Start: 2023-10-19 08:11:54 GMT [buster] Package: gasic Version: 0.0.r19-4 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.r19-4_amd64.deb Size: 20260 MD5sum: 96971d0a1e8887a5cabac3ebac20b47b SHA256: d44088f8b948ca52a0fa6d2236209740b6dc0174a56726626fbaf979811c63e8 [buster-next] Package: gasic Version: 0.0.r19-4 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.r19-4_amd64.deb Size: 20260 MD5sum: 96971d0a1e8887a5cabac3ebac20b47b SHA256: d44088f8b948ca52a0fa6d2236209740b6dc0174a56726626fbaf979811c63e8 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --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/buster_amd64.tar.gz -d buster -d buster-next -B /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat --apt gasic=0.0.r19-4 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 1.1.8~202306121314~1.1.7-9-g57dfbde6 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --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/buster_amd64.tar.gz -d buster -d buster-next -B /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat --apt gasic=0.0.r19-4 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-26-amd64 #1 SMP Debian 5.10.197-1 (2023-09-29) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpzkqsqn2p 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpzkqsqn2p 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m1.9s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/proc'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/proc'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/pts'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/pts'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/ptmx'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/ptmx'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/console'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/console'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/shm'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/shm'] 0m2.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m2.0s DEBUG: Created policy-rc.d and chmodded it. 0m2.0s DEBUG: Created resolv.conf. 0m2.0s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpzkqsqn2p/tmp/scripts/ 0m2.0s INFO: Running scripts post_chroot_unpack 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', 'update'] 0m3.4s DUMP: Hit:1 http://deb.debian.org/debian buster InRelease Reading package lists... 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', 'update'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', '-yf', 'dist-upgrade'] 0m3.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', '-yf', 'dist-upgrade'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.1s DUMP: f6fc0f2636004ef589309651dfd778f4 - 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.1s INFO: Running scripts post_setup 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_setup_dummy_users'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_setup_dummy_users'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_setup_forbid_home'] 0m5.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_setup_forbid_home'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.4s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_setup_minimize'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_setup_minimize'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_setup_zz_backports'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_setup_zz_backports'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.5s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u1 install ok installed libc-bin libc-bin 2.28-10+deb10u1 install ok installed libc6:amd64 libc6 2.28-10+deb10u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u8 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u2 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u8 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u2 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tzdata tzdata 2021a-0+deb10u6 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat 0m5.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m5.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m5.8s INFO: Running scripts is_testable 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/is_testable_uninstallable'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/is_testable_uninstallable'] 0m5.8s INFO: Running scripts pre_test 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_test_exceptions'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_test_exceptions'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_test_root_password'] 0m5.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_test_root_password'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'show', '--no-all-versions', 'gasic'] 0m6.0s DUMP: Package: gasic Version: 0.0.r19-4 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.r19-4_amd64.deb Size: 20260 MD5sum: 96971d0a1e8887a5cabac3ebac20b47b SHA256: d44088f8b948ca52a0fa6d2236209740b6dc0174a56726626fbaf979811c63e8 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'show', '--no-all-versions', 'gasic'] 0m6.0s INFO: apt-cache knows about the following packages: gasic 0m6.0s INFO: Running scripts pre_install 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_database-server'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_database-server'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_exceptions'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_exceptions'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_extras'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_extras'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'policy'] 0m6.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'policy'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'policy', 'gasic'] 0m6.2s DUMP: gasic: Installed: (none) Candidate: 0.0.r19-4 Version table: 0.0.r19-4 500 500 http://deb.debian.org/debian buster/main amd64 Packages 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'policy', 'gasic'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', '-y', 'install', 'gasic'] 0m30.5s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bowtie bowtie2 bwa fonts-lyx libatomic1 libblas3 libcurl3-gnutls libdeflate0 libexpat1 libfreetype6 libgfortran5 libgomp1 libgssapi-krb5-2 libhts2 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libnghttp2-14 libpng16-16 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libtbb2 libtiff5 libwebp6 libwebpdemux2 libwebpmux3 mime-support python python-backports.functools-lru-cache python-biopython python-cycler python-dateutil python-decorator python-kiwisolver python-matplotlib python-matplotlib2-data python-minimal python-numpy python-pil python-pkg-resources python-pyparsing python-pysam python-reportlab python-reportlab-accel python-scipy python-six python-subprocess32 python-tz python2 python2-minimal python2.7 python2.7-minimal readline-common seqan-apps ttf-bitstream-vera Suggested packages: bowtie-examples bowtie2-examples samtools krb5-doc krb5-user libjs-jquery-ui-docs liblcms2-utils python-doc python-tk clustalo clustalw dialign dssp emboss fasttree mafft muscle phylip phyml prank probcons python-mysqldb python-rdflib python-renderpm python-psycopg2 raxml t-coffee wise w3-dtd-mathml python-cycler-doc dvipng ffmpeg gir1.2-gtk-3.0 ghostscript inkscape ipython librsvg2-common python-cairocffi python-configobj python-excelerator python-gi python-gobject-2 python-matplotlib2-doc python-nose python-qt4 python-sip python-tornado python-traits python-wxgtk3.0 texlive-extra-utils texlive-latex-extra ttf-staypuft gcc gfortran python-dev python-pytest python-numpy-dbg python-numpy-doc python-pil-doc python-pil-dbg python-setuptools python-pyparsing-doc pdf-viewer python-egenix-mxtexttools python-reportlab-doc python-scipy-doc python2-doc python2.7-doc binutils binfmt-support readline-doc cwltool | cwl-runner Recommended packages: ca-certificates javascript-common krb5-locales publicsuffix libsasl2-modules bzip2 file xz-utils python-biopython-doc ncbi-blast+ python-tk python-olefile python-renderpm g++ | c++-compiler python-dev The following NEW packages will be installed: bowtie bowtie2 bwa fonts-lyx gasic libatomic1 libblas3 libcurl3-gnutls libdeflate0 libexpat1 libfreetype6 libgfortran5 libgomp1 libgssapi-krb5-2 libhts2 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libnghttp2-14 libpng16-16 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libtbb2 libtiff5 libwebp6 libwebpdemux2 libwebpmux3 mime-support python python-backports.functools-lru-cache python-biopython python-cycler python-dateutil python-decorator python-kiwisolver python-matplotlib python-matplotlib2-data python-minimal python-numpy python-pil python-pkg-resources python-pyparsing python-pysam python-reportlab python-reportlab-accel python-scipy python-six python-subprocess32 python-tz python2 python2-minimal python2.7 python2.7-minimal readline-common seqan-apps ttf-bitstream-vera 0 upgraded, 77 newly installed, 0 to remove and 0 not upgraded. Need to get 55.3 MB of archives. After this operation, 235 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get:2 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get:3 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get:4 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get:5 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u3 [1551 kB] Get:6 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:7 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get:8 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:9 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:10 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get:12 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get:13 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:14 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:15 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:16 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:17 http://deb.debian.org/debian buster/main amd64 libatomic1 amd64 8.3.0-6 [9032 B] Get:18 http://deb.debian.org/debian buster/main amd64 libtbb2 amd64 2018~U6-4 [147 kB] Get:19 http://deb.debian.org/debian buster/main amd64 bowtie amd64 1.2.2+dfsg-4 [1670 kB] Get:20 http://deb.debian.org/debian buster/main amd64 bowtie2 amd64 2.3.4.3-1 [1188 kB] Get:21 http://deb.debian.org/debian buster/main amd64 bwa amd64 0.7.17-3 [195 kB] Get:22 http://deb.debian.org/debian buster/main amd64 fonts-lyx all 2.3.2-1 [199 kB] Get:23 http://deb.debian.org/debian buster/main amd64 python-decorator all 4.3.0-1.1 [14.4 kB] Get:24 http://deb.debian.org/debian buster/main amd64 libquadmath0 amd64 8.3.0-6 [133 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get:26 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get:27 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get:28 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get:29 http://deb.debian.org/debian buster/main amd64 python-numpy amd64 1:1.16.2-1 [2101 kB] Get:30 http://deb.debian.org/debian buster/main amd64 python-scipy amd64 1.1.0-7 [10.1 MB] Get:31 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u3 [380 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get:35 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get:36 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:37 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get:38 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u4 [271 kB] Get:39 http://deb.debian.org/debian buster/main amd64 libwebpdemux2 amd64 0.6.1-2+deb10u1 [87.6 kB] Get:40 http://deb.debian.org/debian buster/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u1 [97.8 kB] Get:41 http://deb.debian.org/debian buster/main amd64 python-pil amd64 5.4.1-2+deb10u3 [395 kB] Get:42 http://deb.debian.org/debian buster/main amd64 python-reportlab-accel amd64 3.5.13-1+deb10u1 [39.8 kB] Get:43 http://deb.debian.org/debian buster/main amd64 python-reportlab all 3.5.13-1+deb10u1 [545 kB] Get:44 http://deb.debian.org/debian buster/main amd64 python-biopython amd64 1.73+dfsg-1 [1334 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:46 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u4 [65.9 kB] Get:47 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u4 [122 kB] Get:48 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u4 [369 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u4 [158 kB] Get:50 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u2 [69.2 kB] Get:51 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u2 [106 kB] Get:52 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u7 [90.1 kB] Get:53 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u7 [224 kB] Get:54 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get:55 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:56 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:57 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:58 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get:59 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get:61 http://deb.debian.org/debian buster/main amd64 python-pysam amd64 0.15.2+ds-2 [1629 kB] Get:62 http://deb.debian.org/debian buster/main amd64 python-backports.functools-lru-cache all 1.5-3 [6704 B] Get:63 http://deb.debian.org/debian buster/main amd64 python-six all 1.12.0-1 [15.7 kB] Get:64 http://deb.debian.org/debian buster/main amd64 python-dateutil all 2.7.3-3 [76.8 kB] Get:65 http://deb.debian.org/debian buster/main amd64 ttf-bitstream-vera all 1.10-8 [352 kB] Get:66 http://deb.debian.org/debian buster/main amd64 python-matplotlib2-data all 2.2.3-6 [4124 kB] Get:67 http://deb.debian.org/debian buster/main amd64 python-pyparsing all 2.2.0+dfsg1-2 [89.5 kB] Get:68 http://deb.debian.org/debian buster/main amd64 python-tz all 2019.1-1 [33.6 kB] Get:69 http://deb.debian.org/debian buster/main amd64 libjs-jquery all 3.3.1~dfsg-3+deb10u1 [332 kB] Get:70 http://deb.debian.org/debian buster/main amd64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get:71 http://deb.debian.org/debian buster/main amd64 python-cycler all 0.10.0-1 [7448 B] Get:72 http://deb.debian.org/debian buster/main amd64 python-kiwisolver amd64 1.0.1-2+b1 [67.3 kB] Get:73 http://deb.debian.org/debian buster/main amd64 python-subprocess32 amd64 3.5.3-1 [29.9 kB] Get:74 http://deb.debian.org/debian buster/main amd64 python-matplotlib amd64 2.2.3-6 [5073 kB] Get:75 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB] Get:76 http://deb.debian.org/debian buster/main amd64 seqan-apps amd64 2.4.0+dfsg-11 [11.4 MB] Get:77 http://deb.debian.org/debian buster/main amd64 gasic amd64 0.0.r19-4 [20.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 55.3 MB in 6s (9369 kB/s) Selecting previously unselected package libpython2.7-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6462 files and directories currently installed.) Preparing to unpack .../00-libpython2.7-minimal_2.7.16-2+deb10u1_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../01-python2.7-minimal_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. 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Unpacking libpython-stdlib:amd64 (2.7.16-1) ... Setting up libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 7299 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... 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Preparing to unpack .../02-libtbb2_2018~U6-4_amd64.deb ... Unpacking libtbb2:amd64 (2018~U6-4) ... Selecting previously unselected package bowtie. Preparing to unpack .../03-bowtie_1.2.2+dfsg-4_amd64.deb ... Unpacking bowtie (1.2.2+dfsg-4) ... Selecting previously unselected package bowtie2. Preparing to unpack .../04-bowtie2_2.3.4.3-1_amd64.deb ... Unpacking bowtie2 (2.3.4.3-1) ... Selecting previously unselected package bwa. Preparing to unpack .../05-bwa_0.7.17-3_amd64.deb ... Unpacking bwa (0.7.17-3) ... Selecting previously unselected package fonts-lyx. Preparing to unpack .../06-fonts-lyx_2.3.2-1_all.deb ... Unpacking fonts-lyx (2.3.2-1) ... Selecting previously unselected package python-decorator. Preparing to unpack .../07-python-decorator_4.3.0-1.1_all.deb ... Unpacking python-decorator (4.3.0-1.1) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../08-libquadmath0_8.3.0-6_amd64.deb ... Unpacking libquadmath0:amd64 (8.3.0-6) ... 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Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../15-libpng16-16_1.6.36-6_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.36-6) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../16-libfreetype6_2.9.1-3+deb10u3_amd64.deb ... Unpacking libfreetype6:amd64 (2.9.1-3+deb10u3) ... Selecting previously unselected package libimagequant0:amd64. Preparing to unpack .../17-libimagequant0_2.12.2-1.1_amd64.deb ... Unpacking libimagequant0:amd64 (2.12.2-1.1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../18-libjpeg62-turbo_1%3a1.5.2-2+deb10u1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../19-liblcms2-2_2.9-3_amd64.deb ... Unpacking liblcms2-2:amd64 (2.9-3) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../20-libjbig0_2.1-3.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-3.1+b2) ... Selecting previously unselected package libwebp6:amd64. Preparing to unpack .../21-libwebp6_0.6.1-2+deb10u1_amd64.deb ... Unpacking libwebp6:amd64 (0.6.1-2+deb10u1) ... Selecting previously unselected package libtiff5:amd64. Preparing to unpack .../22-libtiff5_4.1.0+git191117-2~deb10u4_amd64.deb ... Unpacking libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Selecting previously unselected package libwebpdemux2:amd64. Preparing to unpack .../23-libwebpdemux2_0.6.1-2+deb10u1_amd64.deb ... Unpacking libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../24-libwebpmux3_0.6.1-2+deb10u1_amd64.deb ... Unpacking libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Selecting previously unselected package python-pil:amd64. Preparing to unpack .../25-python-pil_5.4.1-2+deb10u3_amd64.deb ... Unpacking python-pil:amd64 (5.4.1-2+deb10u3) ... Selecting previously unselected package python-reportlab-accel:amd64. Preparing to unpack .../26-python-reportlab-accel_3.5.13-1+deb10u1_amd64.deb ... Unpacking python-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Selecting previously unselected package python-reportlab. Preparing to unpack .../27-python-reportlab_3.5.13-1+deb10u1_all.deb ... Unpacking python-reportlab (3.5.13-1+deb10u1) ... Selecting previously unselected package python-biopython. Preparing to unpack .../28-python-biopython_1.73+dfsg-1_amd64.deb ... Unpacking python-biopython (1.73+dfsg-1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../29-libkeyutils1_1.6-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../30-libkrb5support0_1.17-3+deb10u4_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u4) ... Selecting previously unselected package libk5crypto3:amd64. 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Unpacking libssh2-1:amd64 (1.8.0-2.1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../42-libcurl3-gnutls_7.64.0-4+deb10u2_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../43-libdeflate0_1.2-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.2-1) ... Selecting previously unselected package libhts2:amd64. Preparing to unpack .../44-libhts2_1.9-12~deb10u1_amd64.deb ... Unpacking libhts2:amd64 (1.9-12~deb10u1) ... Selecting previously unselected package python-pysam. Preparing to unpack .../45-python-pysam_0.15.2+ds-2_amd64.deb ... Unpacking python-pysam (0.15.2+ds-2) ... Selecting previously unselected package python-backports.functools-lru-cache. Preparing to unpack .../46-python-backports.functools-lru-cache_1.5-3_all.deb ... Unpacking python-backports.functools-lru-cache (1.5-3) ... Selecting previously unselected package python-six. 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Preparing to unpack .../53-libjs-jquery_3.3.1~dfsg-3+deb10u1_all.deb ... Unpacking libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../54-libjs-jquery-ui_1.12.1+dfsg-5_all.deb ... Unpacking libjs-jquery-ui (1.12.1+dfsg-5) ... Selecting previously unselected package python-cycler. Preparing to unpack .../55-python-cycler_0.10.0-1_all.deb ... Unpacking python-cycler (0.10.0-1) ... Selecting previously unselected package python-kiwisolver. Preparing to unpack .../56-python-kiwisolver_1.0.1-2+b1_amd64.deb ... Unpacking python-kiwisolver (1.0.1-2+b1) ... Selecting previously unselected package python-subprocess32. Preparing to unpack .../57-python-subprocess32_3.5.3-1_amd64.deb ... Unpacking python-subprocess32 (3.5.3-1) ... Selecting previously unselected package python-matplotlib. Preparing to unpack .../58-python-matplotlib_2.2.3-6_amd64.deb ... Unpacking python-matplotlib (2.2.3-6) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../59-libgomp1_8.3.0-6_amd64.deb ... Unpacking libgomp1:amd64 (8.3.0-6) ... Selecting previously unselected package seqan-apps. Preparing to unpack .../60-seqan-apps_2.4.0+dfsg-11_amd64.deb ... Unpacking seqan-apps (2.4.0+dfsg-11) ... Selecting previously unselected package gasic. Preparing to unpack .../61-gasic_0.0.r19-4_amd64.deb ... Unpacking gasic (0.0.r19-4) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u4) ... Setting up liblcms2-2:amd64 (2.9-3) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up ttf-bitstream-vera (1.10-8) ... Setting up mime-support (3.62) ... Setting up bwa (0.7.17-3) ... Setting up libssl1.1:amd64 (1.1.1n-0+deb10u3) ... Setting up fonts-lyx (2.3.2-1) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up libgomp1:amd64 (8.3.0-6) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u7) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u4) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libquadmath0:amd64 (8.3.0-6) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up seqan-apps (2.4.0+dfsg-11) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up libatomic1:amd64 (8.3.0-6) ... Setting up libwebp6:amd64 (0.6.1-2+deb10u1) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u4) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up python-matplotlib2-data (2.2.3-6) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u4) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Setting up libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Setting up libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Setting up readline-common (7.0-5) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Setting up libtbb2:amd64 (2018~U6-4) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up libblas3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up libfreetype6:amd64 (2.9.1-3+deb10u3) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Setting up liblapack3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python2 (2.7.16-1) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up bowtie (1.2.2+dfsg-4) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up python-pil:amd64 (5.4.1-2+deb10u3) ... Setting up bowtie2 (2.3.4.3-1) ... Setting up python-decorator (4.3.0-1.1) ... Setting up python-six (1.12.0-1) ... Setting up python-pyparsing (2.2.0+dfsg1-2) ... Setting up python-dateutil (2.7.3-3) ... Setting up python-subprocess32 (3.5.3-1) ... Setting up python-backports.functools-lru-cache (1.5-3) ... Setting up python-tz (2019.1-1) ... Setting up python-kiwisolver (1.0.1-2+b1) ... Setting up python-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Setting up python-pysam (0.15.2+ds-2) ... Setting up python-numpy (1:1.16.2-1) ... Setting up python-cycler (0.10.0-1) ... Setting up python-reportlab (3.5.13-1+deb10u1) ... Setting up python-scipy (1.1.0-7) ... Setting up python-matplotlib (2.2.3-6) ... Setting up python-biopython (1.73+dfsg-1) ... Setting up gasic (0.0.r19-4) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... 0m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', '-y', 'install', 'gasic'] 0m30.5s INFO: Running scripts post_install 0m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_install_exceptions'] 0m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_install_exceptions'] 0m30.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m31.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m31.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpzkqsqn2p to buster-next 0m31.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main deb http://security.debian.org buster/updates main deb http://deb.debian.org/debian/ buster-updates main deb http://deb.debian.org/debian/ buster-proposed-updates main 0m31.1s INFO: Running scripts pre_distupgrade 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_distupgrade_exceptions'] 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_distupgrade_exceptions'] 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', 'update'] 0m33.2s DUMP: Hit:1 http://deb.debian.org/debian buster InRelease Get:2 http://deb.debian.org/debian buster-updates InRelease [56.6 kB] Get:3 http://security.debian.org buster/updates InRelease [34.8 kB] Get:4 http://deb.debian.org/debian buster-proposed-updates InRelease [59.2 kB] Get:5 http://deb.debian.org/debian buster-updates/main amd64 Packages [8788 B] Get:6 http://deb.debian.org/debian buster-updates/main Translation-en [6915 B] Get:7 http://security.debian.org buster/updates/main amd64 Packages [560 kB] Get:8 http://security.debian.org buster/updates/main Translation-en [303 kB] Get:9 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages [736 B] Get:10 http://deb.debian.org/debian buster-proposed-updates/main Translation-en [859 B] Fetched 1032 kB in 1s (1036 kB/s) Reading package lists... 0m33.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', 'update'] 0m33.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', '-yf', 'dist-upgrade'] 0m41.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: debian-archive-keyring libbz2-1.0 libc-bin libc6 libcurl3-gnutls libexpat1 libgnutls30 libgssapi-krb5-2 libjs-jquery-ui libk5crypto3 libkrb5-3 libkrb5support0 libncursesw6 libnghttp2-14 libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssh2-1 libssl1.1 libsystemd0 libtasn1-6 libtiff5 libtinfo6 libudev1 libwebp6 libwebpdemux2 libwebpmux3 ncurses-base ncurses-bin python-reportlab python-reportlab-accel python2.7 python2.7-minimal tzdata zlib1g 35 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 16.0 MB of archives. After this operation, 63.5 kB of additional disk space will be used. Get:1 http://security.debian.org buster/updates/main amd64 ncurses-bin amd64 6.1+20181013-2+deb10u4 [407 kB] Get:2 http://security.debian.org buster/updates/main amd64 libc6 amd64 2.28-10+deb10u2 [2869 kB] Get:3 http://security.debian.org buster/updates/main amd64 libc-bin amd64 2.28-10+deb10u2 [793 kB] Get:4 http://security.debian.org buster/updates/main amd64 ncurses-base all 6.1+20181013-2+deb10u4 [259 kB] Get:5 http://security.debian.org buster/updates/main amd64 libsystemd0 amd64 241-7~deb10u10 [332 kB] Get:6 http://security.debian.org buster/updates/main amd64 python2.7 amd64 2.7.16-2+deb10u3 [306 kB] Get:7 http://security.debian.org buster/updates/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u6 [1552 kB] Get:8 http://security.debian.org buster/updates/main amd64 libbz2-1.0 amd64 1.0.6-9.2~deb10u2 [45.4 kB] Get:9 http://security.debian.org buster/updates/main amd64 libexpat1 amd64 2.2.6-2+deb10u6 [108 kB] Get:10 http://security.debian.org buster/updates/main amd64 libtinfo6 amd64 6.1+20181013-2+deb10u4 [326 kB] Get:11 http://security.debian.org buster/updates/main amd64 libncursesw6 amd64 6.1+20181013-2+deb10u4 [131 kB] Get:12 http://security.debian.org buster/updates/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u2 [641 kB] Get:13 http://security.debian.org buster/updates/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u3 [1910 kB] Get:14 http://security.debian.org buster/updates/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u3 [1362 kB] Get:15 http://security.debian.org buster/updates/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u3 [397 kB] Get:16 http://security.debian.org buster/updates/main amd64 zlib1g amd64 1:1.2.11.dfsg-1+deb10u2 [90.9 kB] Get:17 http://security.debian.org buster/updates/main amd64 debian-archive-keyring all 2019.1+deb10u2 [110 kB] Get:18 http://security.debian.org buster/updates/main amd64 libudev1 amd64 241-7~deb10u10 [151 kB] Get:19 http://security.debian.org buster/updates/main amd64 libtasn1-6 amd64 4.13-3+deb10u1 [52.0 kB] Get:20 http://security.debian.org buster/updates/main amd64 libgnutls30 amd64 3.6.7-4+deb10u10 [1126 kB] Get:21 http://security.debian.org buster/updates/main amd64 tzdata all 2021a-0+deb10u11 [267 kB] Get:22 http://security.debian.org buster/updates/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u5 [159 kB] Get:23 http://security.debian.org buster/updates/main amd64 libkrb5-3 amd64 1.17-3+deb10u5 [369 kB] Get:24 http://security.debian.org buster/updates/main amd64 libkrb5support0 amd64 1.17-3+deb10u5 [66.0 kB] Get:25 http://security.debian.org buster/updates/main amd64 libk5crypto3 amd64 1.17-3+deb10u5 [122 kB] Get:26 http://security.debian.org buster/updates/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u2 [85.8 kB] Get:27 http://security.debian.org buster/updates/main amd64 libssh2-1 amd64 1.8.0-2.1+deb10u1 [141 kB] Get:28 http://security.debian.org buster/updates/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u7 [333 kB] Get:29 http://security.debian.org buster/updates/main amd64 libjs-jquery-ui all 1.12.1+dfsg-5+deb10u1 [232 kB] Get:30 http://security.debian.org buster/updates/main amd64 libwebp6 amd64 0.6.1-2+deb10u3 [263 kB] Get:31 http://security.debian.org buster/updates/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u8 [273 kB] Get:32 http://security.debian.org buster/updates/main amd64 libwebpdemux2 amd64 0.6.1-2+deb10u3 [87.9 kB] Get:33 http://security.debian.org buster/updates/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u3 [98.1 kB] Get:34 http://security.debian.org buster/updates/main amd64 python-reportlab-accel amd64 3.5.13-1+deb10u2 [40.1 kB] Get:35 http://security.debian.org buster/updates/main amd64 python-reportlab all 3.5.13-1+deb10u2 [545 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.0 MB in 0s (60.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11648 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.1+20181013-2+deb10u4_amd64.deb ... Unpacking ncurses-bin (6.1+20181013-2+deb10u4) over (6.1+20181013-2+deb10u2) ... Setting up ncurses-bin (6.1+20181013-2+deb10u4) ... (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 ... 11648 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.1+20181013-2+deb10u4_all.deb ... Unpacking ncurses-base (6.1+20181013-2+deb10u4) over (6.1+20181013-2+deb10u2) ... Setting up ncurses-base (6.1+20181013-2+deb10u4) ... (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 ... 11648 files and directories currently installed.) Preparing to unpack .../libsystemd0_241-7~deb10u10_amd64.deb ... Unpacking libsystemd0:amd64 (241-7~deb10u10) over (241-7~deb10u8) ... Setting up libsystemd0:amd64 (241-7~deb10u10) ... (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 ... 11648 files and directories currently installed.) Preparing to unpack .../python2.7_2.7.16-2+deb10u3_amd64.deb ... Unpacking python2.7 (2.7.16-2+deb10u3) over (2.7.16-2+deb10u1) ... Preparing to unpack .../libssl1.1_1.1.1n-0+deb10u6_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1n-0+deb10u6) over (1.1.1n-0+deb10u3) ... Preparing to unpack .../libbz2-1.0_1.0.6-9.2~deb10u2_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.6-9.2~deb10u2) over (1.0.6-9.2~deb10u1) ... Setting up libbz2-1.0:amd64 (1.0.6-9.2~deb10u2) ... (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 ... 11648 files and directories currently installed.) Preparing to unpack .../libexpat1_2.2.6-2+deb10u6_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u6) over (2.2.6-2+deb10u4) ... Preparing to unpack .../libtinfo6_6.1+20181013-2+deb10u4_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20181013-2+deb10u4) over (6.1+20181013-2+deb10u2) ... Setting up libtinfo6:amd64 (6.1+20181013-2+deb10u4) ... (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 ... 11648 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.1+20181013-2+deb10u4_amd64.deb ... Unpacking libncursesw6:amd64 (6.1+20181013-2+deb10u4) over (6.1+20181013-2+deb10u2) ... Setting up libncursesw6:amd64 (6.1+20181013-2+deb10u4) ... (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 ... 11648 files and directories currently installed.) Preparing to unpack .../libsqlite3-0_3.27.2-3+deb10u2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.27.2-3+deb10u2) over (3.27.2-3+deb10u1) ... Preparing to unpack .../libpython2.7-stdlib_2.7.16-2+deb10u3_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.16-2+deb10u3) over (2.7.16-2+deb10u1) ... Preparing to unpack .../python2.7-minimal_2.7.16-2+deb10u3_amd64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u3) over (2.7.16-2+deb10u1) ... Preparing to unpack .../libpython2.7-minimal_2.7.16-2+deb10u3_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.16-2+deb10u3) over (2.7.16-2+deb10u1) ... Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-1+deb10u2_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.11.dfsg-1+deb10u2) over (1:1.2.11.dfsg-1+deb10u1) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-1+deb10u2) ... (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 ... 11648 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2019.1+deb10u2_all.deb ... Unpacking debian-archive-keyring (2019.1+deb10u2) over (2019.1+deb10u1) ... Setting up debian-archive-keyring (2019.1+deb10u2) ... (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 ... 11654 files and directories currently installed.) Preparing to unpack .../00-tzdata_2021a-0+deb10u11_all.deb ... Unpacking tzdata (2021a-0+deb10u11) over (2021a-0+deb10u6) ... Preparing to unpack .../01-libgssapi-krb5-2_1.17-3+deb10u5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u5) over (1.17-3+deb10u4) ... Preparing to unpack .../02-libkrb5-3_1.17-3+deb10u5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u5) over (1.17-3+deb10u4) ... Preparing to unpack .../03-libkrb5support0_1.17-3+deb10u5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u5) over (1.17-3+deb10u4) ... Preparing to unpack .../04-libk5crypto3_1.17-3+deb10u5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-3+deb10u5) over (1.17-3+deb10u4) ... Preparing to unpack .../05-libnghttp2-14_1.36.0-2+deb10u2_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.36.0-2+deb10u2) over (1.36.0-2+deb10u1) ... Preparing to unpack .../06-libssh2-1_1.8.0-2.1+deb10u1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1+deb10u1) over (1.8.0-2.1) ... Preparing to unpack .../07-libcurl3-gnutls_7.64.0-4+deb10u7_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.64.0-4+deb10u7) over (7.64.0-4+deb10u2) ... Preparing to unpack .../08-libjs-jquery-ui_1.12.1+dfsg-5+deb10u1_all.deb ... Unpacking libjs-jquery-ui (1.12.1+dfsg-5+deb10u1) over (1.12.1+dfsg-5) ... Preparing to unpack .../09-libwebp6_0.6.1-2+deb10u3_amd64.deb ... Unpacking libwebp6:amd64 (0.6.1-2+deb10u3) over (0.6.1-2+deb10u1) ... Preparing to unpack .../10-libtiff5_4.1.0+git191117-2~deb10u8_amd64.deb ... Unpacking libtiff5:amd64 (4.1.0+git191117-2~deb10u8) over (4.1.0+git191117-2~deb10u4) ... Preparing to unpack .../11-libwebpdemux2_0.6.1-2+deb10u3_amd64.deb ... Unpacking libwebpdemux2:amd64 (0.6.1-2+deb10u3) over (0.6.1-2+deb10u1) ... Preparing to unpack .../12-libwebpmux3_0.6.1-2+deb10u3_amd64.deb ... Unpacking libwebpmux3:amd64 (0.6.1-2+deb10u3) over (0.6.1-2+deb10u1) ... Preparing to unpack .../13-python-reportlab-accel_3.5.13-1+deb10u2_amd64.deb ... Unpacking python-reportlab-accel:amd64 (3.5.13-1+deb10u2) over (3.5.13-1+deb10u1) ... Preparing to unpack .../14-python-reportlab_3.5.13-1+deb10u2_all.deb ... Unpacking python-reportlab (3.5.13-1+deb10u2) over (3.5.13-1+deb10u1) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u6) ... Setting up libssl1.1:amd64 (1.1.1n-0+deb10u6) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u2) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u2) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u5) ... Setting up tzdata (2021a-0+deb10u11) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Oct 19 08:12:34 UTC 2023. Universal Time is now: Thu Oct 19 08:12:34 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython2.7-minimal:amd64 (2.7.16-2+deb10u3) ... Setting up libjs-jquery-ui (1.12.1+dfsg-5+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u3) ... Setting up libwebp6:amd64 (0.6.1-2+deb10u3) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u5) ... Setting up libssh2-1:amd64 (1.8.0-2.1+deb10u1) ... Setting up python-reportlab-accel:amd64 (3.5.13-1+deb10u2) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u5) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u8) ... Setting up libwebpmux3:amd64 (0.6.1-2+deb10u3) ... Setting up libwebpdemux2:amd64 (0.6.1-2+deb10u3) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u3) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u5) ... Setting up python-reportlab (3.5.13-1+deb10u2) ... Setting up python2.7 (2.7.16-2+deb10u3) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u7) ... Processing triggers for libc-bin (2.28-10+deb10u2) ... Processing triggers for mime-support (3.62) ... 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', '-yf', 'dist-upgrade'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m41.8s DUMP: 71756666a73147e06184964192e356da - 0m41.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m41.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'show', '--no-all-versions', 'gasic'] 0m42.0s DUMP: Package: gasic Version: 0.0.r19-4 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.r19-4_amd64.deb Size: 20260 MD5sum: 96971d0a1e8887a5cabac3ebac20b47b SHA256: d44088f8b948ca52a0fa6d2236209740b6dc0174a56726626fbaf979811c63e8 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'show', '--no-all-versions', 'gasic'] 0m42.0s INFO: apt-cache knows about the following packages: gasic 0m42.0s INFO: Running scripts pre_install 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_database-server'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_database-server'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_exceptions'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_exceptions'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_extras'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_extras'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'policy'] 0m42.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages release v=10-updates,o=Debian,a=oldoldstable-proposed-updates,n=buster-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian buster-updates/main amd64 Packages release o=Debian,a=oldoldstable-updates,n=buster-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org buster/updates/main amd64 Packages release v=10,o=Debian,a=oldoldstable,n=buster,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'policy'] 0m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'policy', 'gasic'] 0m42.2s DUMP: gasic: Installed: 0.0.r19-4 Candidate: 0.0.r19-4 Version table: *** 0.0.r19-4 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'policy', 'gasic'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', '-y', 'install', 'gasic'] 0m42.6s DUMP: Reading package lists... Building dependency tree... Reading state information... gasic is already the newest version (0.0.r19-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m42.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', '-y', 'install', 'gasic'] 0m42.6s INFO: Running scripts post_install 0m42.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_install_exceptions'] 0m42.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_install_exceptions'] 0m42.6s INFO: Running scripts post_distupgrade 0m42.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m42.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m42.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_distupgrade_exceptions'] 0m42.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_distupgrade_exceptions'] 0m42.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m42.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m42.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m42.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_distupgrade_zz_backports'] 0m42.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_distupgrade_zz_backports'] 0m42.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m43.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m43.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m43.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m43.6s INFO: Running scripts pre_install 0m43.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_database-server'] 0m43.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_database-server'] 0m43.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_exceptions'] 0m43.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_exceptions'] 0m43.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_extras'] 0m43.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_extras'] 0m43.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_foreign_architecture'] 0m43.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_foreign_architecture'] 0m43.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m43.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m43.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'policy'] 0m43.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages release v=10-updates,o=Debian,a=oldoldstable-proposed-updates,n=buster-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian buster-updates/main amd64 Packages release o=Debian,a=oldoldstable-updates,n=buster-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org buster/updates/main amd64 Packages release v=10,o=Debian,a=oldoldstable,n=buster,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m43.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'policy'] 0m43.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'policy', 'gasic'] 0m43.8s DUMP: gasic: Installed: 0.0.r19-4 Candidate: 0.0.r19-4 Version table: *** 0.0.r19-4 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-cache', 'policy', 'gasic'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', '-y', 'install', 'gasic=0.0.r19-4'] 0m44.3s DUMP: Reading package lists... Building dependency tree... Reading state information... gasic is already the newest version (0.0.r19-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m44.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', '-y', 'install', 'gasic=0.0.r19-4'] 0m44.3s INFO: Running scripts post_install 0m44.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_install_exceptions'] 0m44.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_install_exceptions'] 0m44.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m44.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m45.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', '-ac', '--ignore-obsolete'] 0m46.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', '-ac', '--ignore-obsolete'] 0m46.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m46.9s DUMP: 0.15.6 0m46.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m46.9s INFO: Running adequate version 0.15.6 now. 0m46.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'gasic'] 0m47.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'gasic'] 0m47.1s INFO: Running scripts pre_remove 0m47.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m47.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m47.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_remove_exceptions'] 0m49.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/pre_remove_exceptions'] 0m49.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m49.6s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed bowtie bowtie 1.2.2+dfsg-4 install ok installed bowtie2 bowtie2 2.3.4.3-1 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed bwa bwa 0.7.17-3 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u2 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed fonts-lyx fonts-lyx 2.3.2-1 install ok installed gasic gasic 0.0.r19-4 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libatomic1:amd64 libatomic1 8.3.0-6 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblas3:amd64 libblas3 3.8.0-2 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u2 install ok installed libc-bin libc-bin 2.28-10+deb10u2 install ok installed libc6:amd64 libc6 2.28-10+deb10u2 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.64.0-4+deb10u7 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libdeflate0:amd64 libdeflate0 1.2-1 install ok installed libexpat1:amd64 libexpat1 2.2.6-2+deb10u6 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libfreetype6:amd64 libfreetype6 2.9.1-3+deb10u3 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgfortran5:amd64 libgfortran5 8.3.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u10 install ok installed libgomp1:amd64 libgomp1 8.3.0-6 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.17-3+deb10u5 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libhts2:amd64 libhts2 1.9-12~deb10u1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed libimagequant0:amd64 libimagequant0 2.12.2-1.1 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:1.5.2-2+deb10u1 install ok installed libjs-jquery libjs-jquery 3.3.1~dfsg-3+deb10u1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.12.1+dfsg-5+deb10u1 install ok installed libk5crypto3:amd64 libk5crypto3 1.17-3+deb10u5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.17-3+deb10u5 install ok installed libkrb5support0:amd64 libkrb5support0 1.17-3+deb10u5 install ok installed liblapack3:amd64 liblapack3 3.8.0-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.9-3 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.47+dfsg-3+deb10u7 install ok installed libldap-common libldap-common 2.4.47+dfsg-3+deb10u7 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u4 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.36.0-2+deb10u2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libpng16-16:amd64 libpng16-16 1.6.36-6 install ok installed libpsl5:amd64 libpsl5 0.20.2-2 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.16-1 install ok installed libpython2-stdlib:amd64 libpython2-stdlib 2.7.16-1 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.16-2+deb10u3 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.16-2+deb10u3 install ok installed libquadmath0:amd64 libquadmath0 8.3.0-6 install ok installed libreadline7:amd64 libreadline7 7.0-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-1+deb10u2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-1+deb10u2 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.27.2-3+deb10u2 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libssh2-1:amd64 libssh2-1 1.8.0-2.1+deb10u1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1n-0+deb10u6 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u10 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3+deb10u1 install ok installed libtbb2:amd64 libtbb2 2018~U6-4 install ok installed libtiff5:amd64 libtiff5 4.1.0+git191117-2~deb10u8 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u4 install ok installed libudev1:amd64 libudev1 241-7~deb10u10 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2+deb10u3 install ok installed libwebpdemux2:amd64 libwebpdemux2 0.6.1-2+deb10u3 install ok installed libwebpmux3:amd64 libwebpmux3 0.6.1-2+deb10u3 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mime-support mime-support 3.62 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u4 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u4 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed python python 2.7.16-1 install ok installed python-backports.functools-lru-cache python-backports.functools-lru-cache 1.5-3 install ok installed python-biopython python-biopython 1.73+dfsg-1 install ok installed python-cycler python-cycler 0.10.0-1 install ok installed python-dateutil python-dateutil 2.7.3-3 install ok installed python-decorator python-decorator 4.3.0-1.1 install ok installed python-kiwisolver python-kiwisolver 1.0.1-2+b1 install ok installed python-matplotlib python-matplotlib 2.2.3-6 install ok installed python-matplotlib2-data python-matplotlib2-data 2.2.3-6 install ok installed python-minimal python-minimal 2.7.16-1 install ok installed python-numpy python-numpy 1:1.16.2-1 install ok installed python-pil:amd64 python-pil 5.4.1-2+deb10u3 install ok installed python-pkg-resources python-pkg-resources 40.8.0-1 install ok installed python-pyparsing python-pyparsing 2.2.0+dfsg1-2 install ok installed python-pysam python-pysam 0.15.2+ds-2 install ok installed python-reportlab python-reportlab 3.5.13-1+deb10u2 install ok installed python-reportlab-accel:amd64 python-reportlab-accel 3.5.13-1+deb10u2 install ok installed python-scipy python-scipy 1.1.0-7 install ok installed python-six python-six 1.12.0-1 install ok installed python-subprocess32 python-subprocess32 3.5.3-1 install ok installed python-tz python-tz 2019.1-1 install ok installed python2 python2 2.7.16-1 install ok installed python2-minimal python2-minimal 2.7.16-1 install ok installed python2.7 python2.7 2.7.16-2+deb10u3 install ok installed python2.7-minimal python2.7-minimal 2.7.16-2+deb10u3 install ok installed readline-common readline-common 7.0-5 install ok installed sed sed 4.7-1 install ok installed seqan-apps seqan-apps 2.4.0+dfsg-11 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed ttf-bitstream-vera ttf-bitstream-vera 1.10-8 install ok installed tzdata tzdata 2021a-0+deb10u11 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u2 0m49.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m49.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', 'remove', 'bowtie', 'bowtie2', 'bwa', 'fonts-lyx', 'libatomic1:amd64', 'libblas3:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhts2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libnghttp2-14:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'libtiff5:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'mime-support', 'python', 'python-backports.functools-lru-cache', 'python-biopython', 'python-cycler', 'python-dateutil', 'python-decorator', 'python-kiwisolver', 'python-matplotlib', 'python-matplotlib2-data', 'python-minimal', 'python-numpy', 'python-pil:amd64', 'python-pkg-resources', 'python-pyparsing', 'python-pysam', 'python-reportlab', 'python-reportlab-accel:amd64', 'python-scipy', 'python-six', 'python-subprocess32', 'python-tz', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'seqan-apps', 'ttf-bitstream-vera', 'gasic'] 0m52.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bowtie bowtie2 bwa fonts-lyx gasic libatomic1 libblas3 libcurl3-gnutls libdeflate0 libexpat1 libfreetype6 libgfortran5 libgomp1 libgssapi-krb5-2 libhts2 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libnghttp2-14 libpng16-16 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libtbb2 libtiff5 libwebp6 libwebpdemux2 libwebpmux3 mime-support python python-backports.functools-lru-cache python-biopython python-cycler python-dateutil python-decorator python-kiwisolver python-matplotlib python-matplotlib2-data python-minimal python-numpy python-pil python-pkg-resources python-pyparsing python-pysam python-reportlab python-reportlab-accel python-scipy python-six python-subprocess32 python-tz python2 python2-minimal python2.7 python2.7-minimal readline-common seqan-apps ttf-bitstream-vera 0 upgraded, 0 newly installed, 77 to remove and 0 not upgraded. After this operation, 235 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 ... 11657 files and directories currently installed.) Removing gasic (0.0.r19-4) ... Removing bowtie (1.2.2+dfsg-4) ... Removing bowtie2 (2.3.4.3-1) ... Removing bwa (0.7.17-3) ... Removing python-matplotlib (2.2.3-6) ... Removing python-matplotlib2-data (2.2.3-6) ... Removing fonts-lyx (2.3.2-1) ... Removing libtbb2:amd64 (2018~U6-4) ... Removing libatomic1:amd64 (8.3.0-6) ... Removing python-scipy (1.1.0-7) ... Removing python-biopython (1.73+dfsg-1) ... Removing python-numpy (1:1.16.2-1) ... Removing liblapack3:amd64 (3.8.0-2) ... Removing libblas3:amd64 (3.8.0-2) ... Removing python-pysam (0.15.2+ds-2) ... Removing libhts2:amd64 (1.9-12~deb10u1) ... Removing libcurl3-gnutls:amd64 (7.64.0-4+deb10u7) ... Removing libdeflate0:amd64 (1.2-1) ... Removing python-reportlab (3.5.13-1+deb10u2) ... Removing python-reportlab-accel:amd64 (3.5.13-1+deb10u2) ... Removing python-dateutil (2.7.3-3) ... Removing python-cycler (0.10.0-1) ... Removing python-six (1.12.0-1) ... Removing python-subprocess32 (3.5.3-1) ... Removing python-tz (2019.1-1) ... Removing python-pil:amd64 (5.4.1-2+deb10u3) ... Removing libfreetype6:amd64 (2.9.1-3+deb10u3) ... Removing libgfortran5:amd64 (8.3.0-6) ... Removing seqan-apps (2.4.0+dfsg-11) ... Removing libgomp1:amd64 (8.3.0-6) ... Removing libgssapi-krb5-2:amd64 (1.17-3+deb10u5) ... Removing libimagequant0:amd64 (2.12.2-1.1) ... Removing libtiff5:amd64 (4.1.0+git191117-2~deb10u8) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Removing libjs-jquery-ui (1.12.1+dfsg-5+deb10u1) ... Removing libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Removing libkrb5-3:amd64 (1.17-3+deb10u5) ... Removing libk5crypto3:amd64 (1.17-3+deb10u5) ... Removing libkrb5support0:amd64 (1.17-3+deb10u5) ... Removing libkeyutils1:amd64 (1.6-6) ... Removing liblcms2-2:amd64 (2.9-3) ... Removing libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Removing libldap-common (2.4.47+dfsg-3+deb10u7) ... Removing libnghttp2-14:amd64 (1.36.0-2+deb10u2) ... Removing libpng16-16:amd64 (1.6.36-6) ... Removing libpsl5:amd64 (0.20.2-2) ... Removing libquadmath0:amd64 (8.3.0-6) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libssh2-1:amd64 (1.8.0-2.1+deb10u1) ... Removing libwebpmux3:amd64 (0.6.1-2+deb10u3) ... Removing libwebpdemux2:amd64 (0.6.1-2+deb10u3) ... Removing libwebp6:amd64 (0.6.1-2+deb10u3) ... Removing python-backports.functools-lru-cache (1.5-3) ... Removing python-decorator (4.3.0-1.1) ... Removing python-kiwisolver (1.0.1-2+b1) ... Removing python-pkg-resources (40.8.0-1) ... Removing python-pyparsing (2.2.0+dfsg1-2) ... Removing ttf-bitstream-vera (1.10-8) ... Removing python (2.7.16-1) ... Removing python2 (2.7.16-1) ... Removing python2.7 (2.7.16-2+deb10u3) ... Removing libpython-stdlib:amd64 (2.7.16-1) ... Removing libpython2-stdlib:amd64 (2.7.16-1) ... Removing python-minimal (2.7.16-1) ... Removing python2-minimal (2.7.16-1) ... Removing python2.7-minimal (2.7.16-2+deb10u3) ... Removing libpython2.7-stdlib:amd64 (2.7.16-2+deb10u3) ... Removing libexpat1:amd64 (2.2.6-2+deb10u6) ... Removing libpython2.7-minimal:amd64 (2.7.16-2+deb10u3) ... find: '/usr/lib/python2.7': No such file or directory Removing libreadline7:amd64 (7.0-5) ... Removing libsqlite3-0:amd64 (3.27.2-3+deb10u2) ... Removing libssl1.1:amd64 (1.1.1n-0+deb10u6) ... Removing mime-support (3.62) ... Removing readline-common (7.0-5) ... Processing triggers for libc-bin (2.28-10+deb10u2) ... 0m52.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', 'remove', 'bowtie', 'bowtie2', 'bwa', 'fonts-lyx', 'libatomic1:amd64', 'libblas3:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhts2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libnghttp2-14:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'libtiff5:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'mime-support', 'python', 'python-backports.functools-lru-cache', 'python-biopython', 'python-cycler', 'python-dateutil', 'python-decorator', 'python-kiwisolver', 'python-matplotlib', 'python-matplotlib2-data', 'python-minimal', 'python-numpy', 'python-pil:amd64', 'python-pkg-resources', 'python-pyparsing', 'python-pysam', 'python-reportlab', 'python-reportlab-accel:amd64', 'python-scipy', 'python-six', 'python-subprocess32', 'python-tz', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'seqan-apps', 'ttf-bitstream-vera', 'gasic'] 0m52.5s INFO: Running scripts post_remove 0m52.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_remove_exceptions'] 0m52.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_remove_exceptions'] 0m52.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg', '--purge', 'bowtie', 'bowtie2', 'bwa', 'fonts-lyx', 'libatomic1:amd64', 'libblas3:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhts2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libnghttp2-14:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'libtiff5:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'mime-support', 'python', 'python-backports.functools-lru-cache', 'python-biopython', 'python-cycler', 'python-dateutil', 'python-decorator', 'python-kiwisolver', 'python-matplotlib', 'python-matplotlib2-data', 'python-minimal', 'python-numpy', 'python-pil:amd64', 'python-pkg-resources', 'python-pyparsing', 'python-pysam', 'python-reportlab', 'python-reportlab-accel:amd64', 'python-scipy', 'python-six', 'python-subprocess32', 'python-tz', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'seqan-apps', 'ttf-bitstream-vera'] 0m52.7s DUMP: dpkg: warning: ignoring request to remove bowtie which isn't installed dpkg: warning: ignoring request to remove bowtie2 which isn't installed dpkg: warning: ignoring request to remove bwa which isn't installed dpkg: warning: ignoring request to remove fonts-lyx which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed (Reading database ... 6478 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.17-3+deb10u5) ... dpkg: warning: ignoring request to remove libhts2 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 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-5+deb10u1) ... dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.47+dfsg-3+deb10u7) ... dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython2-stdlib which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.16-2+deb10u3) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline7 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed Purging configuration files for libssl1.1:amd64 (1.1.1n-0+deb10u6) ... dpkg: warning: ignoring request to remove libtbb2 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed Purging configuration files for mime-support (3.62) ... Purging configuration files for python (2.7.16-1) ... dpkg: warning: ignoring request to remove python-backports.functools-lru-cache which isn't installed 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-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python-matplotlib which isn't installed Purging configuration files for python-matplotlib2-data (2.2.3-6) ... 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-pil which isn't installed dpkg: warning: ignoring request to remove python-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python-pyparsing 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 which isn't installed dpkg: warning: ignoring request to remove python2-minimal which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed Purging configuration files for python2.7-minimal (2.7.16-2+deb10u3) ... Purging configuration files for readline-common (7.0-5) ... dpkg: warning: ignoring request to remove seqan-apps which isn't installed dpkg: warning: ignoring request to remove ttf-bitstream-vera which isn't installed 0m52.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg', '--purge', 'bowtie', 'bowtie2', 'bwa', 'fonts-lyx', 'libatomic1:amd64', 'libblas3:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhts2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libnghttp2-14:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'libtiff5:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'mime-support', 'python', 'python-backports.functools-lru-cache', 'python-biopython', 'python-cycler', 'python-dateutil', 'python-decorator', 'python-kiwisolver', 'python-matplotlib', 'python-matplotlib2-data', 'python-minimal', 'python-numpy', 'python-pil:amd64', 'python-pkg-resources', 'python-pyparsing', 'python-pysam', 'python-reportlab', 'python-reportlab-accel:amd64', 'python-scipy', 'python-six', 'python-subprocess32', 'python-tz', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'seqan-apps', 'ttf-bitstream-vera'] 0m52.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg', '--purge', 'gasic'] 0m52.7s DUMP: dpkg: warning: ignoring request to remove gasic which isn't installed 0m52.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg', '--purge', 'gasic'] 0m52.7s INFO: Running scripts post_purge 0m52.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_purge_exceptions'] 0m52.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_purge_exceptions'] 0m52.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg', '--purge', '--pending'] 0m52.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg', '--purge', '--pending'] 0m52.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg', '--remove', '--pending'] 0m52.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg', '--remove', '--pending'] 0m52.7s INFO: Running scripts post_test 0m52.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_test_exceptions'] 0m52.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'tmp/scripts/post_test_exceptions'] 0m52.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m53.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m53.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg-divert', '--list'] 0m53.1s 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 0m53.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'dpkg-divert', '--list'] 0m53.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', 'clean'] 0m53.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p', 'apt-get', 'clean'] 0m53.1s DEBUG: Recording chroot state 0m54.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/shm'] 0m54.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/shm'] 0m54.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/console'] 0m54.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/console'] 0m54.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/ptmx'] 0m54.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/ptmx'] 0m54.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/pts'] 0m54.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/dev/pts'] 0m54.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/proc'] 0m54.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p/proc'] 0m54.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m54.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpzkqsqn2p'] 0m54.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpzkqsqn2p 0m54.2s INFO: PASS: Upgrading between Debian distributions. 0m54.2s INFO: PASS: All tests. 0m54.2s INFO: piuparts run ends. ret=0 End: 2023-10-19 08:12:49 GMT