib_2.7.9-2+deb8u1_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.9-2+deb8u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../python2.7_2.7.9-2+deb8u1_amd64.deb ... Unpacking python2.7 (2.7.9-2+deb8u1) ... Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../libpython-stdlib_2.7.9-1_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.9-1) ... Setting up libpython2.7-minimal:amd64 (2.7.9-2+deb8u1) ... Setting up python2.7-minimal (2.7.9-2+deb8u1) ... Setting up python-minimal (2.7.9-1) ... Selecting previously unselected package python. (Reading database ... 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Unpacking libgfortran3:amd64 (4.9.2-10+deb8u1) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../libgomp1_4.9.2-10+deb8u1_amd64.deb ... Unpacking libgomp1:amd64 (4.9.2-10+deb8u1) ... Selecting previously unselected package bwa. Preparing to unpack .../bwa_0.7.10-1_amd64.deb ... Unpacking bwa (0.7.10-1) ... Selecting previously unselected package cython. Preparing to unpack .../cython_0.21.1-1_amd64.deb ... Unpacking cython (0.21.1-1) ... Selecting previously unselected package python-decorator. Preparing to unpack .../python-decorator_3.4.0-2_all.deb ... Unpacking python-decorator (3.4.0-2) ... Selecting previously unselected package libblas-common. Preparing to unpack .../libblas-common_1.2.20110419-10_amd64.deb ... Unpacking libblas-common (1.2.20110419-10) ... Selecting previously unselected package libblas3. Preparing to unpack .../libblas3_1.2.20110419-10_amd64.deb ... Unpacking libblas3 (1.2.20110419-10) ... Selecting previously unselected package liblapack3. Preparing to unpack .../liblapack3_3.5.0-4_amd64.deb ... Unpacking liblapack3 (3.5.0-4) ... Selecting previously unselected package python-numpy. Preparing to unpack .../python-numpy_1%3a1.8.2-2_amd64.deb ... Unpacking python-numpy (1:1.8.2-2) ... Selecting previously unselected package python-scipy. Preparing to unpack .../python-scipy_0.14.0-2_amd64.deb ... Unpacking python-scipy (0.14.0-2) ... Selecting previously unselected package python-reportlab-accel:amd64. Preparing to unpack .../python-reportlab-accel_3.1.8-3+deb8u1_amd64.deb ... Unpacking python-reportlab-accel:amd64 (3.1.8-3+deb8u1) ... Selecting previously unselected package python-reportlab. Preparing to unpack .../python-reportlab_3.1.8-3+deb8u1_all.deb ... Unpacking python-reportlab (3.1.8-3+deb8u1) ... Selecting previously unselected package python-biopython. Preparing to unpack .../python-biopython_1.64+dfsg-5_amd64.deb ... Unpacking python-biopython (1.64+dfsg-5) ... Selecting previously unselected package python-pyrex. Preparing to unpack .../python-pyrex_0.9.8.5-2.1_all.deb ... Unpacking python-pyrex (0.9.8.5-2.1) ... Selecting previously unselected package python-pysam. Preparing to unpack .../python-pysam_0.7.7-1_amd64.deb ... Unpacking python-pysam (0.7.7-1) ... Selecting previously unselected package bowtie. Preparing to unpack .../bowtie_1.1.1-2_amd64.deb ... Unpacking bowtie (1.1.1-2) ... Selecting previously unselected package bowtie2. Preparing to unpack .../bowtie2_2.2.4-1_amd64.deb ... Unpacking bowtie2 (2.2.4-1) ... Selecting previously unselected package seqan-apps. Preparing to unpack .../seqan-apps_1.4.1+dfsg-2_amd64.deb ... Unpacking seqan-apps (1.4.1+dfsg-2) ... Selecting previously unselected package gasic. Preparing to unpack .../gasic_0.0.r18-2_amd64.deb ... Unpacking gasic (0.0.r18-2) ... Setting up libssl1.0.0:amd64 (1.0.1t-1+deb8u8) ... Setting up libsqlite3-0:amd64 (3.8.7.1-1+deb8u2) ... Setting up mime-support (3.58) ... Setting up libexpat1:amd64 (2.1.0-6+deb8u4) ... Setting up libffi6:amd64 (3.1-2+deb8u1) ... Setting up libpython2.7-stdlib:amd64 (2.7.9-2+deb8u1) ... Setting up python2.7 (2.7.9-2+deb8u1) ... Setting up libpython-stdlib:amd64 (2.7.9-1) ... Setting up python (2.7.9-1) ... Setting up libquadmath0:amd64 (4.9.2-10+deb8u1) ... Setting up libgfortran3:amd64 (4.9.2-10+deb8u1) ... Setting up libgomp1:amd64 (4.9.2-10+deb8u1) ... Setting up bwa (0.7.10-1) ... Setting up cython (0.21.1-1) ... Setting up python-decorator (3.4.0-2) ... Setting up libblas-common (1.2.20110419-10) ... Setting up libblas3 (1.2.20110419-10) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up liblapack3 (3.5.0-4) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up python-numpy (1:1.8.2-2) ... Setting up python-scipy (0.14.0-2) ... Setting up python-reportlab-accel:amd64 (3.1.8-3+deb8u1) ... Setting up python-reportlab (3.1.8-3+deb8u1) ... Setting up python-biopython (1.64+dfsg-5) ... Setting up python-pyrex (0.9.8.5-2.1) ... Setting up python-pysam (0.7.7-1) ... Setting up bowtie (1.1.1-2) ... Setting up bowtie2 (2.2.4-1) ... Setting up seqan-apps (1.4.1+dfsg-2) ... Setting up gasic (0.0.r18-2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', '-y', 'install', 'gasic'] 0m15.4s INFO: Running scripts post_install 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_install_exceptions'] 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_install_exceptions'] 0m15.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 0m16.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 0m16.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpwf4utdmp to stretch 0m16.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m16.0s INFO: Running scripts pre_distupgrade 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', 'update'] 0m18.6s DUMP: Ign http://deb.debian.org stretch InRelease Get:1 http://deb.debian.org stretch Release.gpg [3177 B] Get:2 http://deb.debian.org stretch Release [118 kB] Get:3 http://deb.debian.org stretch/main amd64 Packages [7080 kB] Get:4 http://deb.debian.org stretch/main Translation-en [5377 kB] Fetched 12.6 MB in 1s (7958 kB/s) Reading package lists... W: There is no public key available for the following key IDs: 648ACFD622F3D138 NO_PUBKEY 0E98404D386FA1D9 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', 'update'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', '-y', 'upgrade'] 0m32.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages have been kept back: apt bowtie bowtie2 gasic gnupg init initscripts libaudit1 libgcc1 libgfortran3 libgomp1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libstdc++6 libsystemd0 libudev1 procps python python-minimal python-pyrex python-pysam python-scipy python2.7 python2.7-minimal seqan-apps systemd sysv-rc sysvinit-utils udev util-linux The following packages will be upgraded: acl adduser base-files base-passwd bash bsdutils bwa coreutils cython dash debconf debconf-i18n debian-archive-keyring debianutils diffutils dmsetup dpkg e2fslibs e2fsprogs findutils gpgv grep gzip hostname insserv libacl1 libattr1 libaudit-common libblas-common libblas3 libblkid1 libbz2-1.0 libc-bin libc6 libcap2 libcap2-bin libcomerr2 libcryptsetup4 libdb5.3 libdebconfclient0 libdevmapper1.02.1 libexpat1 libffi6 libgcrypt20 libgpg-error0 libkmod2 liblapack3 liblocale-gettext-perl liblzma5 libmount1 libncurses5 libncursesw5 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre3 libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libss2 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtinfo5 libusb-0.1-4 libustr-1.0-1 libuuid1 login lsb-base mawk mime-support mount multiarch-support ncurses-base ncurses-bin passwd perl-base python-biopython python-decorator python-numpy python-reportlab python-reportlab-accel readline-common sed sensible-utils startpar systemd-sysv tar tzdata zlib1g 95 upgraded, 0 newly installed, 0 to remove and 32 not upgraded. Need to get 34.4 MB of archives. After this operation, 15.7 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian/ stretch/main base-files amd64 9.9+deb9u13 [67.6 kB] Get:2 http://deb.debian.org/debian/ stretch/main libc6 amd64 2.24-11+deb9u4 [2694 kB] Get:3 http://deb.debian.org/debian/ stretch/main libc-bin amd64 2.24-11+deb9u4 [782 kB] Get:4 http://deb.debian.org/debian/ stretch/main libtinfo5 amd64 6.0+20161126-1+deb9u2 [300 kB] Get:5 http://deb.debian.org/debian/ stretch/main libncurses5 amd64 6.0+20161126-1+deb9u2 [93.4 kB] Get:6 http://deb.debian.org/debian/ stretch/main libncursesw5 amd64 6.0+20161126-1+deb9u2 [115 kB] Get:7 http://deb.debian.org/debian/ stretch/main sensible-utils all 0.0.9+deb9u1 [10.8 kB] Get:8 http://deb.debian.org/debian/ stretch/main debianutils amd64 4.8.1.1 [100 kB] Get:9 http://deb.debian.org/debian/ stretch/main bash amd64 4.4-5 [1427 kB] Get:10 http://deb.debian.org/debian/ stretch/main bsdutils amd64 1:2.29.2-1+deb9u1 [112 kB] Get:11 http://deb.debian.org/debian/ stretch/main coreutils amd64 8.26-3 [2870 kB] Get:12 http://deb.debian.org/debian/ stretch/main tar amd64 1.29b-1.1 [759 kB] Get:13 http://deb.debian.org/debian/ stretch/main liblzma5 amd64 5.2.2-1.2+b1 [234 kB] Get:14 http://deb.debian.org/debian/ stretch/main dpkg amd64 1.18.25 [2115 kB] Get:15 http://deb.debian.org/debian/ stretch/main dash amd64 0.5.8-2.4 [109 kB] Get:16 http://deb.debian.org/debian/ stretch/main diffutils amd64 1:3.5-3 [314 kB] Get:17 http://deb.debian.org/debian/ stretch/main e2fslibs amd64 1.43.4-2+deb9u1 [208 kB] Get:18 http://deb.debian.org/debian/ stretch/main e2fsprogs amd64 1.43.4-2+deb9u1 [947 kB] Get:19 http://deb.debian.org/debian/ stretch/main findutils amd64 4.6.0+git+20161106-2 [622 kB] Get:20 http://deb.debian.org/debian/ stretch/main grep amd64 2.27-2 [382 kB] Get:21 http://deb.debian.org/debian/ stretch/main gzip amd64 1.6-5+b1 [114 kB] Get:22 http://deb.debian.org/debian/ stretch/main hostname amd64 3.18+b1 [14.9 kB] Get:23 http://deb.debian.org/debian/ stretch/main login amd64 1:4.4-4.1 [790 kB] Get:24 http://deb.debian.org/debian/ stretch/main libpcre3 amd64 2:8.39-3 [337 kB] Get:25 http://deb.debian.org/debian/ stretch/main libselinux1 amd64 2.6-3+b3 [101 kB] Get:26 http://deb.debian.org/debian/ stretch/main libsmartcols1 amd64 2.29.2-1+deb9u1 [126 kB] Get:27 http://deb.debian.org/debian/ stretch/main mount amd64 2.29.2-1+deb9u1 [189 kB] Get:28 http://deb.debian.org/debian/ stretch/main ncurses-bin amd64 6.0+20161126-1+deb9u2 [366 kB] Get:29 http://deb.debian.org/debian/ stretch/main libtext-charwidth-perl amd64 0.04-7+b5 [9870 B] Get:30 http://deb.debian.org/debian/ stretch/main libtext-iconv-perl amd64 1.7-5+b4 [15.3 kB] Get:31 http://deb.debian.org/debian/ stretch/main perl-base amd64 5.24.1-3+deb9u7 [1346 kB] Get:32 http://deb.debian.org/debian/ stretch/main liblocale-gettext-perl amd64 1.07-3+b1 [18.7 kB] Get:33 http://deb.debian.org/debian/ stretch/main sed amd64 4.4-1 [280 kB] Get:34 http://deb.debian.org/debian/ stretch/main libdebconfclient0 amd64 0.227 [47.8 kB] Get:35 http://deb.debian.org/debian/ stretch/main base-passwd amd64 3.5.43 [57.7 kB] Get:36 http://deb.debian.org/debian/ stretch/main ncurses-base all 6.0+20161126-1+deb9u2 [238 kB] Get:37 http://deb.debian.org/debian/ stretch/main systemd-sysv amd64 232-25+deb9u12 [82.5 kB] Get:38 http://deb.debian.org/debian/ stretch/main libtext-wrapi18n-perl all 0.06-7.1 [8644 B] Get:39 http://deb.debian.org/debian/ stretch/main debconf-i18n all 1.5.61 [205 kB] Get:40 http://deb.debian.org/debian/ stretch/main debconf all 1.5.61 [159 kB] Get:41 http://deb.debian.org/debian/ stretch/main libpam0g amd64 1.1.8-3.6 [125 kB] Get:42 http://deb.debian.org/debian/ stretch/main libpam-modules-bin amd64 1.1.8-3.6 [105 kB] Get:43 http://deb.debian.org/debian/ stretch/main libpam-modules amd64 1.1.8-3.6 [308 kB] Get:44 http://deb.debian.org/debian/ stretch/main mawk amd64 1.3.3-17+b3 [84.6 kB] Get:45 http://deb.debian.org/debian/ stretch/main libsepol1 amd64 2.6-2 [241 kB] Get:46 http://deb.debian.org/debian/ stretch/main libsemanage-common all 2.6-2 [26.9 kB] Get:47 http://deb.debian.org/debian/ stretch/main libsemanage1 amd64 2.6-2 [103 kB] Get:48 http://deb.debian.org/debian/ stretch/main libbz2-1.0 amd64 1.0.6-8.1 [43.5 kB] Get:49 http://deb.debian.org/debian/ stretch/main libustr-1.0-1 amd64 1.0.4-6 [76.3 kB] Get:50 http://deb.debian.org/debian/ stretch/main passwd amd64 1:4.4-4.1 [996 kB] Get:51 http://deb.debian.org/debian/ stretch/main adduser all 3.115 [241 kB] Get:52 http://deb.debian.org/debian/ stretch/main libgpg-error0 amd64 1.26-2 [112 kB] Get:53 http://deb.debian.org/debian/ stretch/main libgcrypt20 amd64 1.7.6-2+deb9u3 [524 kB] Get:54 http://deb.debian.org/debian/ stretch/main zlib1g amd64 1:1.2.8.dfsg-5 [87.5 kB] Get:55 http://deb.debian.org/debian/ stretch/main gpgv amd64 2.1.18-8~deb9u4 [481 kB] Get:56 http://deb.debian.org/debian/ stretch/main debian-archive-keyring all 2017.5+deb9u1 [73.9 kB] Get:57 http://deb.debian.org/debian/ stretch/main libkmod2 amd64 23-2 [48.1 kB] Get:58 http://deb.debian.org/debian/ stretch/main libslang2 amd64 2.3.1-5 [503 kB] Get:59 http://deb.debian.org/debian/ stretch/main readline-common all 7.0-3 [70.4 kB] Get:60 http://deb.debian.org/debian/ stretch/main libattr1 amd64 1:2.4.47-2+b2 [18.4 kB] Get:61 http://deb.debian.org/debian/ stretch/main libacl1 amd64 2.2.52-3+b1 [28.1 kB] Get:62 http://deb.debian.org/debian/ stretch/main acl amd64 2.2.52-3+b1 [59.5 kB] Get:63 http://deb.debian.org/debian/ stretch/main libuuid1 amd64 2.29.2-1+deb9u1 [70.1 kB] Get:64 http://deb.debian.org/debian/ stretch/main libblkid1 amd64 2.29.2-1+deb9u1 [168 kB] Get:65 http://deb.debian.org/debian/ stretch/main libcomerr2 amd64 1.43.4-2+deb9u1 [63.5 kB] Get:66 http://deb.debian.org/debian/ stretch/main libmount1 amd64 2.29.2-1+deb9u1 [178 kB] Get:67 http://deb.debian.org/debian/ stretch/main libpam-runtime all 1.1.8-3.6 [212 kB] Get:68 http://deb.debian.org/debian/ stretch/main libss2 amd64 1.43.4-2+deb9u1 [67.8 kB] Get:69 http://deb.debian.org/debian/ stretch/main lsb-base all 9.20161125 [27.9 kB] Get:70 http://deb.debian.org/debian/ stretch/main multiarch-support amd64 2.24-11+deb9u4 [201 kB] Get:71 http://deb.debian.org/debian/ stretch/main tzdata all 2020a-0+deb9u1 [278 kB] Get:72 http://deb.debian.org/debian/ stretch/main libcap2 amd64 1:2.25-1 [16.8 kB] Get:73 http://deb.debian.org/debian/ stretch/main libdb5.3 amd64 5.3.28-12+deb9u1 [679 kB] Get:74 http://deb.debian.org/debian/ stretch/main dmsetup amd64 2:1.02.137-2 [107 kB] Get:75 http://deb.debian.org/debian/ stretch/main libdevmapper1.02.1 amd64 2:1.02.137-2 [170 kB] Get:76 http://deb.debian.org/debian/ stretch/main insserv amd64 1.14.0-5.4+b1 [61.8 kB] Get:77 http://deb.debian.org/debian/ stretch/main libaudit-common all 1:2.6.7-2 [18.1 kB] Get:78 http://deb.debian.org/debian/ stretch/main libcap2-bin amd64 1:2.25-1 [26.5 kB] Get:79 http://deb.debian.org/debian/ stretch/main libcryptsetup4 amd64 2:1.7.3-4 [109 kB] Get:80 http://deb.debian.org/debian/ stretch/main libusb-0.1-4 amd64 2:0.1.12-30 [22.9 kB] Get:81 http://deb.debian.org/debian/ stretch/main startpar amd64 0.59-3.1 [22.5 kB] Get:82 http://deb.debian.org/debian/ stretch/main libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:83 http://deb.debian.org/debian/ stretch/main mime-support all 3.60 [36.7 kB] Get:84 http://deb.debian.org/debian/ stretch/main bwa amd64 0.7.15-2+deb9u1 [194 kB] Get:85 http://deb.debian.org/debian/ stretch/main cython amd64 0.25.2-1 [1863 kB] Get:86 http://deb.debian.org/debian/ stretch/main libblas-common amd64 3.7.0-2 [14.2 kB] Get:87 http://deb.debian.org/debian/ stretch/main libblas3 amd64 3.7.0-2 [155 kB] Get:88 http://deb.debian.org/debian/ stretch/main libexpat1 amd64 2.2.0-2+deb9u3 [83.7 kB] Get:89 http://deb.debian.org/debian/ stretch/main libffi6 amd64 3.2.1-6 [20.4 kB] Get:90 http://deb.debian.org/debian/ stretch/main liblapack3 amd64 3.7.0-2 [2141 kB] Get:91 http://deb.debian.org/debian/ stretch/main python-numpy amd64 1:1.12.1-3 [1936 kB] Get:92 http://deb.debian.org/debian/ stretch/main python-reportlab-accel amd64 3.3.0-2+deb9u1 [36.8 kB] Get:93 http://deb.debian.org/debian/ stretch/main python-reportlab all 3.3.0-2+deb9u1 [478 kB] Get:94 http://deb.debian.org/debian/ stretch/main python-biopython amd64 1.68+dfsg-3 [1201 kB] Get:95 http://deb.debian.org/debian/ stretch/main python-decorator all 4.0.11-1 [13.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 34.4 MB in 1s (26.0 MB/s) (Reading database ... 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Updating /root/.profile to current default. (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 ... 14095 files and directories currently installed.) Preparing to unpack .../libc6_2.24-11+deb9u4_amd64.deb ... Unpacking libc6:amd64 (2.24-11+deb9u4) over (2.19-18+deb8u10) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... Setting up libc6:amd64 (2.24-11+deb9u4) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (Reading database ... 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Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\${ <-- HERE ([^}]+)}/ at /usr/share/perl5/Debconf/Config.pm line 30. (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 ... 14146 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.0+20161126-1+deb9u2_all.deb ... Unpacking ncurses-base (6.0+20161126-1+deb9u2) over (5.9+20140913-1+deb8u3) ... Setting up ncurses-base (6.0+20161126-1+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 ... 14147 files and directories currently installed.) Preparing to unpack .../systemd-sysv_232-25+deb9u12_amd64.deb ... Unpacking systemd-sysv (232-25+deb9u12) over (215-17+deb8u7) ... Setting up systemd-sysv (232-25+deb9u12) ... (Reading database ... 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Removing obsolete conffile /etc/bash_completion.d/debconf ... (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 ... 14148 files and directories currently installed.) Preparing to unpack .../libpam0g_1.1.8-3.6_amd64.deb ... Unpacking libpam0g:amd64 (1.1.8-3.6) over (1.1.8-3.1+deb8u2+b1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libpam0g:amd64 (1.1.8-3.6) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... (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 ... 14148 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.115_all.deb ... Unpacking adduser (3.115) over (3.113+nmu3) ... Setting up adduser (3.115) ... (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 ... 14147 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.7.6-2+deb9u3_amd64.deb ... Unpacking libgcrypt20:amd64 (1.7.6-2+deb9u3) over (1.6.3-2+deb8u4) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libgcrypt20:amd64 (1.7.6-2+deb9u3) ... Processing triggers for libc-bin (2.24-11+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 ... 14147 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.8.dfsg-5_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.8.dfsg-5) over (1:1.2.8.dfsg-2+b1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up zlib1g:amd64 (1:1.2.8.dfsg-5) ... Processing triggers for libc-bin (2.24-11+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 ... 14146 files and directories currently installed.) Preparing to unpack .../gpgv_2.1.18-8~deb9u4_amd64.deb ... Unpacking gpgv (2.1.18-8~deb9u4) over (1.4.18-7+deb8u5) ... Setting up gpgv (2.1.18-8~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 ... 14147 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2017.5+deb9u1_all.deb ... Unpacking debian-archive-keyring (2017.5+deb9u1) over (2017.5~deb8u1) ... Setting up debian-archive-keyring (2017.5+deb9u1) ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-wheezy-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-wheezy-stable.gpg ... (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 ... 14148 files and directories currently installed.) Preparing to unpack .../libkmod2_23-2_amd64.deb ... Unpacking libkmod2:amd64 (23-2) over (18-3) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libkmod2:amd64 (23-2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... (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 ... 14148 files and directories currently installed.) Preparing to unpack .../lsb-base_9.20161125_all.deb ... Unpacking lsb-base (9.20161125) over (4.1+Debian13+nmu1) ... Setting up lsb-base (9.20161125) ... (Reading database ... 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Setting up dmsetup (2:1.02.137-2) ... Processing triggers for libc-bin (2.24-11+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 ... 14160 files and directories currently installed.) Preparing to unpack .../insserv_1.14.0-5.4+b1_amd64.deb ... Unpacking insserv (1.14.0-5.4+b1) over (1.14.0-5) ... Setting up insserv (1.14.0-5.4+b1) ... (Reading database ... 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Unpacking cython (0.25.2-1) over (0.21.1-1) ... Preparing to unpack .../libblas-common_3.7.0-2_amd64.deb ... Unpacking libblas-common (3.7.0-2) over (1.2.20110419-10) ... Preparing to unpack .../libblas3_3.7.0-2_amd64.deb ... Unpacking libblas3 (3.7.0-2) over (1.2.20110419-10) ... Preparing to unpack .../libexpat1_2.2.0-2+deb9u3_amd64.deb ... Unpacking libexpat1:amd64 (2.2.0-2+deb9u3) over (2.1.0-6+deb8u4) ... Preparing to unpack .../libffi6_3.2.1-6_amd64.deb ... Unpacking libffi6:amd64 (3.2.1-6) over (3.1-2+deb8u1) ... Preparing to unpack .../liblapack3_3.7.0-2_amd64.deb ... Unpacking liblapack3 (3.7.0-2) over (3.5.0-4) ... Preparing to unpack .../python-numpy_1%3a1.12.1-3_amd64.deb ... Unpacking python-numpy (1:1.12.1-3) over (1:1.8.2-2) ... Preparing to unpack .../python-reportlab-accel_3.3.0-2+deb9u1_amd64.deb ... Unpacking python-reportlab-accel:amd64 (3.3.0-2+deb9u1) over (3.1.8-3+deb8u1) ... Preparing to unpack .../python-reportlab_3.3.0-2+deb9u1_all.deb ... Unpacking python-reportlab (3.3.0-2+deb9u1) over (3.1.8-3+deb8u1) ... Preparing to unpack .../python-biopython_1.68+dfsg-3_amd64.deb ... Unpacking python-biopython (1.68+dfsg-3) over (1.64+dfsg-5) ... Preparing to unpack .../python-decorator_4.0.11-1_all.deb ... Unpacking python-decorator (4.0.11-1) over (3.4.0-2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libtext-charwidth-perl (0.04-7+b5) ... Setting up libtext-iconv-perl (1.7-5+b4) ... Setting up liblocale-gettext-perl (1.07-3+b1) ... Setting up libtext-wrapi18n-perl (0.06-7.1) ... Setting up debconf-i18n (1.5.61) ... Setting up mawk (1.3.3-17+b3) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up mime-support (3.60) ... Installing new version of config file /etc/mime.types ... Setting up bwa (0.7.15-2+deb9u1) ... Setting up cython (0.25.2-1) ... Setting up libblas-common (3.7.0-2) ... Setting up libblas3 (3.7.0-2) ... update-alternatives: warning: forcing reinstallation of alternative /usr/lib/libblas/libblas.so.3 because link group libblas.so.3 is broken Setting up libexpat1:amd64 (2.2.0-2+deb9u3) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up liblapack3 (3.7.0-2) ... update-alternatives: warning: forcing reinstallation of alternative /usr/lib/lapack/liblapack.so.3 because link group liblapack.so.3 is broken Setting up python-numpy (1:1.12.1-3) ... Setting up python-reportlab-accel:amd64 (3.3.0-2+deb9u1) ... Setting up python-reportlab (3.3.0-2+deb9u1) ... Setting up python-biopython (1.68+dfsg-3) ... Setting up python-decorator (4.0.11-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', '-y', 'upgrade'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', '-yf', 'dist-upgrade'] 1m0.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: cython libssl1.0.0 python-pyrex Use 'apt-get autoremove' to remove them. The following NEW packages will be installed: fontconfig fontconfig-config fonts-lyx gcc-6-base gnome-icon-theme gnupg-agent gtk-update-icon-cache hicolor-icon-theme init-system-helpers libapparmor1 libapt-pkg5.0 libassuan0 libatk1.0-0 libatk1.0-data libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbsd0 libc-dev-bin libc6-dev libcairo2 libcap-ng0 libcroco3 libcups2 libcurl3-gnutls libdatrie1 libdbus-1-3 libexpat1-dev libfdisk1 libfontconfig1 libfreetype6 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libglib2.0-0 libgmp10 libgnutls30 libgraphite2-3 libgssapi-krb5-2 libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhogweed4 libhts1 libicu57 libidn11 libidn2-0 libip4tc0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libksba8 libldap-2.4-2 libldap-common liblz4-1 libnettle6 libnghttp2-14 libnpth0 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpixman-1-0 libpng16-16 libprocps6 libpsl5 libpython-dev libpython2.7 libpython2.7-dev libreadline7 librsvg2-2 librsvg2-common librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libssh2-1 libssl1.1 libtasn1-6 libtbb2 libthai-data libthai0 libtiff5 libunistring0 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxinerama1 libxml2 libxrandr2 libxrender1 linux-libc-dev pinentry-curses python-cycler python-dateutil python-dev python-functools32 python-matplotlib python-matplotlib-data python-pyparsing python-six python-subprocess32 python-tz python2.7-dev shared-mime-info ttf-bitstream-vera ucf The following packages will be upgraded: apt bowtie bowtie2 gasic gnupg init initscripts libaudit1 libgcc1 libgfortran3 libgomp1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libstdc++6 libsystemd0 libudev1 procps python python-minimal python-pyrex python-pysam python-scipy python2.7 python2.7-minimal seqan-apps systemd sysv-rc sysvinit-utils udev util-linux 32 upgraded, 122 newly installed, 0 to remove and 0 not upgraded. Need to get 122 MB of archives. After this operation, 245 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian/ stretch/main libfdisk1 amd64 2.29.2-1+deb9u1 [203 kB] Get:2 http://deb.debian.org/debian/ stretch/main init-system-helpers all 1.48 [44.0 kB] Get:3 http://deb.debian.org/debian/ stretch/main util-linux amd64 2.29.2-1+deb9u1 [981 kB] Get:4 http://deb.debian.org/debian/ stretch/main sysvinit-utils amd64 2.88dsf-59.9 [68.4 kB] Get:5 http://deb.debian.org/debian/ stretch/main initscripts amd64 2.88dsf-59.9 [84.5 kB] Get:6 http://deb.debian.org/debian/ stretch/main sysv-rc all 2.88dsf-59.9 [67.4 kB] Get:7 http://deb.debian.org/debian/ stretch/main init amd64 1.48 [12.0 kB] Get:8 http://deb.debian.org/debian/ stretch/main liblz4-1 amd64 0.0~r131-2+b1 [33.3 kB] Get:9 http://deb.debian.org/debian/ stretch/main gcc-6-base amd64 6.3.0-18+deb9u1 [180 kB] Get:10 http://deb.debian.org/debian/ stretch/main libreadline7 amd64 7.0-3 [151 kB] Get:11 http://deb.debian.org/debian/ stretch/main libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:12 http://deb.debian.org/debian/ stretch/main python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:13 http://deb.debian.org/debian/ stretch/main libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:14 http://deb.debian.org/debian/ stretch/main python2.7-minimal amd64 2.7.13-2+deb9u3 [1382 kB] Get:15 http://deb.debian.org/debian/ stretch/main libpython2.7-minimal amd64 2.7.13-2+deb9u3 [389 kB] Get:16 http://deb.debian.org/debian/ stretch/main python-minimal amd64 2.7.13-2 [40.5 kB] Get:17 http://deb.debian.org/debian/ stretch/main python amd64 2.7.13-2 [154 kB] Get:18 http://deb.debian.org/debian/ stretch/main libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:19 http://deb.debian.org/debian/ stretch/main libgcc1 amd64 1:6.3.0-18+deb9u1 [38.0 kB] Get:20 http://deb.debian.org/debian/ stretch/main libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:21 http://deb.debian.org/debian/ stretch/main libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:22 http://deb.debian.org/debian/ stretch/main python-scipy amd64 0.18.1-2 [8933 kB] Get:23 http://deb.debian.org/debian/ stretch/main libstdc++6 amd64 6.3.0-18+deb9u1 [396 kB] Get:24 http://deb.debian.org/debian/ stretch/main libapt-pkg5.0 amd64 1.4.10 [917 kB] Get:25 http://deb.debian.org/debian/ stretch/main apt amd64 1.4.10 [1232 kB] Get:26 http://deb.debian.org/debian/ stretch/main libapparmor1 amd64 2.11.0-3+deb9u2 [78.9 kB] Get:27 http://deb.debian.org/debian/ stretch/main libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:28 http://deb.debian.org/debian/ stretch/main libip4tc0 amd64 1.6.0+snapshot20161117-6 [67.8 kB] Get:29 http://deb.debian.org/debian/ stretch/main libseccomp2 amd64 2.3.1-2.1+deb9u1 [40.7 kB] Get:30 http://deb.debian.org/debian/ stretch/main libudev1 amd64 232-25+deb9u12 [126 kB] Get:31 http://deb.debian.org/debian/ stretch/main libsystemd0 amd64 232-25+deb9u12 [282 kB] Get:32 http://deb.debian.org/debian/ stretch/main systemd amd64 232-25+deb9u12 [2469 kB] Get:33 http://deb.debian.org/debian/ stretch/main udev amd64 232-25+deb9u12 [1113 kB] Get:34 http://deb.debian.org/debian/ stretch/main libprocps6 amd64 2:3.3.12-3+deb9u1 [58.5 kB] Get:35 http://deb.debian.org/debian/ stretch/main procps amd64 2:3.3.12-3+deb9u1 [250 kB] Get:36 http://deb.debian.org/debian/ stretch/main libcap-ng0 amd64 0.7.7-3+b1 [13.8 kB] Get:37 http://deb.debian.org/debian/ stretch/main libaudit1 amd64 1:2.6.7-2 [51.3 kB] Get:38 http://deb.debian.org/debian/ stretch/main libpng16-16 amd64 1.6.28-1+deb9u1 [280 kB] Get:39 http://deb.debian.org/debian/ stretch/main libfreetype6 amd64 2.6.3-3.2+deb9u1 [438 kB] Get:40 http://deb.debian.org/debian/ stretch/main ucf all 3.0036 [70.2 kB] Get:41 http://deb.debian.org/debian/ stretch/main ttf-bitstream-vera all 1.10-8 [352 kB] Get:42 http://deb.debian.org/debian/ stretch/main fontconfig-config all 2.11.0-6.7 [271 kB] Get:43 http://deb.debian.org/debian/ stretch/main libfontconfig1 amd64 2.11.0-6.7+b1 [331 kB] Get:44 http://deb.debian.org/debian/ stretch/main fontconfig amd64 2.11.0-6.7+b1 [404 kB] Get:45 http://deb.debian.org/debian/ stretch/main libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:46 http://deb.debian.org/debian/ stretch/main libassuan0 amd64 2.4.3-2 [42.5 kB] Get:47 http://deb.debian.org/debian/ stretch/main pinentry-curses amd64 1.0.0-2 [50.5 kB] Get:48 http://deb.debian.org/debian/ stretch/main libnpth0 amd64 1.3-1 [14.6 kB] Get:49 http://deb.debian.org/debian/ stretch/main gnupg-agent amd64 2.1.18-8~deb9u4 [554 kB] Get:50 http://deb.debian.org/debian/ stretch/main libksba8 amd64 1.3.5-2 [99.7 kB] Get:51 http://deb.debian.org/debian/ stretch/main gnupg amd64 2.1.18-8~deb9u4 [1128 kB] Get:52 http://deb.debian.org/debian/ stretch/main libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:53 http://deb.debian.org/debian/ stretch/main libnettle6 amd64 3.3-1+b2 [192 kB] Get:54 http://deb.debian.org/debian/ stretch/main libhogweed4 amd64 3.3-1+b2 [136 kB] Get:55 http://deb.debian.org/debian/ stretch/main libp11-kit0 amd64 0.23.3-2 [111 kB] Get:56 http://deb.debian.org/debian/ stretch/main libtasn1-6 amd64 4.10-1.1+deb9u1 [50.6 kB] Get:57 http://deb.debian.org/debian/ stretch/main libgnutls30 amd64 3.5.8-5+deb9u5 [896 kB] Get:58 http://deb.debian.org/debian/ stretch/main libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:59 http://deb.debian.org/debian/ stretch/main libkrb5support0 amd64 1.15-1+deb9u1 [61.9 kB] Get:60 http://deb.debian.org/debian/ stretch/main libk5crypto3 amd64 1.15-1+deb9u1 [119 kB] Get:61 http://deb.debian.org/debian/ stretch/main libkrb5-3 amd64 1.15-1+deb9u1 [311 kB] Get:62 http://deb.debian.org/debian/ stretch/main libgssapi-krb5-2 amd64 1.15-1+deb9u1 [155 kB] Get:63 http://deb.debian.org/debian/ stretch/main libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [68.4 kB] Get:64 http://deb.debian.org/debian/ stretch/main libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [105 kB] Get:65 http://deb.debian.org/debian/ stretch/main libldap-common all 2.4.44+dfsg-5+deb9u4 [85.7 kB] Get:66 http://deb.debian.org/debian/ stretch/main libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u4 [219 kB] Get:67 http://deb.debian.org/debian/ stretch/main libicu57 amd64 57.1-6+deb9u4 [7699 kB] Get:68 http://deb.debian.org/debian/ stretch/main libxml2 amd64 2.9.4+dfsg1-2.2+deb9u2 [920 kB] Get:69 http://deb.debian.org/debian/ stretch/main fonts-lyx all 2.2.2-1 [197 kB] Get:70 http://deb.debian.org/debian/ stretch/main libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:71 http://deb.debian.org/debian/ stretch/main libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:72 http://deb.debian.org/debian/ stretch/main libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:73 http://deb.debian.org/debian/ stretch/main libpsl5 amd64 0.17.0-3 [41.8 kB] Get:74 http://deb.debian.org/debian/ stretch/main librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:75 http://deb.debian.org/debian/ stretch/main libssh2-1 amd64 1.7.0-1+deb9u1 [139 kB] Get:76 http://deb.debian.org/debian/ stretch/main libcurl3-gnutls amd64 7.52.1-5+deb9u10 [290 kB] Get:77 http://deb.debian.org/debian/ stretch/main libhts1 amd64 1.3.2-2 [257 kB] Get:78 http://deb.debian.org/debian/ stretch/main python-pysam amd64 0.10.0+ds-2 [1301 kB] Get:79 http://deb.debian.org/debian/ stretch/main python-six all 1.10.0-3 [14.4 kB] Get:80 http://deb.debian.org/debian/ stretch/main python-dateutil all 2.5.3-2 [51.3 kB] Get:81 http://deb.debian.org/debian/ stretch/main python-matplotlib-data all 2.0.0+dfsg1-2 [4414 kB] Get:82 http://deb.debian.org/debian/ stretch/main python-pyparsing all 2.1.10+dfsg1-1 [88.5 kB] Get:83 http://deb.debian.org/debian/ stretch/main python-tz all 2016.7-0.3 [33.7 kB] Get:84 http://deb.debian.org/debian/ stretch/main libjs-jquery all 3.1.1-2+deb9u1 [154 kB] Get:85 http://deb.debian.org/debian/ stretch/main libjs-jquery-ui all 1.12.1+dfsg-4 [232 kB] Get:86 http://deb.debian.org/debian/ stretch/main python-cycler all 0.10.0-1 [7448 B] Get:87 http://deb.debian.org/debian/ stretch/main python-functools32 all 3.2.3.2-3 [11.0 kB] Get:88 http://deb.debian.org/debian/ stretch/main python-subprocess32 amd64 3.2.7-2 [28.9 kB] Get:89 http://deb.debian.org/debian/ stretch/main libglib2.0-0 amd64 2.50.3-2+deb9u2 [2692 kB] Get:90 http://deb.debian.org/debian/ stretch/main libatk1.0-data all 2.22.0-1 [172 kB] Get:91 http://deb.debian.org/debian/ stretch/main libatk1.0-0 amd64 2.22.0-1 [78.4 kB] Get:92 http://deb.debian.org/debian/ stretch/main libpixman-1-0 amd64 0.34.0-1 [530 kB] Get:93 http://deb.debian.org/debian/ stretch/main libbsd0 amd64 0.8.3-1 [83.0 kB] Get:94 http://deb.debian.org/debian/ stretch/main libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:95 http://deb.debian.org/debian/ stretch/main libxcb1 amd64 1.12-1 [133 kB] Get:96 http://deb.debian.org/debian/ stretch/main libx11-data all 2:1.6.4-3+deb9u1 [287 kB] Get:97 http://deb.debian.org/debian/ stretch/main libx11-6 amd64 2:1.6.4-3+deb9u1 [748 kB] Get:98 http://deb.debian.org/debian/ stretch/main libxcb-render0 amd64 1.12-1 [105 kB] Get:99 http://deb.debian.org/debian/ stretch/main libxcb-shm0 amd64 1.12-1 [95.9 kB] Get:100 http://deb.debian.org/debian/ stretch/main libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:101 http://deb.debian.org/debian/ stretch/main libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:102 http://deb.debian.org/debian/ stretch/main libcairo2 amd64 1.14.8-1 [771 kB] Get:103 http://deb.debian.org/debian/ stretch/main libjpeg62-turbo amd64 1:1.5.1-2 [134 kB] Get:104 http://deb.debian.org/debian/ stretch/main libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:105 http://deb.debian.org/debian/ stretch/main libtiff5 amd64 4.0.8-2+deb9u5 [239 kB] Get:106 http://deb.debian.org/debian/ stretch/main shared-mime-info amd64 1.8-1+deb9u1 [731 kB] Get:107 http://deb.debian.org/debian/ stretch/main libgdk-pixbuf2.0-common all 2.36.5-2+deb9u2 [311 kB] Get:108 http://deb.debian.org/debian/ stretch/main libgdk-pixbuf2.0-0 amd64 2.36.5-2+deb9u2 [170 kB] Get:109 http://deb.debian.org/debian/ stretch/main libgtk2.0-common all 2.24.31-2 [2693 kB] Get:110 http://deb.debian.org/debian/ stretch/main libavahi-common-data amd64 0.6.32-2 [118 kB] Get:111 http://deb.debian.org/debian/ stretch/main libavahi-common3 amd64 0.6.32-2 [52.0 kB] Get:112 http://deb.debian.org/debian/ stretch/main libdbus-1-3 amd64 1.10.32-0+deb9u1 [196 kB] Get:113 http://deb.debian.org/debian/ stretch/main libavahi-client3 amd64 0.6.32-2 [55.3 kB] Get:114 http://deb.debian.org/debian/ stretch/main libcups2 amd64 2.2.1-8+deb9u6 [307 kB] Get:115 http://deb.debian.org/debian/ stretch/main libthai-data all 0.1.26-1 [166 kB] Get:116 http://deb.debian.org/debian/ stretch/main libdatrie1 amd64 0.2.10-4+b1 [36.4 kB] Get:117 http://deb.debian.org/debian/ stretch/main libthai0 amd64 0.1.26-1 [52.1 kB] Get:118 http://deb.debian.org/debian/ stretch/main libpango-1.0-0 amd64 1.40.5-1 [320 kB] Get:119 http://deb.debian.org/debian/ stretch/main libgraphite2-3 amd64 1.3.10-1 [84.2 kB] Get:120 http://deb.debian.org/debian/ stretch/main libharfbuzz0b amd64 1.4.2-1 [671 kB] Get:121 http://deb.debian.org/debian/ stretch/main libpangoft2-1.0-0 amd64 1.40.5-1 [205 kB] Get:122 http://deb.debian.org/debian/ stretch/main libpangocairo-1.0-0 amd64 1.40.5-1 [193 kB] Get:123 http://deb.debian.org/debian/ stretch/main libxcomposite1 amd64 1:0.4.4-2 [16.5 kB] Get:124 http://deb.debian.org/debian/ stretch/main libxfixes3 amd64 1:5.0.3-1 [21.9 kB] Get:125 http://deb.debian.org/debian/ stretch/main libxcursor1 amd64 1:1.1.14-1+deb9u2 [34.9 kB] Get:126 http://deb.debian.org/debian/ stretch/main libxdamage1 amd64 1:1.1.4-2+b3 [14.5 kB] Get:127 http://deb.debian.org/debian/ stretch/main libxi6 amd64 2:1.7.9-1 [82.6 kB] Get:128 http://deb.debian.org/debian/ stretch/main libxinerama1 amd64 2:1.1.3-1+b3 [16.7 kB] Get:129 http://deb.debian.org/debian/ stretch/main libxrandr2 amd64 2:1.5.1-1 [37.5 kB] Get:130 http://deb.debian.org/debian/ stretch/main hicolor-icon-theme all 0.15-1 [9550 B] Get:131 http://deb.debian.org/debian/ stretch/main gtk-update-icon-cache amd64 3.22.11-1 [76.6 kB] Get:132 http://deb.debian.org/debian/ stretch/main libcroco3 amd64 0.6.11-3 [143 kB] Get:133 http://deb.debian.org/debian/ stretch/main librsvg2-2 amd64 2.40.16-1+b1 [281 kB] Get:134 http://deb.debian.org/debian/ stretch/main librsvg2-common amd64 2.40.16-1+b1 [194 kB] Get:135 http://deb.debian.org/debian/ stretch/main gnome-icon-theme all 3.12.0-2 [9890 kB] Get:136 http://deb.debian.org/debian/ stretch/main libgtk2.0-0 amd64 2.24.31-2 [1800 kB] Get:137 http://deb.debian.org/debian/ stretch/main python-matplotlib amd64 2.0.0+dfsg1-2 [1598 kB] Get:138 http://deb.debian.org/debian/ stretch/main bowtie amd64 1.1.2-6 [1618 kB] Get:139 http://deb.debian.org/debian/ stretch/main libatomic1 amd64 6.3.0-18+deb9u1 [8966 B] Get:140 http://deb.debian.org/debian/ stretch/main libtbb2 amd64 4.3~20150611-2 [136 kB] Get:141 http://deb.debian.org/debian/ stretch/main bowtie2 amd64 2.3.0-2 [1166 kB] Get:142 http://deb.debian.org/debian/ stretch/main libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:143 http://deb.debian.org/debian/ stretch/main seqan-apps amd64 2.3.1+dfsg-4 [11.5 MB] Get:144 http://deb.debian.org/debian/ stretch/main gasic amd64 0.0.r19-1 [19.9 kB] Get:145 http://deb.debian.org/debian/ stretch/main libc-dev-bin amd64 2.24-11+deb9u4 [259 kB] Get:146 http://deb.debian.org/debian/ stretch/main linux-libc-dev amd64 4.9.228-1 [1511 kB] Get:147 http://deb.debian.org/debian/ stretch/main libc6-dev amd64 2.24-11+deb9u4 [2364 kB] Get:148 http://deb.debian.org/debian/ stretch/main libexpat1-dev amd64 2.2.0-2+deb9u3 [134 kB] Get:149 http://deb.debian.org/debian/ stretch/main libpython2.7 amd64 2.7.13-2+deb9u3 [1071 kB] Get:150 http://deb.debian.org/debian/ stretch/main libpython2.7-dev amd64 2.7.13-2+deb9u3 [28.2 MB] Get:151 http://deb.debian.org/debian/ stretch/main libpython-dev amd64 2.7.13-2 [20.1 kB] Get:152 http://deb.debian.org/debian/ stretch/main python2.7-dev amd64 2.7.13-2+deb9u3 [290 kB] Get:153 http://deb.debian.org/debian/ stretch/main python-dev amd64 2.7.13-2 [1126 B] Get:154 http://deb.debian.org/debian/ stretch/main python-pyrex all 0.9.9-1 [191 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 122 MB in 3s (39.3 MB/s) Selecting previously unselected package libfdisk1: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 ... 14118 files and directories currently installed.) Preparing to unpack .../libfdisk1_2.29.2-1+deb9u1_amd64.deb ... Unpacking libfdisk1:amd64 (2.29.2-1+deb9u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libfdisk1:amd64 (2.29.2-1+deb9u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... (Reading database ... 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Setting up init-system-helpers (1.48) ... (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 ... 14128 files and directories currently installed.) Preparing to unpack .../util-linux_2.29.2-1+deb9u1_amd64.deb ... Unpacking util-linux (2.29.2-1+deb9u1) over (2.25.2-6) ... Replacing files in old package initscripts (2.88dsf-59) ... Processing triggers for mime-support (3.60) ... Setting up util-linux (2.29.2-1+deb9u1) ... Installing new version of config file /etc/init.d/hwclock.sh ... Processing triggers for systemd (215-17+deb8u7) ... (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 ... 14159 files and directories currently installed.) Preparing to unpack .../initscripts_2.88dsf-59.9_amd64.deb ... Unpacking initscripts (2.88dsf-59.9) over (2.88dsf-59) ... Setting up sysvinit-utils (2.88dsf-59.9) ... Setting up initscripts (2.88dsf-59.9) ... Installing new version of config file /etc/init.d/checkfs.sh ... Installing new version of config file /etc/init.d/checkroot.sh ... Installing new version of config file /etc/init.d/mountall.sh ... Installing new version of config file /etc/init.d/umountfs ... Installing new version of config file /etc/init.d/umountroot ... Installing new version of config file /etc/default/rcS ... Installing new version of config file /etc/default/tmpfs ... Processing triggers for systemd (215-17+deb8u7) ... (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 ... 14159 files and directories currently installed.) Preparing to unpack .../sysv-rc_2.88dsf-59.9_all.deb ... Unpacking sysv-rc (2.88dsf-59.9) over (2.88dsf-59) ... Setting up sysv-rc (2.88dsf-59.9) ... Processing triggers for systemd (215-17+deb8u7) ... (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 ... 14157 files and directories currently installed.) Preparing to unpack .../archives/init_1.48_amd64.deb ... Unpacking init (1.48) over (1.22) ... Setting up init (1.48) ... Selecting previously unselected package liblz4-1: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 ... 14157 files and directories currently installed.) Preparing to unpack .../liblz4-1_0.0~r131-2+b1_amd64.deb ... Unpacking liblz4-1:amd64 (0.0~r131-2+b1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up liblz4-1:amd64 (0.0~r131-2+b1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Selecting previously unselected package gcc-6-base: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 ... 14163 files and directories currently installed.) Preparing to unpack .../gcc-6-base_6.3.0-18+deb9u1_amd64.deb ... Unpacking gcc-6-base:amd64 (6.3.0-18+deb9u1) ... Setting up gcc-6-base:amd64 (6.3.0-18+deb9u1) ... Selecting previously unselected package libreadline7: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 ... 14170 files and directories currently installed.) Preparing to unpack .../libreadline7_7.0-3_amd64.deb ... Unpacking libreadline7:amd64 (7.0-3) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../libssl1.1_1.1.0l-1~deb9u1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Preparing to unpack .../python2.7_2.7.13-2+deb9u3_amd64.deb ... Unpacking python2.7 (2.7.13-2+deb9u3) over (2.7.9-2+deb8u1) ... Preparing to unpack .../libpython2.7-stdlib_2.7.13-2+deb9u3_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) over (2.7.9-2+deb8u1) ... Preparing to unpack .../python2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking python2.7-minimal (2.7.13-2+deb9u3) over (2.7.9-2+deb8u1) ... Preparing to unpack .../libpython2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) over (2.7.9-2+deb8u1) ... Preparing to unpack .../python-minimal_2.7.13-2_amd64.deb ... Unpacking python-minimal (2.7.13-2) over (2.7.9-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Processing triggers for mime-support (3.60) ... Setting up libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Setting up python2.7-minimal (2.7.13-2+deb9u3) ... Setting up python-minimal (2.7.13-2) ... (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 ... 14190 files and directories currently installed.) Preparing to unpack .../python_2.7.13-2_amd64.deb ... Unpacking python (2.7.13-2) over (2.7.9-1) ... Preparing to unpack .../libpython-stdlib_2.7.13-2_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.13-2) over (2.7.9-1) ... Preparing to unpack .../libgcc1_1%3a6.3.0-18+deb9u1_amd64.deb ... Unpacking libgcc1:amd64 (1:6.3.0-18+deb9u1) over (1:4.9.2-10+deb8u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libgcc1:amd64 (1:6.3.0-18+deb9u1) ... Processing triggers for libc-bin (2.24-11+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 ... 14190 files and directories currently installed.) Preparing to unpack .../libquadmath0_6.3.0-18+deb9u1_amd64.deb ... Unpacking libquadmath0:amd64 (6.3.0-18+deb9u1) over (4.9.2-10+deb8u1) ... Preparing to unpack .../libgfortran3_6.3.0-18+deb9u1_amd64.deb ... Unpacking libgfortran3:amd64 (6.3.0-18+deb9u1) over (4.9.2-10+deb8u1) ... Preparing to unpack .../python-scipy_0.18.1-2_amd64.deb ... Unpacking python-scipy (0.18.1-2) over (0.14.0-2) ... Preparing to unpack .../libstdc++6_6.3.0-18+deb9u1_amd64.deb ... Unpacking libstdc++6:amd64 (6.3.0-18+deb9u1) over (4.9.2-10+deb8u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libstdc++6:amd64 (6.3.0-18+deb9u1) ... Processing triggers for libc-bin (2.24-11+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 ... 14247 files and directories currently installed.) Preparing to unpack .../archives/apt_1.4.10_amd64.deb ... Unpacking apt (1.4.10) over (1.0.9.8.4) ... Selecting previously unselected package libapt-pkg5.0:amd64. Preparing to unpack .../libapt-pkg5.0_1.4.10_amd64.deb ... Unpacking libapt-pkg5.0:amd64 (1.4.10) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libapt-pkg5.0:amd64 (1.4.10) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Selecting previously unselected package libapparmor1: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 ... 14302 files and directories currently installed.) Preparing to unpack .../libapparmor1_2.11.0-3+deb9u2_amd64.deb ... Unpacking libapparmor1:amd64 (2.11.0-3+deb9u2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libapparmor1:amd64 (2.11.0-3+deb9u2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Selecting previously unselected package libidn11: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 ... 14308 files and directories currently installed.) Preparing to unpack .../libidn11_1.33-1+deb9u1_amd64.deb ... Unpacking libidn11:amd64 (1.33-1+deb9u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libidn11:amd64 (1.33-1+deb9u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Selecting previously unselected package libip4tc0: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 ... 14314 files and directories currently installed.) Preparing to unpack .../libip4tc0_1.6.0+snapshot20161117-6_amd64.deb ... Unpacking libip4tc0:amd64 (1.6.0+snapshot20161117-6) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libip4tc0:amd64 (1.6.0+snapshot20161117-6) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Selecting previously unselected package libseccomp2: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 ... 14320 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.3.1-2.1+deb9u1_amd64.deb ... Unpacking libseccomp2:amd64 (2.3.1-2.1+deb9u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libseccomp2:amd64 (2.3.1-2.1+deb9u1) ... Processing triggers for libc-bin (2.24-11+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 ... 14326 files and directories currently installed.) Preparing to unpack .../libudev1_232-25+deb9u12_amd64.deb ... Unpacking libudev1:amd64 (232-25+deb9u12) over (215-17+deb8u7) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libudev1:amd64 (232-25+deb9u12) ... Processing triggers for libc-bin (2.24-11+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 ... 14325 files and directories currently installed.) Preparing to unpack .../libsystemd0_232-25+deb9u12_amd64.deb ... Unpacking libsystemd0:amd64 (232-25+deb9u12) over (215-17+deb8u7) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libsystemd0:amd64 (232-25+deb9u12) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... dpkg: considering deconfiguration of systemd, which would be broken by installation of udev ... dpkg: yes, will deconfigure systemd (broken by udev) (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 ... 14325 files and directories currently installed.) Preparing to unpack .../udev_232-25+deb9u12_amd64.deb ... De-configuring systemd (215-17+deb8u7) ... Unpacking udev (232-25+deb9u12) over (215-17+deb8u7) ... Replacing files in old package systemd (215-17+deb8u7) ... dpkg: warning: unable to delete old directory '/etc/modprobe.d': Directory not empty Preparing to unpack .../systemd_232-25+deb9u12_amd64.deb ... Unpacking systemd (232-25+deb9u12) over (215-17+deb8u7) ... Setting up systemd (232-25+deb9u12) ... Installing new version of config file /etc/dbus-1/system.d/org.freedesktop.login1.conf ... Installing new version of config file /etc/dbus-1/system.d/org.freedesktop.systemd1.conf ... Installing new version of config file /etc/pam.d/systemd-user ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/resolved.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/timesyncd.conf ... Installing new version of config file /etc/systemd/user.conf ... Created symlink /etc/systemd/system/sysinit.target.wants/systemd-timesyncd.service → /lib/systemd/system/systemd-timesyncd.service. addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.machine1.conf ... Removing obsolete conffile /etc/systemd/bootchart.conf ... Selecting previously unselected package libprocps6: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 ... 14386 files and directories currently installed.) Preparing to unpack .../libprocps6_2%3a3.3.12-3+deb9u1_amd64.deb ... Unpacking libprocps6:amd64 (2:3.3.12-3+deb9u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libprocps6:amd64 (2:3.3.12-3+deb9u1) ... Processing triggers for libc-bin (2.24-11+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 ... 14393 files and directories currently installed.) Preparing to unpack .../procps_2%3a3.3.12-3+deb9u1_amd64.deb ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Unpacking procps (2:3.3.12-3+deb9u1) over (2:3.3.9-9+deb8u1) ... Setting up procps (2:3.3.12-3+deb9u1) ... Installing new version of config file /etc/init.d/procps ... Installing new version of config file /etc/sysctl.conf ... Processing triggers for systemd (232-25+deb9u12) ... Selecting previously unselected package libcap-ng0: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 ... 14395 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.7.7-3+b1_amd64.deb ... Unpacking libcap-ng0:amd64 (0.7.7-3+b1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libcap-ng0:amd64 (0.7.7-3+b1) ... Processing triggers for libc-bin (2.24-11+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 ... 14402 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a2.6.7-2_amd64.deb ... Unpacking libaudit1:amd64 (1:2.6.7-2) over (1:2.4-1+b1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libaudit1:amd64 (1:2.6.7-2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Selecting previously unselected package libpng16-16: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 ... 14401 files and directories currently installed.) Preparing to unpack .../libpng16-16_1.6.28-1+deb9u1_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.28-1+deb9u1) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../libfreetype6_2.6.3-3.2+deb9u1_amd64.deb ... Unpacking libfreetype6:amd64 (2.6.3-3.2+deb9u1) ... Selecting previously unselected package ucf. Preparing to unpack .../archives/ucf_3.0036_all.deb ... Moving old data out of the way Unpacking ucf (3.0036) ... Selecting previously unselected package ttf-bitstream-vera. Preparing to unpack .../ttf-bitstream-vera_1.10-8_all.deb ... Unpacking ttf-bitstream-vera (1.10-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../fontconfig-config_2.11.0-6.7_all.deb ... Unpacking fontconfig-config (2.11.0-6.7) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../libfontconfig1_2.11.0-6.7+b1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.11.0-6.7+b1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../fontconfig_2.11.0-6.7+b1_amd64.deb ... Unpacking fontconfig (2.11.0-6.7+b1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../libxau6_1%3a1.0.8-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.8-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../libassuan0_2.4.3-2_amd64.deb ... Unpacking libassuan0:amd64 (2.4.3-2) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../pinentry-curses_1.0.0-2_amd64.deb ... Unpacking pinentry-curses (1.0.0-2) ... Selecting previously unselected package libnpth0:amd64. Preparing to unpack .../libnpth0_1.3-1_amd64.deb ... Unpacking libnpth0:amd64 (1.3-1) ... Selecting previously unselected package gnupg-agent. Preparing to unpack .../gnupg-agent_2.1.18-8~deb9u4_amd64.deb ... Unpacking gnupg-agent (2.1.18-8~deb9u4) ... Selecting previously unselected package libksba8:amd64. Preparing to unpack .../libksba8_1.3.5-2_amd64.deb ... Unpacking libksba8:amd64 (1.3.5-2) ... Preparing to unpack .../gnupg_2.1.18-8~deb9u4_amd64.deb ... Unpacking gnupg (2.1.18-8~deb9u4) over (1.4.18-7+deb8u5) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libassuan0:amd64 (2.4.3-2) ... Setting up pinentry-curses (1.0.0-2) ... Setting up libnpth0:amd64 (1.3-1) ... Setting up libreadline7:amd64 (7.0-3) ... Setting up gnupg-agent (2.1.18-8~deb9u4) ... Setting up libksba8:amd64 (1.3.5-2) ... Setting up gnupg (2.1.18-8~deb9u4) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Selecting previously unselected package libgmp10: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 ... 14614 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.1.2+dfsg-1_amd64.deb ... Unpacking libgmp10:amd64 (2:6.1.2+dfsg-1) ... 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Selecting previously unselected package libpython-dev:amd64. Preparing to unpack .../libpython-dev_2.7.13-2_amd64.deb ... Unpacking libpython-dev:amd64 (2.7.13-2) ... Selecting previously unselected package python2.7-dev. Preparing to unpack .../python2.7-dev_2.7.13-2+deb9u3_amd64.deb ... Unpacking python2.7-dev (2.7.13-2+deb9u3) ... Selecting previously unselected package python-dev. Preparing to unpack .../python-dev_2.7.13-2_amd64.deb ... Unpacking python-dev (2.7.13-2) ... Preparing to unpack .../python-pyrex_0.9.9-1_all.deb ... Unpacking python-pyrex (0.9.9-1) over (0.9.8.5-2.1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up python (2.7.13-2) ... Setting up libquadmath0:amd64 (6.3.0-18+deb9u1) ... Setting up libgfortran3:amd64 (6.3.0-18+deb9u1) ... Setting up python-scipy (0.18.1-2) ... Setting up apt (1.4.10) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/kernel/postinst.d/apt-auto-removal ... usermod: no changes Created symlink /etc/systemd/system/timers.target.wants/apt-daily-upgrade.timer → /lib/systemd/system/apt-daily-upgrade.timer. Created symlink /etc/systemd/system/timers.target.wants/apt-daily.timer → /lib/systemd/system/apt-daily.timer. Removing obsolete conffile /etc/cron.daily/apt ... Setting up udev (232-25+deb9u12) ... Installing new version of config file /etc/init.d/udev ... Installing new version of config file /etc/init/udevmonitor.conf ... Installing new version of config file /etc/udev/udev.conf ... addgroup: The group `input' already exists as a system group. Exiting. A chroot environment has been detected, udev not started. Removing obsolete conffile /etc/init.d/udev-finish ... Removing obsolete conffile /etc/init/udev-finish.conf ... Removing obsolete conffile /etc/init/udev-fallback-graphics.conf ... Removing obsolete conffile /etc/modprobe.d/fbdev-blacklist.conf ... Setting up libpng16-16:amd64 (1.6.28-1+deb9u1) ... Setting up libfreetype6:amd64 (2.6.3-3.2+deb9u1) ... Setting up ucf (3.0036) ... Setting up ttf-bitstream-vera (1.10-8) ... Setting up fontconfig-config (2.11.0-6.7) ... Setting up libfontconfig1:amd64 (2.11.0-6.7+b1) ... Setting up fontconfig (2.11.0-6.7+b1) ... Regenerating fonts cache... done. Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-1) ... Setting up libnettle6:amd64 (3.3-1+b2) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u1) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u1) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+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 libldap-common (2.4.44+dfsg-5+deb9u4) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Setting up libicu57:amd64 (57.1-6+deb9u4) ... Setting up libxml2:amd64 (2.9.4+dfsg1-2.2+deb9u2) ... Setting up fonts-lyx (2.2.2-1) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up libssh2-1:amd64 (1.7.0-1+deb9u1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Setting up libhts1:amd64 (1.3.2-2) ... Setting up python-pysam (0.10.0+ds-2) ... Setting up python-six (1.10.0-3) ... Setting up python-dateutil (2.5.3-2) ... Setting up python-matplotlib-data (2.0.0+dfsg1-2) ... Setting up python-pyparsing (2.1.10+dfsg1-1) ... Setting up python-tz (2016.7-0.3) ... Setting up libjs-jquery (3.1.1-2+deb9u1) ... Setting up libjs-jquery-ui (1.12.1+dfsg-4) ... Setting up python-cycler (0.10.0-1) ... Setting up python-functools32 (3.2.3.2-3) ... Setting up python-subprocess32 (3.2.7-2) ... Setting up libglib2.0-0:amd64 (2.50.3-2+deb9u2) ... No schema files found: doing nothing. Setting up libatk1.0-data (2.22.0-1) ... Setting up libatk1.0-0:amd64 (2.22.0-1) ... Setting up libpixman-1-0:amd64 (0.34.0-1) ... Setting up libbsd0:amd64 (0.8.3-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.12-1) ... Setting up libx11-data (2:1.6.4-3+deb9u1) ... Setting up libx11-6:amd64 (2:1.6.4-3+deb9u1) ... Setting up libxcb-render0:amd64 (1.12-1) ... Setting up libxcb-shm0:amd64 (1.12-1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libcairo2:amd64 (1.14.8-1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.1-2) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libtiff5:amd64 (4.0.8-2+deb9u5) ... Setting up shared-mime-info (1.8-1+deb9u1) ... Setting up libgdk-pixbuf2.0-common (2.36.5-2+deb9u2) ... Setting up libgdk-pixbuf2.0-0:amd64 (2.36.5-2+deb9u2) ... Setting up libgtk2.0-common (2.24.31-2) ... Setting up libavahi-common-data:amd64 (0.6.32-2) ... Setting up libavahi-common3:amd64 (0.6.32-2) ... Setting up libdbus-1-3:amd64 (1.10.32-0+deb9u1) ... Setting up libavahi-client3:amd64 (0.6.32-2) ... Setting up libcups2:amd64 (2.2.1-8+deb9u6) ... Setting up libthai-data (0.1.26-1) ... Setting up libdatrie1:amd64 (0.2.10-4+b1) ... Setting up libthai0:amd64 (0.1.26-1) ... Setting up libpango-1.0-0:amd64 (1.40.5-1) ... Setting up libgraphite2-3:amd64 (1.3.10-1) ... Setting up libharfbuzz0b:amd64 (1.4.2-1) ... Setting up libpangoft2-1.0-0:amd64 (1.40.5-1) ... Setting up libpangocairo-1.0-0:amd64 (1.40.5-1) ... Setting up libxcomposite1:amd64 (1:0.4.4-2) ... Setting up libxfixes3:amd64 (1:5.0.3-1) ... Setting up libxcursor1:amd64 (1:1.1.14-1+deb9u2) ... Setting up libxdamage1:amd64 (1:1.1.4-2+b3) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libxinerama1:amd64 (2:1.1.3-1+b3) ... Setting up libxrandr2:amd64 (2:1.5.1-1) ... Setting up hicolor-icon-theme (0.15-1) ... Setting up gtk-update-icon-cache (3.22.11-1) ... Setting up libcroco3:amd64 (0.6.11-3) ... Setting up librsvg2-2:amd64 (2.40.16-1+b1) ... Setting up librsvg2-common:amd64 (2.40.16-1+b1) ... Setting up gnome-icon-theme (3.12.0-2) ... update-alternatives: using /usr/share/icons/gnome/scalable/places/debian-swirl.svg to provide /usr/share/icons/gnome/scalable/places/start-here.svg (start-here.svg) in auto mode Setting up libgtk2.0-0:amd64 (2.24.31-2) ... Setting up python-matplotlib (2.0.0+dfsg1-2) ... Setting up bowtie (1.1.2-6) ... Setting up libatomic1:amd64 (6.3.0-18+deb9u1) ... Setting up libtbb2:amd64 (4.3~20150611-2) ... Setting up bowtie2 (2.3.0-2) ... Setting up libgomp1:amd64 (6.3.0-18+deb9u1) ... Setting up seqan-apps (2.3.1+dfsg-4) ... Setting up gasic (0.0.r19-1) ... Setting up libc-dev-bin (2.24-11+deb9u4) ... Setting up linux-libc-dev:amd64 (4.9.228-1) ... Setting up libc6-dev:amd64 (2.24-11+deb9u4) ... Setting up libexpat1-dev:amd64 (2.2.0-2+deb9u3) ... Setting up libpython2.7:amd64 (2.7.13-2+deb9u3) ... Setting up libpython2.7-dev:amd64 (2.7.13-2+deb9u3) ... Setting up libpython-dev:amd64 (2.7.13-2) ... Setting up python2.7-dev (2.7.13-2+deb9u3) ... Setting up python-dev (2.7.13-2) ... Setting up python-pyrex (0.9.9-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Processing triggers for systemd (232-25+deb9u12) ... Processing triggers for libgdk-pixbuf2.0-0:amd64 (2.36.5-2+deb9u2) ... 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', '-yf', 'dist-upgrade'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m1.1s DUMP: 660e5103244a20b75ca08c3f8741e16e - 1m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'show', '--no-all-versions', 'gasic'] 1m1.3s DUMP: Package: gasic Version: 0.0.r19-1 Installed-Size: 74 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python:any (>= 2.6.6-7~), python-scipy, python-numpy, python-biopython, python-pysam, python-matplotlib, bowtie, bowtie2, bwa, seqan-apps Description-en: genome abundance similarity correction One goal of sequencing based metagenomic analysis is the quantitative taxonomic assessment of microbial community compositions. However, the majority of approaches either quantify at low resolution (e.g. at phylum level) or have severe problems discerning highly similar species. Yet, accurate quantification on species level is desirable in applications such as metagenomic diagnostics or community comparison. GASiC is a method to correct read alignment results for the ambiguities imposed by similarities of genomes. It has superior performance over existing methods. Description-md5: bdb1fbe60cfde219955bdb0d4f72e27c Homepage: http://sourceforge.net/projects/gasic/ Section: science Priority: optional Filename: pool/main/g/gasic/gasic_0.0.r19-1_amd64.deb Size: 19922 MD5sum: 72c96ac61c52ec65dab1caeee027c422 SHA256: cf8500919e647641eba13e8fc31d18a0d74640eb895016f01ce0e83316b16bc1 1m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'show', '--no-all-versions', 'gasic'] 1m1.3s INFO: apt-cache knows about the following packages: gasic 1m1.3s INFO: Running scripts pre_install 1m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_database-server'] 1m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_database-server'] 1m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_exceptions'] 1m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_exceptions'] 1m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_extras'] 1m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_extras'] 1m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_foreign_architecture'] 1m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_foreign_architecture'] 1m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'policy'] 1m1.3s 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: 1m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'policy'] 1m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'policy', 'gasic'] 1m1.4s DUMP: gasic: Installed: 0.0.r19-1 Candidate: 0.0.r19-1 Version table: *** 0.0.r19-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 1m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'policy', 'gasic'] 1m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', '-y', 'install', 'gasic'] 1m1.6s DUMP: Reading package lists... Building dependency tree... Reading state information... gasic is already the newest version (0.0.r19-1). The following packages were automatically installed and are no longer required: cython libssl1.0.0 python-pyrex Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', '-y', 'install', 'gasic'] 1m1.6s INFO: Running scripts post_install 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_install_exceptions'] 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_install_exceptions'] 1m1.6s INFO: Running scripts post_distupgrade 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_distupgrade_exceptions'] 1m1.6s DUMP: mode of '/usr/share/man/sl' changed from 0775 (rwxrwxr-x) to 0755 (rwxr-xr-x) mode of '/usr/share/man/sl/man1' changed from 0775 (rwxrwxr-x) to 0755 (rwxr-xr-x) mode of '/usr/share/man/sl/man8' changed from 0775 (rwxrwxr-x) to 0755 (rwxr-xr-x) 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_distupgrade_exceptions'] 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_distupgrade_zz_backports'] 1m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_distupgrade_zz_backports'] 1m1.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 1m3.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 1m3.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 1m4.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 1m4.6s INFO: Running scripts pre_install 1m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_database-server'] 1m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_database-server'] 1m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_exceptions'] 1m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_exceptions'] 1m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_extras'] 1m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_extras'] 1m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_foreign_architecture'] 1m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_foreign_architecture'] 1m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'policy'] 1m4.7s 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: 1m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'policy'] 1m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'policy', 'gasic'] 1m4.7s DUMP: gasic: Installed: 0.0.r19-1 Candidate: 0.0.r19-1 Version table: *** 0.0.r19-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 1m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-cache', 'policy', 'gasic'] 1m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', '-y', 'install', 'gasic=0.0.r19-1'] 1m4.9s DUMP: Reading package lists... Building dependency tree... Reading state information... gasic is already the newest version (0.0.r19-1). The following packages were automatically installed and are no longer required: cython libssl1.0.0 python-pyrex Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', '-y', 'install', 'gasic=0.0.r19-1'] 1m4.9s INFO: Running scripts post_install 1m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_install_exceptions'] 1m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_install_exceptions'] 1m5.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 1m6.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 1m7.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', '-ac', '--ignore-obsolete'] 1m9.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', '-ac', '--ignore-obsolete'] 1m9.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m9.7s DUMP: 0.15.6 1m9.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m9.7s INFO: Running adequate version 0.15.6 now. 1m9.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'gasic'] 1m9.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'gasic'] 1m9.8s INFO: Running scripts pre_remove 1m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_remove_exceptions'] 1m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/pre_remove_exceptions'] 1m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m13.6s DUMP: install ok installed acl acl 2.2.52-3+b1 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 bowtie bowtie 1.1.2-6 install ok installed bowtie2 bowtie2 2.3.0-2 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed bwa bwa 0.7.15-2+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed cython cython 0.25.2-1 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debconf-i18n debconf-i18n 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 dmsetup dmsetup 2:1.02.137-2 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 fontconfig fontconfig 2.11.0-6.7+b1 install ok installed fontconfig-config fontconfig-config 2.11.0-6.7 install ok installed fonts-lyx fonts-lyx 2.2.2-1 install ok installed gasic gasic 0.0.r19-1 install ok installed gcc-4.9-base:amd64 gcc-4.9-base 4.9.2-10+deb8u1 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gnome-icon-theme gnome-icon-theme 3.12.0-2 install ok installed gnupg gnupg 2.1.18-8~deb9u4 install ok installed gnupg-agent gnupg-agent 2.1.18-8~deb9u4 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gtk-update-icon-cache gtk-update-icon-cache 3.22.11-1 install ok installed gzip gzip 1.6-5+b1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.15-1 install ok installed hostname hostname 3.18+b1 install ok installed init init 1.48 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed initscripts initscripts 2.88dsf-59.9 install ok installed insserv insserv 1.14.0-5.4+b1 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapparmor1:amd64 libapparmor1 2.11.0-3+deb9u2 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 1.0.9.8.4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libassuan0:amd64 libassuan0 2.4.3-2 install ok installed libatk1.0-0:amd64 libatk1.0-0 2.22.0-1 install ok installed libatk1.0-data libatk1.0-data 2.22.0-1 install ok installed libatomic1:amd64 libatomic1 6.3.0-18+deb9u1 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libavahi-client3:amd64 libavahi-client3 0.6.32-2 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.6.32-2 install ok installed libavahi-common3:amd64 libavahi-common3 0.6.32-2 install ok installed libblas-common libblas-common 3.7.0-2 install ok installed libblas3 libblas3 3.7.0-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbsd0:amd64 libbsd0 0.8.3-1 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 libc-dev-bin libc-dev-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libc6-dev:amd64 libc6-dev 2.24-11+deb9u4 install ok installed libcairo2:amd64 libcairo2 1.14.8-1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcap2:amd64 libcap2 1:2.25-1 install ok installed libcap2-bin libcap2-bin 1:2.25-1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libcroco3:amd64 libcroco3 0.6.11-3 install ok installed libcryptsetup4:amd64 libcryptsetup4 2:1.7.3-4 install ok installed libcups2:amd64 libcups2 2.2.1-8+deb9u6 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.52.1-5+deb9u10 install ok installed libdatrie1:amd64 libdatrie1 0.2.10-4+b1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.10.32-0+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libdevmapper1.02.1:amd64 libdevmapper1.02.1 2:1.02.137-2 install ok installed libexpat1:amd64 libexpat1 2.2.0-2+deb9u3 install ok installed libexpat1-dev:amd64 libexpat1-dev 2.2.0-2+deb9u3 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libffi6:amd64 libffi6 3.2.1-6 install ok installed libfontconfig1:amd64 libfontconfig1 2.11.0-6.7+b1 install ok installed libfreetype6:amd64 libfreetype6 2.6.3-3.2+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 libgdk-pixbuf2.0-0:amd64 libgdk-pixbuf2.0-0 2.36.5-2+deb9u2 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.36.5-2+deb9u2 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.50.3-2+deb9u2 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-1 install ok installed libgnutls30:amd64 libgnutls30 3.5.8-5+deb9u5 install ok installed libgomp1:amd64 libgomp1 6.3.0-18+deb9u1 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.10-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.15-1+deb9u1 install ok installed libgtk2.0-0:amd64 libgtk2.0-0 2.24.31-2 install ok installed libgtk2.0-common libgtk2.0-common 2.24.31-2 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 1.4.2-1 install ok installed libhogweed4:amd64 libhogweed4 3.3-1+b2 install ok installed libhts1:amd64 libhts1 1.3.2-2 install ok installed libicu57:amd64 libicu57 57.1-6+deb9u4 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 libip4tc0:amd64 libip4tc0 1.6.0+snapshot20161117-6 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:1.5.1-2 install ok installed libjs-jquery libjs-jquery 3.1.1-2+deb9u1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.12.1+dfsg-4 install ok installed libk5crypto3:amd64 libk5crypto3 1.15-1+deb9u1 install ok installed libkeyutils1:amd64 libkeyutils1 1.5.9-9 install ok installed libkmod2:amd64 libkmod2 23-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.15-1+deb9u1 install ok installed libkrb5support0:amd64 libkrb5support0 1.15-1+deb9u1 install ok installed libksba8:amd64 libksba8 1.3.5-2 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+deb9u4 install ok installed libldap-common libldap-common 2.4.44+dfsg-5+deb9u4 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.07-3+b1 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 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+b2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.18.1-1+deb9u1 install ok installed libnpth0:amd64 libnpth0 1.3-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.3-2 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 libpango-1.0-0:amd64 libpango-1.0-0 1.40.5-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.40.5-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.40.5-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.34.0-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.28-1+deb9u1 install ok installed libprocps3:amd64 libprocps3 2:3.3.9-9+deb8u1 install ok installed libprocps6:amd64 libprocps6 2:3.3.12-3+deb9u1 install ok installed libpsl5:amd64 libpsl5 0.17.0-3 install ok installed libpython-dev:amd64 libpython-dev 2.7.13-2 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.13-2 install ok installed libpython2.7:amd64 libpython2.7 2.7.13-2+deb9u3 install ok installed libpython2.7-dev:amd64 libpython2.7-dev 2.7.13-2+deb9u3 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.13-2+deb9u3 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.13-2+deb9u3 install ok installed libquadmath0:amd64 libquadmath0 6.3.0-18+deb9u1 install ok installed libreadline6:amd64 libreadline6 6.3-8+b3 install ok installed libreadline7:amd64 libreadline7 7.0-3 install ok installed librsvg2-2:amd64 librsvg2-2 2.40.16-1+b1 install ok installed librsvg2-common:amd64 librsvg2-common 2.40.16-1+b1 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+deb9u1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27~101-g0780600+dfsg-3+deb9u1 install ok installed libseccomp2:amd64 libseccomp2 2.3.1-2.1+deb9u1 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 libslang2:amd64 libslang2 2.3.1-5 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.16.2-5+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libssh2-1:amd64 libssh2-1 1.7.0-1+deb9u1 install ok installed libssl1.0.0:amd64 libssl1.0.0 1.0.1t-1+deb8u8 install ok installed libssl1.1:amd64 libssl1.1 1.1.0l-1~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 libtasn1-6:amd64 libtasn1-6 4.10-1.1+deb9u1 install ok installed libtbb2:amd64 libtbb2 4.3~20150611-2 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b5 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5+b4 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7.1 install ok installed libthai-data libthai-data 0.1.26-1 install ok installed libthai0:amd64 libthai0 0.1.26-1 install ok installed libtiff5:amd64 libtiff5 4.0.8-2+deb9u5 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libunistring0:amd64 libunistring0 0.9.6+really0.9.3-0.1 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-30 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed libx11-6:amd64 libx11-6 2:1.6.4-3+deb9u1 install ok installed libx11-data libx11-data 2:1.6.4-3+deb9u1 install ok installed libxau6:amd64 libxau6 1:1.0.8-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.12-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.12-1 install ok installed libxcb1:amd64 libxcb1 1.12-1 install ok installed libxcomposite1:amd64 libxcomposite1 1:0.4.4-2 install ok installed libxcursor1:amd64 libxcursor1 1:1.1.14-1+deb9u2 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.4-2+b3 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.3-1+b2 install ok installed libxfixes3:amd64 libxfixes3 1:5.0.3-1 install ok installed libxi6:amd64 libxi6 2:1.7.9-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.3-1+b3 install ok installed libxml2:amd64 libxml2 2.9.4+dfsg1-2.2+deb9u2 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.1-1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1 install ok installed linux-libc-dev:amd64 linux-libc-dev 4.9.228-1 install ok installed login login 1:4.4-4.1 install ok installed lsb-base lsb-base 9.20161125 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mime-support mime-support 3.60 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed 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 pinentry-curses pinentry-curses 1.0.0-2 install ok installed procps procps 2:3.3.12-3+deb9u1 install ok installed python python 2.7.13-2 install ok installed python-biopython python-biopython 1.68+dfsg-3 install ok installed python-cycler python-cycler 0.10.0-1 install ok installed python-dateutil python-dateutil 2.5.3-2 install ok installed python-decorator python-decorator 4.0.11-1 install ok installed python-dev python-dev 2.7.13-2 install ok installed python-functools32 python-functools32 3.2.3.2-3 install ok installed python-matplotlib python-matplotlib 2.0.0+dfsg1-2 install ok installed python-matplotlib-data python-matplotlib-data 2.0.0+dfsg1-2 install ok installed python-minimal python-minimal 2.7.13-2 install ok installed python-numpy python-numpy 1:1.12.1-3 install ok installed python-pyparsing python-pyparsing 2.1.10+dfsg1-1 install ok installed python-pyrex python-pyrex 0.9.9-1 install ok installed python-pysam python-pysam 0.10.0+ds-2 install ok installed python-reportlab python-reportlab 3.3.0-2+deb9u1 install ok installed python-reportlab-accel:amd64 python-reportlab-accel 3.3.0-2+deb9u1 install ok installed python-scipy python-scipy 0.18.1-2 install ok installed python-six python-six 1.10.0-3 install ok installed python-subprocess32 python-subprocess32 3.2.7-2 install ok installed python-tz python-tz 2016.7-0.3 install ok installed python2.7 python2.7 2.7.13-2+deb9u3 install ok installed python2.7-dev python2.7-dev 2.7.13-2+deb9u3 install ok installed python2.7-minimal python2.7-minimal 2.7.13-2+deb9u3 install ok installed readline-common readline-common 7.0-3 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed seqan-apps seqan-apps 2.3.1+dfsg-4 install ok installed shared-mime-info shared-mime-info 1.8-1+deb9u1 install ok installed startpar startpar 0.59-3.1 install ok installed systemd systemd 232-25+deb9u12 install ok installed systemd-sysv systemd-sysv 232-25+deb9u12 install ok installed sysv-rc sysv-rc 2.88dsf-59.9 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed ttf-bitstream-vera ttf-bitstream-vera 1.10-8 install ok installed tzdata tzdata 2020a-0+deb9u1 install ok installed ucf ucf 3.0036 install ok installed udev udev 232-25+deb9u12 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 1m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', 'remove', 'bowtie', 'bowtie2', 'bwa', 'cython', 'fontconfig', 'fontconfig-config', 'fonts-lyx', 'gnome-icon-theme', 'gnupg', 'gnupg-agent', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'libatk1.0-0:amd64', 'libatk1.0-data', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libblas-common', 'libblas3', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcroco3:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libffi6:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdk-pixbuf2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran3:amd64', 'libglib2.0-0:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libicu57:amd64', 'libidn2-0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps3:amd64', 'libpsl5:amd64', 'libpython-dev:amd64', 'libpython-stdlib:amd64', 'libpython2.7:amd64', 'libpython2.7-dev:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'librsvg2-2:amd64', 'librsvg2-common:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1:amd64', 'libssl1.0.0:amd64', 'libssl1.1:amd64', 'libtasn1-6:amd64', 'libtbb2:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libunistring0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'linux-libc-dev:amd64', 'mime-support', 'pinentry-curses', 'python', 'python-biopython', 'python-cycler', 'python-dateutil', 'python-decorator', 'python-dev', 'python-functools32', 'python-matplotlib', 'python-matplotlib-data', 'python-minimal', 'python-numpy', 'python-pyparsing', 'python-pyrex', 'python-pysam', 'python-reportlab', 'python-reportlab-accel:amd64', 'python-scipy', 'python-six', 'python-subprocess32', 'python-tz', 'python2.7', 'python2.7-dev', 'python2.7-minimal', 'seqan-apps', 'shared-mime-info', 'ttf-bitstream-vera', 'ucf', 'gasic'] 1m16.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libassuan0 libksba8 libnpth0 libreadline7 libsqlite3-0 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: bowtie bowtie2 bwa cython fontconfig fontconfig-config fonts-lyx gasic gnome-icon-theme gnupg gnupg-agent gtk-update-icon-cache hicolor-icon-theme libatk1.0-0 libatk1.0-data libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libblas-common libblas3 libbsd0 libc-dev-bin libc6-dev libcairo2 libcroco3 libcups2 libcurl3-gnutls libdatrie1 libdbus-1-3 libexpat1 libexpat1-dev libffi6 libfontconfig1 libfreetype6 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran3 libglib2.0-0 libgmp10 libgnutls30 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhogweed4 libhts1 libicu57 libidn2-0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libnettle6 libnghttp2-14 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpixman-1-0 libpng16-16 libprocps3 libpsl5 libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libquadmath0 librsvg2-2 librsvg2-common librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1 libssl1.0.0 libssl1.1 libtasn1-6 libtbb2 libthai-data libthai0 libtiff5 libunistring0 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxinerama1 libxml2 libxrandr2 libxrender1 linux-libc-dev mime-support pinentry-curses python python-biopython python-cycler python-dateutil python-decorator python-dev python-functools32 python-matplotlib python-matplotlib-data python-minimal python-numpy python-pyparsing python-pyrex python-pysam python-reportlab python-reportlab-accel python-scipy python-six python-subprocess32 python-tz python2.7 python2.7-dev python2.7-minimal seqan-apps shared-mime-info ttf-bitstream-vera ucf 0 upgraded, 0 newly installed, 140 to remove and 0 not upgraded. After this operation, 409 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 ... 22538 files and directories currently installed.) Removing gasic (0.0.r19-1) ... Removing bowtie (1.1.2-6) ... Removing bowtie2 (2.3.0-2) ... Removing bwa (0.7.15-2+deb9u1) ... Removing cython (0.25.2-1) ... Removing python-matplotlib (2.0.0+dfsg1-2) ... Removing libgtk2.0-0:amd64 (2.24.31-2) ... Removing gnome-icon-theme (3.12.0-2) ... update-alternatives: using /usr/share/icons/gnome/scalable/places/gnome-foot.svg to provide /usr/share/icons/gnome/scalable/places/start-here.svg (start-here.svg) in auto mode update-alternatives: warning: skip creation of /usr/share/icons/gnome/256x256/places/start-here.png because associated file /usr/share/icons/gnome/256x256/places/gnome-foot.png (of link group start-here.svg) doesn't exist Removing librsvg2-common:amd64 (2.40.16-1+b1) ... Removing librsvg2-2:amd64 (2.40.16-1+b1) ... Removing libpangocairo-1.0-0:amd64 (1.40.5-1) ... Removing libpangoft2-1.0-0:amd64 (1.40.5-1) ... Removing libpango-1.0-0:amd64 (1.40.5-1) ... Removing fontconfig (2.11.0-6.7+b1) ... Removing libcairo2:amd64 (1.14.8-1) ... Removing libfontconfig1:amd64 (2.11.0-6.7+b1) ... Removing fontconfig-config (2.11.0-6.7) ... Removing python-matplotlib-data (2.0.0+dfsg1-2) ... Removing fonts-lyx (2.2.2-1) ... Removing gnupg (2.1.18-8~deb9u4) ... Removing gnupg-agent (2.1.18-8~deb9u4) ... Removing gtk-update-icon-cache (3.22.11-1) ... Removing hicolor-icon-theme (0.15-1) ... Removing libatk1.0-0:amd64 (2.22.0-1) ... Removing libatk1.0-data (2.22.0-1) ... Removing libtbb2:amd64 (4.3~20150611-2) ... Removing libatomic1:amd64 (6.3.0-18+deb9u1) ... Removing libcups2:amd64 (2.2.1-8+deb9u6) ... Removing libavahi-client3:amd64 (0.6.32-2) ... Removing libavahi-common3:amd64 (0.6.32-2) ... Removing libavahi-common-data:amd64 (0.6.32-2) ... Removing python-scipy (0.18.1-2) ... Removing python-biopython (1.68+dfsg-3) ... 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 libxrandr2:amd64 (2:1.5.1-1) ... Removing libxcursor1:amd64 (1:1.1.14-1+deb9u2) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing libxinerama1:amd64 (2:1.1.3-1+b3) ... Removing libxcb-shm0:amd64 (1.12-1) ... Removing python-pyrex (0.9.9-1) ... Removing python-dev (2.7.13-2) ... Removing python2.7-dev (2.7.13-2+deb9u3) ... Removing libpython-dev:amd64 (2.7.13-2) ... Removing libpython2.7-dev:amd64 (2.7.13-2+deb9u3) ... Removing libexpat1-dev:amd64 (2.2.0-2+deb9u3) ... Removing libc6-dev:amd64 (2.24-11+deb9u4) ... Removing libc-dev-bin (2.24-11+deb9u4) ... Removing libcroco3:amd64 (0.6.11-3) ... Removing python-pysam (0.10.0+ds-2) ... Removing libhts1:amd64 (1.3.2-2) ... Removing libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Removing libthai0:amd64 (0.1.26-1) ... Removing libdatrie1:amd64 (0.2.10-4+b1) ... Removing libdbus-1-3:amd64 (1.10.32-0+deb9u1) ... Removing python-subprocess32 (3.2.7-2) ... Removing python-dateutil (2.5.3-2) ... Removing python-cycler (0.10.0-1) ... Removing python-six (1.10.0-3) ... Removing python-reportlab (3.3.0-2+deb9u1) ... Removing python-reportlab-accel:amd64 (3.3.0-2+deb9u1) ... Removing python-tz (2016.7-0.3) ... Removing libpython2.7:amd64 (2.7.13-2+deb9u3) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Removing libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Removing libgnutls30:amd64 (3.5.8-5+deb9u5) ... Removing libp11-kit0:amd64 (0.23.3-2) ... Removing libgdk-pixbuf2.0-0:amd64 (2.36.5-2+deb9u2) ... Removing shared-mime-info (1.8-1+deb9u1) ... Removing libharfbuzz0b:amd64 (1.4.2-1) ... Removing libfreetype6:amd64 (2.6.3-3.2+deb9u1) ... Removing libgdk-pixbuf2.0-common (2.36.5-2+deb9u2) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libhogweed4:amd64 (3.3-1+b2) ... Removing libgmp10:amd64 (2:6.1.2+dfsg-1) ... Removing seqan-apps (2.3.1+dfsg-4) ... Removing libgomp1:amd64 (6.3.0-18+deb9u1) ... Removing libgraphite2-3:amd64 (1.3.10-1) ... Removing libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Removing libgtk2.0-common (2.24.31-2) ... Removing libxml2:amd64 (2.9.4+dfsg1-2.2+deb9u2) ... Removing libicu57:amd64 (57.1-6+deb9u4) ... Removing libpsl5:amd64 (0.17.0-3) ... Removing libidn2-0:amd64 (0.16-1+deb9u1) ... Removing libtiff5:amd64 (4.0.8-2+deb9u5) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:1.5.1-2) ... Removing libjs-jquery-ui (1.12.1+dfsg-4) ... Removing libjs-jquery (3.1.1-2+deb9u1) ... Removing libkrb5-3:amd64 (1.15-1+deb9u1) ... Removing libk5crypto3:amd64 (1.15-1+deb9u1) ... Removing libkrb5support0:amd64 (1.15-1+deb9u1) ... Removing libkeyutils1:amd64 (1.5.9-9) ... Removing libldap-common (2.4.44+dfsg-5+deb9u4) ... Removing libnettle6:amd64 (3.3-1+b2) ... Removing libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Removing libpixman-1-0:amd64 (0.34.0-1) ... Removing libpng16-16:amd64 (1.6.28-1+deb9u1) ... Removing libprocps3:amd64 (2:3.3.9-9+deb8u1) ... Removing libquadmath0:amd64 (6.3.0-18+deb9u1) ... Removing libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Removing libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Removing libssh2-1:amd64 (1.7.0-1+deb9u1) ... Removing libssl1.0.0:amd64 (1.0.1t-1+deb8u8) ... Removing libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Removing libthai-data (0.1.26-1) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing libxcb-render0:amd64 (1.12-1) ... Removing libxcomposite1:amd64 (1:0.4.4-2) ... Removing libxdamage1:amd64 (1:1.1.4-2+b3) ... Removing libxi6:amd64 (2:1.7.9-1) ... Removing libxext6:amd64 (2:1.3.3-1+b2) ... Removing libxfixes3:amd64 (1:5.0.3-1) ... Removing linux-libc-dev:amd64 (4.9.228-1) ... Removing pinentry-curses (1.0.0-2) ... Removing python-decorator (4.0.11-1) ... Removing python-functools32 (3.2.3.2-3) ... Removing python-pyparsing (2.1.10+dfsg1-1) ... Removing ttf-bitstream-vera (1.10-8) ... Removing ucf (3.0036) ... Removing libx11-6:amd64 (2:1.6.4-3+deb9u1) ... Removing libxcb1:amd64 (1.12-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.8.3-1) ... Removing python (2.7.13-2) ... Removing python2.7 (2.7.13-2+deb9u3) ... Removing libglib2.0-0:amd64 (2.50.3-2+deb9u2) ... Removing libpython-stdlib:amd64 (2.7.13-2) ... Removing python-minimal (2.7.13-2) ... Removing python2.7-minimal (2.7.13-2+deb9u3) ... Removing libx11-data (2:1.6.4-3+deb9u1) ... Removing libxau6:amd64 (1:1.0.8-1) ... Removing libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Removing libexpat1:amd64 (2.2.0-2+deb9u3) ... Removing libffi6:amd64 (3.2.1-6) ... Removing libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Removing libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Removing mime-support (3.60) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 1m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', 'remove', 'bowtie', 'bowtie2', 'bwa', 'cython', 'fontconfig', 'fontconfig-config', 'fonts-lyx', 'gnome-icon-theme', 'gnupg', 'gnupg-agent', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'libatk1.0-0:amd64', 'libatk1.0-data', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libblas-common', 'libblas3', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcroco3:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libffi6:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdk-pixbuf2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran3:amd64', 'libglib2.0-0:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libicu57:amd64', 'libidn2-0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps3:amd64', 'libpsl5:amd64', 'libpython-dev:amd64', 'libpython-stdlib:amd64', 'libpython2.7:amd64', 'libpython2.7-dev:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'librsvg2-2:amd64', 'librsvg2-common:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1:amd64', 'libssl1.0.0:amd64', 'libssl1.1:amd64', 'libtasn1-6:amd64', 'libtbb2:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libunistring0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'linux-libc-dev:amd64', 'mime-support', 'pinentry-curses', 'python', 'python-biopython', 'python-cycler', 'python-dateutil', 'python-decorator', 'python-dev', 'python-functools32', 'python-matplotlib', 'python-matplotlib-data', 'python-minimal', 'python-numpy', 'python-pyparsing', 'python-pyrex', 'python-pysam', 'python-reportlab', 'python-reportlab-accel:amd64', 'python-scipy', 'python-six', 'python-subprocess32', 'python-tz', 'python2.7', 'python2.7-dev', 'python2.7-minimal', 'seqan-apps', 'shared-mime-info', 'ttf-bitstream-vera', 'ucf', 'gasic'] 1m16.3s INFO: Running scripts post_remove 1m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_remove_exceptions'] 1m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_remove_exceptions'] 1m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg', '--purge', 'bowtie', 'bowtie2', 'bwa', 'cython', 'fontconfig', 'fontconfig-config', 'fonts-lyx', 'gnome-icon-theme', 'gnupg', 'gnupg-agent', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'libatk1.0-0:amd64', 'libatk1.0-data', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libblas-common', 'libblas3', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcroco3:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libffi6:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdk-pixbuf2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran3:amd64', 'libglib2.0-0:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libicu57:amd64', 'libidn2-0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps3:amd64', 'libpsl5:amd64', 'libpython-dev:amd64', 'libpython-stdlib:amd64', 'libpython2.7:amd64', 'libpython2.7-dev:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'librsvg2-2:amd64', 'librsvg2-common:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1:amd64', 'libssl1.0.0:amd64', 'libssl1.1:amd64', 'libtasn1-6:amd64', 'libtbb2:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libunistring0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'linux-libc-dev:amd64', 'mime-support', 'pinentry-curses', 'python', 'python-biopython', 'python-cycler', 'python-dateutil', 'python-decorator', 'python-dev', 'python-functools32', 'python-matplotlib', 'python-matplotlib-data', 'python-minimal', 'python-numpy', 'python-pyparsing', 'python-pyrex', 'python-pysam', 'python-reportlab', 'python-reportlab-accel:amd64', 'python-scipy', 'python-six', 'python-subprocess32', 'python-tz', 'python2.7', 'python2.7-dev', 'python2.7-minimal', 'seqan-apps', 'shared-mime-info', 'ttf-bitstream-vera', 'ucf'] 1m16.8s DUMP: dpkg: warning: ignoring request to remove bowtie which isn't installed dpkg: warning: ignoring request to remove bowtie2 which isn't installed (Reading database ... 7718 files and directories currently installed.) Purging configuration files for bwa (0.7.15-2+deb9u1) ... dpkg: warning: ignoring request to remove cython which isn't installed Purging configuration files for fontconfig (2.11.0-6.7+b1) ... Purging configuration files for fontconfig-config (2.11.0-6.7) ... dpkg: warning: ignoring request to remove fonts-lyx which isn't installed dpkg: warning: ignoring request to remove gnome-icon-theme which isn't installed dpkg: warning: ignoring request to remove gnupg which isn't installed Purging configuration files for gnupg-agent (2.1.18-8~deb9u4) ... dpkg: warning: ignoring request to remove gtk-update-icon-cache which isn't installed dpkg: warning: ignoring request to remove hicolor-icon-theme which isn't installed dpkg: warning: ignoring request to remove libatk1.0-0 which isn't installed dpkg: warning: ignoring request to remove libatk1.0-data which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libavahi-client3 which isn't installed dpkg: warning: ignoring request to remove libavahi-common-data which isn't installed dpkg: warning: ignoring request to remove libavahi-common3 which isn't installed dpkg: warning: ignoring request to remove libblas-common which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcroco3 which isn't installed dpkg: warning: ignoring request to remove libcups2 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdbus-1-3 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libexpat1-dev which isn't installed dpkg: warning: ignoring request to remove libffi6 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed Purging configuration files for libgdk-pixbuf2.0-0:amd64 (2.36.5-2+deb9u2) ... dpkg: warning: ignoring request to remove libgdk-pixbuf2.0-common which isn't installed dpkg: warning: ignoring request to remove libgfortran3 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.50.3-2+deb9u2) ... dpkg: warning: ignoring request to remove libgmp10 which isn't installed dpkg: warning: ignoring request to remove libgnutls30 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Purging configuration files for libgtk2.0-0:amd64 (2.24.31-2) ... Purging configuration files for libgtk2.0-common (2.24.31-2) ... dpkg: warning: ignoring request to remove libharfbuzz0b 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 libicu57 which isn't installed dpkg: warning: ignoring request to remove libidn2-0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjs-jquery which isn't installed Purging configuration files for libjs-jquery-ui (1.12.1+dfsg-4) ... 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+deb9u4) ... 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 libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed Purging configuration files for libprocps3:amd64 (2:3.3.9-9+deb8u1) ... dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython-dev which isn't installed dpkg: warning: ignoring request to remove libpython-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython2.7 which isn't installed dpkg: warning: ignoring request to remove libpython2.7-dev which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... 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 librsvg2-2 which isn't installed dpkg: warning: ignoring request to remove librsvg2-common 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 libssl1.0.0:amd64 (1.0.1t-1+deb8u8) ... Purging configuration files for libssl1.1:amd64 (1.1.0l-1~deb9u1) ... dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libtbb2 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libunistring0 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed Purging configuration files for libxau6:amd64 (1:1.0.8-1) ... dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxcomposite1 which isn't installed dpkg: warning: ignoring request to remove libxcursor1 which isn't installed dpkg: warning: ignoring request to remove libxdamage1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxfixes3 which isn't installed dpkg: warning: ignoring request to remove libxi6 which isn't installed dpkg: warning: ignoring request to remove libxinerama1 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrandr2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed Purging configuration files for mime-support (3.60) ... dpkg: warning: ignoring request to remove pinentry-curses which isn't installed Purging configuration files for python (2.7.13-2) ... dpkg: warning: ignoring request to remove python-biopython which isn't installed dpkg: warning: ignoring request to remove python-cycler which isn't installed dpkg: warning: ignoring request to remove python-dateutil which isn't installed dpkg: warning: ignoring request to remove python-decorator which isn't installed dpkg: warning: ignoring request to remove python-dev which isn't installed dpkg: warning: ignoring request to remove python-functools32 which isn't installed dpkg: warning: ignoring request to remove python-matplotlib which isn't installed Purging configuration files for python-matplotlib-data (2.0.0+dfsg1-2) ... dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python-numpy which isn't installed dpkg: warning: ignoring request to remove python-pyparsing which isn't installed dpkg: warning: ignoring request to remove python-pyrex which isn't installed dpkg: warning: ignoring request to remove python-pysam which isn't installed dpkg: warning: ignoring request to remove python-reportlab which isn't installed dpkg: warning: ignoring request to remove python-reportlab-accel which isn't installed dpkg: warning: ignoring request to remove python-scipy which isn't installed dpkg: warning: ignoring request to remove python-six which isn't installed dpkg: warning: ignoring request to remove python-subprocess32 which isn't installed dpkg: warning: ignoring request to remove python-tz which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed dpkg: warning: ignoring request to remove python2.7-dev which isn't installed Purging configuration files for python2.7-minimal (2.7.13-2+deb9u3) ... dpkg: warning: ignoring request to remove seqan-apps which isn't installed Purging configuration files for shared-mime-info (1.8-1+deb9u1) ... dpkg: warning: ignoring request to remove ttf-bitstream-vera which isn't installed Purging configuration files for ucf (3.0036) ... 1m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg', '--purge', 'bowtie', 'bowtie2', 'bwa', 'cython', 'fontconfig', 'fontconfig-config', 'fonts-lyx', 'gnome-icon-theme', 'gnupg', 'gnupg-agent', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'libatk1.0-0:amd64', 'libatk1.0-data', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libblas-common', 'libblas3', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcroco3:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libffi6:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgdk-pixbuf2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran3:amd64', 'libglib2.0-0:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libicu57:amd64', 'libidn2-0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps3:amd64', 'libpsl5:amd64', 'libpython-dev:amd64', 'libpython-stdlib:amd64', 'libpython2.7:amd64', 'libpython2.7-dev:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'librsvg2-2:amd64', 'librsvg2-common:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1:amd64', 'libssl1.0.0:amd64', 'libssl1.1:amd64', 'libtasn1-6:amd64', 'libtbb2:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libunistring0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'linux-libc-dev:amd64', 'mime-support', 'pinentry-curses', 'python', 'python-biopython', 'python-cycler', 'python-dateutil', 'python-decorator', 'python-dev', 'python-functools32', 'python-matplotlib', 'python-matplotlib-data', 'python-minimal', 'python-numpy', 'python-pyparsing', 'python-pyrex', 'python-pysam', 'python-reportlab', 'python-reportlab-accel:amd64', 'python-scipy', 'python-six', 'python-subprocess32', 'python-tz', 'python2.7', 'python2.7-dev', 'python2.7-minimal', 'seqan-apps', 'shared-mime-info', 'ttf-bitstream-vera', 'ucf'] 1m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg', '--purge', 'gasic'] 1m16.8s DUMP: dpkg: warning: ignoring request to remove gasic which isn't installed 1m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg', '--purge', 'gasic'] 1m16.8s INFO: Running scripts post_purge 1m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_purge_exceptions'] 1m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_purge_exceptions'] 1m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg', '--purge', '--pending'] 1m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg', '--purge', '--pending'] 1m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg', '--remove', '--pending'] 1m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg', '--remove', '--pending'] 1m16.8s INFO: Running scripts post_test 1m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_test_exceptions'] 1m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'tmp/scripts/post_test_exceptions'] 1m16.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 1m17.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 1m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg-divert', '--list'] 1m17.3s 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 1m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'dpkg-divert', '--list'] 1m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', 'clean'] 1m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp', 'apt-get', 'clean'] 1m17.3s DEBUG: Recording chroot state 1m18.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/shm'] 1m18.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/shm'] 1m18.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/console'] 1m18.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/console'] 1m18.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/ptmx'] 1m18.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/ptmx'] 1m18.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/pts'] 1m18.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/dev/pts'] 1m18.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/proc'] 1m18.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp/proc'] 1m18.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 1m18.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpwf4utdmp'] 1m18.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpwf4utdmp 1m18.5s INFO: PASS: Upgrading between Debian distributions. 1m18.5s INFO: PASS: All tests. 1m18.5s INFO: piuparts run ends. ret=0 End: 2022-11-13 02:25:35 GMT