Start: 2023-04-16 18:18:07 GMT [stretch] Package: gubbins Version: 2.2.0-1 Installed-Size: 204 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), zlib1g (>= 1:1.1.4), python3-biopython, python3-dendropy, python3-nose, python3-reportlab, python3:any (>= 3.3.2-2~), python3, fasttree, raxml (>= 8) Description: phylogenetic analysis of genome sequences Homepage: https://sanger-pathogens.github.io/gubbins/ Description-md5: cc258d495d1b902fa507e53b5cc3902e Section: science Priority: optional Filename: pool/main/g/gubbins/gubbins_2.2.0-1_amd64.deb Size: 53106 MD5sum: b0c79c64904d6691e3b0f90efc291044 SHA256: 0969c992900e02061dbd508de57ac143e27615a55581abcaaddf8437a4387733 [buster] Package: gubbins Version: 2.3.4-1 Installed-Size: 187 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), zlib1g (>= 1:1.1.4), python3-biopython, python3-dendropy, python3-nose, python3-reportlab, python3:any, python3, fasttree, raxml (>= 8) Description: phylogenetic analysis of genome sequences Homepage: https://sanger-pathogens.github.io/gubbins/ Description-md5: cc258d495d1b902fa507e53b5cc3902e Section: science Priority: optional Filename: pool/main/g/gubbins/gubbins_2.3.4-1_amd64.deb Size: 48528 MD5sum: 46836e385ecc89d2dfcccd092f3cbdeb SHA256: 3587556fb6ef7f72a6856b7b9a96b0e0517b3e41351d2172dd1483d160bc33da Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --install-recommends --upgrade-before-dist-upgrade --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster-rcmd/reference-chroot-metadata.dat --apt gubbins=2.3.4-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --install-recommends --upgrade-before-dist-upgrade --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster-rcmd/reference-chroot-metadata.dat --apt gubbins=2.3.4-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp8jjk8g56 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp8jjk8g56 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/proc'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/proc'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/pts'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/pts'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/ptmx'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/ptmx'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/console'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/console'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/shm'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/shm'] 0m1.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.6s DEBUG: Created policy-rc.d and chmodded it. 0m1.6s DEBUG: Created resolv.conf. 0m1.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp8jjk8g56/tmp/scripts/ 0m1.6s INFO: Running scripts post_chroot_unpack 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', 'update'] 0m2.6s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', 'update'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', '-yf', 'dist-upgrade'] 0m3.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', '-yf', 'dist-upgrade'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s INFO: Running scripts post_setup 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_setup_dummy_users'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_setup_dummy_users'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_setup_forbid_home'] 0m4.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_setup_forbid_home'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.4s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_setup_minimize'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_setup_minimize'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster-rcmd/reference-chroot-metadata.dat 0m4.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 0m4.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 0m4.8s INFO: Running scripts is_testable 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/is_testable_uninstallable'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/is_testable_uninstallable'] 0m4.8s INFO: Running scripts pre_test 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_test_exceptions'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_test_exceptions'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_test_root_password'] 0m4.9s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_test_root_password'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'show', '--no-all-versions', 'gubbins'] 0m5.1s DUMP: Package: gubbins Version: 2.2.0-1 Installed-Size: 204 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), zlib1g (>= 1:1.1.4), python3-biopython, python3-dendropy, python3-nose, python3-reportlab, python3:any (>= 3.3.2-2~), python3, fasttree, raxml (>= 8) Description-en: phylogenetic analysis of genome sequences Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. . Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences. Description-md5: cc258d495d1b902fa507e53b5cc3902e Homepage: https://sanger-pathogens.github.io/gubbins/ Section: science Priority: optional Filename: pool/main/g/gubbins/gubbins_2.2.0-1_amd64.deb Size: 53106 MD5sum: b0c79c64904d6691e3b0f90efc291044 SHA256: 0969c992900e02061dbd508de57ac143e27615a55581abcaaddf8437a4387733 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'show', '--no-all-versions', 'gubbins'] 0m5.1s INFO: apt-cache knows about the following packages: gubbins 0m5.1s INFO: Running scripts pre_install 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_database-server'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_database-server'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_exceptions'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_exceptions'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_extras'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_extras'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'policy'] 0m5.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'policy'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'policy', 'gubbins'] 0m5.3s DUMP: gubbins: Installed: (none) Candidate: 2.2.0-1 Version table: 2.2.0-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'policy', 'gubbins'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', '-y', 'install', 'gubbins'] 0m36.2s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bzip2 dh-python fasttree file gsfonts libart-2.0-2 libblas-common libblas3 libexpat1 libffi6 libfreetype6 libgdbm3 libgfortran3 libgmp10 libgnutls30 libgomp1 libhogweed4 libidn11 libjbig0 libjpeg62-turbo liblapack3 liblcms2-2 libmagic-mgc libmagic1 libmpdec2 libnettle6 libp11-kit0 libperl5.24 libpng16-16 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libquadmath0 libreadline7 libsqlite3-0 libssl1.1 libtasn1-6 libtiff5 libwebp6 libwebpdemux2 libwebpmux2 mime-support ncbi-blast+ ncbi-data netbase perl perl-modules-5.24 python python-biopython python-biopython-doc python-minimal python-numpy python-pil python-renderpm python-reportlab python-reportlab-accel python2.7 python2.7-minimal python3 python3-biopython python3-dendropy python3-minimal python3-nose python3-numpy python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3.5 python3.5-minimal raxml readline-common rename xz-utils Suggested packages: bzip2-doc libdpkg-perl gnutls-bin liblcms2-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make python-doc python-tk bwa clustalo clustalw dialign dssp emboss mafft muscle phylip phyml prank probcons python-mysqldb python-matplotlib python-rdflib python-psycopg2 python-scipy samtools t-coffee wise gcc gfortran python-dev python-nose python-numpy-dbg python-numpy-doc python-pil-doc python-pil-dbg python-renderpm-dbg pdf-viewer python-egenix-mxtexttools python-reportlab-doc python2.7-doc binutils binfmt-support python3-doc python3-tk python3-venv python3-matplotlib python3-rdflib python3-psycopg2 python3-scipy python-nose-doc python3-dev python3-numpy-dbg python3-pil-dbg python3-setuptools python3-renderpm-dbg python3-egenix-mxtexttools python3.5-venv python3.5-doc readline-doc The following NEW packages will be installed: bzip2 dh-python fasttree file gsfonts gubbins libart-2.0-2 libblas-common libblas3 libexpat1 libffi6 libfreetype6 libgdbm3 libgfortran3 libgmp10 libgnutls30 libgomp1 libhogweed4 libidn11 libjbig0 libjpeg62-turbo liblapack3 liblcms2-2 libmagic-mgc libmagic1 libmpdec2 libnettle6 libp11-kit0 libperl5.24 libpng16-16 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libquadmath0 libreadline7 libsqlite3-0 libssl1.1 libtasn1-6 libtiff5 libwebp6 libwebpdemux2 libwebpmux2 mime-support ncbi-blast+ ncbi-data netbase perl perl-modules-5.24 python python-biopython python-biopython-doc python-minimal python-numpy python-pil python-renderpm python-reportlab python-reportlab-accel python2.7 python2.7-minimal python3 python3-biopython python3-dendropy python3-minimal python3-nose python3-numpy python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3.5 python3.5-minimal raxml readline-common rename xz-utils 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. Need to get 70.3 MB of archives. After this operation, 319 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 perl-modules-5.24 all 5.24.1-3+deb9u7 [2723 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 libgdbm3 amd64 1.8.3-14 [30.0 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 libperl5.24 amd64 5.24.1-3+deb9u7 [3527 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 perl amd64 5.24.1-3+deb9u7 [218 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u3 [389 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u3 [1382 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u3 [83.7 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 python amd64 2.7.13-2 [154 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 libart-2.0-2 amd64 2.3.21-2 [72.7 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libpython3.5-minimal amd64 3.5.3-1+deb9u1 [573 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 python3.5-minimal amd64 3.5.3-1+deb9u1 [1691 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 python3-minimal amd64 3.5.3-1 [35.3 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 libmpdec2 amd64 2.4.2-1 [85.2 kB] Get:24 http://deb.debian.org/debian stretch/main amd64 libpython3.5-stdlib amd64 3.5.3-1+deb9u1 [2167 kB] Get:25 http://deb.debian.org/debian stretch/main amd64 python3.5 amd64 3.5.3-1+deb9u1 [229 kB] Get:26 http://deb.debian.org/debian stretch/main amd64 libpython3-stdlib amd64 3.5.3-1 [18.6 kB] Get:27 http://deb.debian.org/debian stretch/main amd64 dh-python all 2.20170125 [86.8 kB] Get:28 http://deb.debian.org/debian stretch/main amd64 python3 amd64 3.5.3-1 [21.6 kB] Get:29 http://deb.debian.org/debian stretch/main amd64 netbase all 5.4 [19.1 kB] Get:30 http://deb.debian.org/debian stretch/main amd64 bzip2 amd64 1.0.6-8.1 [47.5 kB] Get:31 http://deb.debian.org/debian stretch/main amd64 libmagic-mgc amd64 1:5.30-1+deb9u3 [222 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libmagic1 amd64 1:5.30-1+deb9u3 [111 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 file amd64 1:5.30-1+deb9u3 [64.2 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b2 [192 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b2 [136 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 libtasn1-6 amd64 4.10-1.1+deb9u1 [50.6 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 libgnutls30 amd64 3.5.8-5+deb9u5 [896 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 xz-utils amd64 5.2.2-1.2+b1 [266 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 gsfonts all 1:8.11+urwcyr1.0.7~pre44-4.3 [3126 kB] Get:43 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 libblas-common amd64 3.7.0-2 [14.2 kB] Get:46 http://deb.debian.org/debian stretch/main amd64 libblas3 amd64 3.7.0-2 [155 kB] Get:47 http://deb.debian.org/debian stretch/main amd64 liblapack3 amd64 3.7.0-2 [2141 kB] Get:48 http://deb.debian.org/debian stretch/main amd64 python3-numpy amd64 1:1.12.1-3 [1934 kB] Get:49 http://deb.debian.org/debian stretch/main amd64 python3-reportlab-accel amd64 3.3.0-2+deb9u1 [32.1 kB] Get:50 http://deb.debian.org/debian stretch/main amd64 python3-reportlab all 3.3.0-2+deb9u1 [474 kB] Get:51 http://deb.debian.org/debian stretch/main amd64 python3-biopython amd64 1.68+dfsg-3 [1163 kB] Get:52 http://deb.debian.org/debian stretch/main amd64 python3-pkg-resources all 33.1.1-1 [137 kB] Get:53 http://deb.debian.org/debian stretch/main amd64 python3-dendropy all 4.2.0+dfsg-1 [7494 kB] Get:54 http://deb.debian.org/debian stretch/main amd64 python3-nose all 1.3.7-2 [132 kB] Get:55 http://deb.debian.org/debian stretch/main amd64 libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:56 http://deb.debian.org/debian stretch/main amd64 fasttree amd64 2.1.9-1 [132 kB] Get:57 http://deb.debian.org/debian stretch/main amd64 raxml amd64 8.2.9+dfsg-1+b1 [1278 kB] Get:58 http://deb.debian.org/debian stretch/main amd64 gubbins amd64 2.2.0-1 [53.1 kB] Get:59 http://deb.debian.org/debian stretch/main amd64 libpng16-16 amd64 1.6.28-1+deb9u1 [280 kB] Get:60 http://deb.debian.org/debian stretch/main amd64 libfreetype6 amd64 2.6.3-3.2+deb9u1 [438 kB] Get:61 http://deb.debian.org/debian stretch/main amd64 libjpeg62-turbo amd64 1:1.5.1-2 [134 kB] Get:62 http://deb.debian.org/debian stretch/main amd64 liblcms2-2 amd64 2.8-4+deb9u1 [143 kB] Get:63 http://deb.debian.org/debian stretch/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:64 http://deb.debian.org/debian stretch/main amd64 libtiff5 amd64 4.0.8-2+deb9u5 [239 kB] Get:65 http://deb.debian.org/debian stretch/main amd64 libwebp6 amd64 0.5.2-1 [235 kB] Get:66 http://deb.debian.org/debian stretch/main amd64 libwebpdemux2 amd64 0.5.2-1 [73.7 kB] Get:67 http://deb.debian.org/debian stretch/main amd64 libwebpmux2 amd64 0.5.2-1 [83.9 kB] Get:68 http://deb.debian.org/debian stretch/main amd64 ncbi-data all 6.1.20170106+dfsg1-0+deb9u1 [3555 kB] Get:69 http://deb.debian.org/debian stretch/main amd64 ncbi-blast+ amd64 2.6.0-1 [9591 kB] Get:70 http://deb.debian.org/debian stretch/main amd64 python-numpy amd64 1:1.12.1-3 [1936 kB] Get:71 http://deb.debian.org/debian stretch/main amd64 python-reportlab-accel amd64 3.3.0-2+deb9u1 [36.8 kB] Get:72 http://deb.debian.org/debian stretch/main amd64 python-reportlab all 3.3.0-2+deb9u1 [478 kB] Get:73 http://deb.debian.org/debian stretch/main amd64 python-biopython amd64 1.68+dfsg-3 [1201 kB] Get:74 http://deb.debian.org/debian stretch/main amd64 python-biopython-doc all 1.68+dfsg-3 [11.8 MB] Get:75 http://deb.debian.org/debian stretch/main amd64 python-pil amd64 4.0.0-4+deb9u1 [376 kB] Get:76 http://deb.debian.org/debian stretch/main amd64 python-renderpm amd64 3.3.0-2+deb9u1 [47.3 kB] Get:77 http://deb.debian.org/debian stretch/main amd64 python3-pil amd64 4.0.0-4+deb9u1 [377 kB] Get:78 http://deb.debian.org/debian stretch/main amd64 python3-renderpm amd64 3.3.0-2+deb9u1 [47.4 kB] Get:79 http://deb.debian.org/debian stretch/main amd64 rename all 0.20-4 [12.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 70.3 MB in 6s (10.9 MB/s) Selecting previously unselected package perl-modules-5.24. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4411 files and directories currently installed.) Preparing to unpack .../00-perl-modules-5.24_5.24.1-3+deb9u7_all.deb ... Unpacking perl-modules-5.24 (5.24.1-3+deb9u7) ... Selecting previously unselected package libgdbm3:amd64. Preparing to unpack .../01-libgdbm3_1.8.3-14_amd64.deb ... Unpacking libgdbm3:amd64 (1.8.3-14) ... Selecting previously unselected package libperl5.24:amd64. 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Selecting previously unselected package python3-reportlab-accel:amd64. Preparing to unpack .../21-python3-reportlab-accel_3.3.0-2+deb9u1_amd64.deb ... Unpacking python3-reportlab-accel:amd64 (3.3.0-2+deb9u1) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../22-python3-reportlab_3.3.0-2+deb9u1_all.deb ... Unpacking python3-reportlab (3.3.0-2+deb9u1) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../23-python3-biopython_1.68+dfsg-3_amd64.deb ... Unpacking python3-biopython (1.68+dfsg-3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../24-python3-pkg-resources_33.1.1-1_all.deb ... Unpacking python3-pkg-resources (33.1.1-1) ... Selecting previously unselected package python3-dendropy. Preparing to unpack .../25-python3-dendropy_4.2.0+dfsg-1_all.deb ... Unpacking python3-dendropy (4.2.0+dfsg-1) ... Selecting previously unselected package python3-nose. 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Unpacking python-reportlab-accel:amd64 (3.3.0-2+deb9u1) ... Selecting previously unselected package python-reportlab. Preparing to unpack .../44-python-reportlab_3.3.0-2+deb9u1_all.deb ... Unpacking python-reportlab (3.3.0-2+deb9u1) ... Selecting previously unselected package python-biopython. Preparing to unpack .../45-python-biopython_1.68+dfsg-3_amd64.deb ... Unpacking python-biopython (1.68+dfsg-3) ... Selecting previously unselected package python-biopython-doc. Preparing to unpack .../46-python-biopython-doc_1.68+dfsg-3_all.deb ... Unpacking python-biopython-doc (1.68+dfsg-3) ... Selecting previously unselected package python-pil:amd64. Preparing to unpack .../47-python-pil_4.0.0-4+deb9u1_amd64.deb ... Unpacking python-pil:amd64 (4.0.0-4+deb9u1) ... Selecting previously unselected package python-renderpm:amd64. Preparing to unpack .../48-python-renderpm_3.3.0-2+deb9u1_amd64.deb ... Unpacking python-renderpm:amd64 (3.3.0-2+deb9u1) ... Selecting previously unselected package python3-pil:amd64. Preparing to unpack .../49-python3-pil_4.0.0-4+deb9u1_amd64.deb ... Unpacking python3-pil:amd64 (4.0.0-4+deb9u1) ... Selecting previously unselected package python3-renderpm:amd64. Preparing to unpack .../50-python3-renderpm_3.3.0-2+deb9u1_amd64.deb ... Unpacking python3-renderpm:amd64 (3.3.0-2+deb9u1) ... Selecting previously unselected package rename. Preparing to unpack .../51-rename_0.20-4_all.deb ... Unpacking rename (0.20-4) ... Setting up libquadmath0:amd64 (6.3.0-18+deb9u1) ... Setting up libart-2.0-2:amd64 (2.3.21-2) ... Setting up libgomp1:amd64 (6.3.0-18+deb9u1) ... Setting up readline-common (7.0-3) ... Setting up perl-modules-5.24 (5.24.1-3+deb9u7) ... Setting up libgdbm3:amd64 (1.8.3-14) ... Setting up libperl5.24:amd64 (5.24.1-3+deb9u7) ... Setting up libnettle6:amd64 (3.3-1+b2) ... Setting up libjpeg62-turbo:amd64 (1:1.5.1-2) ... Setting up mime-support (3.60) ... Setting up gsfonts (1:8.11+urwcyr1.0.7~pre44-4.3) ... Setting up libpng16-16:amd64 (1.6.28-1+deb9u1) ... Setting up liblcms2-2:amd64 (2.8-4+deb9u1) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libreadline7:amd64 (7.0-3) ... Setting up libblas-common (3.7.0-2) ... Setting up libgfortran3:amd64 (6.3.0-18+deb9u1) ... Setting up libtiff5:amd64 (4.0.8-2+deb9u5) ... Setting up python-biopython-doc (1.68+dfsg-3) ... Setting up libfreetype6:amd64 (2.6.3-3.2+deb9u1) ... Setting up libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Setting up libmagic-mgc (1:5.30-1+deb9u3) ... Setting up bzip2 (1.0.6-8.1) ... Setting up libmagic1:amd64 (1:5.30-1+deb9u3) ... Setting up raxml (8.2.9+dfsg-1+b1) ... Setting up perl (5.24.1-3+deb9u7) ... update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode Setting up libgmp10:amd64 (2:6.1.2+dfsg-1) ... Setting up ncbi-data (6.1.20170106+dfsg1-0+deb9u1) ... Setting up libblas3 (3.7.0-2) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up fasttree (2.1.9-1) ... Setting up xz-utils (5.2.2-1.2+b1) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up libidn11:amd64 (1.33-1+deb9u1) ... Setting up libmpdec2:amd64 (2.4.2-1) ... Setting up netbase (5.4) ... Setting up libwebp6:amd64 (0.5.2-1) ... Setting up rename (0.20-4) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up liblapack3 (3.7.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libpython3.5-stdlib:amd64 (3.5.3-1+deb9u1) ... Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up libwebpmux2:amd64 (0.5.2-1) ... Setting up file (1:5.30-1+deb9u3) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up libwebpdemux2:amd64 (0.5.2-1) ... Setting up python (2.7.13-2) ... Setting up python3.5 (3.5.3-1+deb9u1) ... Setting up libpython3-stdlib:amd64 (3.5.3-1) ... Setting up python-reportlab-accel:amd64 (3.3.0-2+deb9u1) ... Setting up python-reportlab (3.3.0-2+deb9u1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up python-numpy (1:1.12.1-3) ... Setting up python-renderpm:amd64 (3.3.0-2+deb9u1) ... Setting up python-pil:amd64 (4.0.0-4+deb9u1) ... Setting up python-biopython (1.68+dfsg-3) ... Setting up ncbi-blast+ (2.6.0-1) ... Setting up python3 (3.5.3-1) ... Setting up python3-numpy (1:1.12.1-3) ... Setting up python3-pkg-resources (33.1.1-1) ... Setting up python3-nose (1.3.7-2) ... Setting up python3-reportlab-accel:amd64 (3.3.0-2+deb9u1) ... Setting up python3-dendropy (4.2.0+dfsg-1) ... Setting up dh-python (2.20170125) ... Setting up python3-renderpm:amd64 (3.3.0-2+deb9u1) ... Setting up python3-pil:amd64 (4.0.0-4+deb9u1) ... Setting up python3-reportlab (3.3.0-2+deb9u1) ... Setting up python3-biopython (1.68+dfsg-3) ... Setting up gubbins (2.2.0-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m36.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', '-y', 'install', 'gubbins'] 0m36.2s INFO: Running scripts post_install 0m36.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_install_exceptions'] 0m36.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_install_exceptions'] 0m36.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 0m37.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 0m37.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp8jjk8g56 to buster 0m37.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m37.0s INFO: Running scripts pre_distupgrade 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_distupgrade_exceptions'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_distupgrade_exceptions'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', 'update'] 0m41.1s DUMP: Get:1 http://deb.debian.org/debian buster InRelease [122 kB] Get:2 http://deb.debian.org/debian buster/main amd64 Packages [7909 kB] Get:3 http://deb.debian.org/debian buster/main Translation-en [5969 kB] Fetched 14.0 MB in 3s (4426 kB/s) Reading package lists... 0m41.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', 'update'] 0m41.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', '-y', 'upgrade'] 0m52.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages have been kept back: apt bash coreutils dash dpkg e2fslibs e2fsprogs gpgv libapt-pkg5.0 libblas3 libblkid1 libc-bin libc6 libcomerr2 libexpat1 libfdisk1 libgcc1 libgnutls30 libgomp1 libgpg-error0 liblapack3 libmount1 libncursesw5 libp11-kit0 libpam-modules libpam-modules-bin libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libquadmath0 libreadline7 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++6 libsystemd0 libtiff5 libtinfo5 libudev1 libuuid1 login mount ncbi-blast+ ncurses-base ncurses-bin perl perl-base python python-biopython python-biopython-doc python-minimal python-numpy python-pil python2.7 python2.7-minimal python3 python3-biopython python3-minimal python3-numpy python3-pil python3-renderpm python3-reportlab python3-reportlab-accel rename util-linux The following packages will be upgraded: adduser base-files base-passwd bsdutils bzip2 debconf debian-archive-keyring debianutils dh-python diffutils fasttree file findutils grep gsfonts gubbins gzip hostname init-system-helpers libacl1 libart-2.0-2 libattr1 libaudit-common libaudit1 libbz2-1.0 libcap-ng0 libdb5.3 libdebconfclient0 libffi6 libfreetype6 libgcrypt20 libgmp10 libhogweed4 libidn11 libjpeg62-turbo liblcms2-2 liblz4-1 liblzma5 libmagic-mgc libmagic1 libmpdec2 libnettle6 libpam-runtime libpam0g libpcre3 libpng16-16 libselinux1 libsemanage-common libsemanage1 libsepol1 libtasn1-6 libwebp6 libwebpdemux2 mime-support multiarch-support ncbi-data netbase passwd python-renderpm python-reportlab python-reportlab-accel python3-dendropy python3-nose python3-pkg-resources raxml readline-common sed sensible-utils sysvinit-utils tar xz-utils zlib1g 72 upgraded, 0 newly installed, 0 to remove and 67 not upgraded. Need to get 20.3 MB of archives. After this operation, 64.7 MB disk space will be freed. Get:1 http://deb.debian.org/debian buster/main amd64 base-files amd64 10.3+deb10u13 [69.9 kB] Get:2 http://deb.debian.org/debian buster/main amd64 bsdutils amd64 1:2.33.1-0.1 [121 kB] Get:3 http://deb.debian.org/debian buster/main amd64 debianutils amd64 4.8.6.1 [100 kB] Get:4 http://deb.debian.org/debian buster/main amd64 diffutils amd64 1:3.7-3 [371 kB] Get:5 http://deb.debian.org/debian buster/main amd64 findutils amd64 4.6.0+git+20190209-2 [684 kB] Get:6 http://deb.debian.org/debian buster/main amd64 grep amd64 3.3-1 [373 kB] Get:7 http://deb.debian.org/debian buster/main amd64 gzip amd64 1.9-3+deb10u1 [128 kB] Get:8 http://deb.debian.org/debian buster/main amd64 hostname amd64 3.21 [14.8 kB] Get:9 http://deb.debian.org/debian buster/main amd64 sed amd64 4.7-1 [310 kB] Get:10 http://deb.debian.org/debian buster/main amd64 tar amd64 1.30+dfsg-6 [780 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libdebconfclient0 amd64 0.249 [49.1 kB] Get:12 http://deb.debian.org/debian buster/main amd64 base-passwd amd64 3.5.46 [56.7 kB] Get:13 http://deb.debian.org/debian buster/main amd64 init-system-helpers all 1.56+nmu1 [46.8 kB] Get:14 http://deb.debian.org/debian buster/main amd64 sysvinit-utils amd64 2.93-8 [78.4 kB] Get:15 http://deb.debian.org/debian buster/main amd64 debconf all 1.5.71+deb10u1 [145 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libpam-runtime all 1.3.1-5 [211 kB] Get:17 http://deb.debian.org/debian buster/main amd64 libaudit-common all 1:2.8.4-3 [22.4 kB] Get:18 http://deb.debian.org/debian buster/main amd64 libcap-ng0 amd64 0.7.9-2 [14.3 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libaudit1 amd64 1:2.8.4-3 [57.3 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libpam0g amd64 1.3.1-5 [126 kB] Get:21 http://deb.debian.org/debian buster/main amd64 libpcre3 amd64 2:8.39-12 [341 kB] Get:22 http://deb.debian.org/debian buster/main amd64 libselinux1 amd64 2.8-1+b1 [86.9 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libsepol1 amd64 2.8-1 [263 kB] Get:24 http://deb.debian.org/debian buster/main amd64 libsemanage-common all 2.8-2 [17.7 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libsemanage1 amd64 2.8-2 [96.5 kB] Get:26 http://deb.debian.org/debian buster/main amd64 bzip2 amd64 1.0.6-9.2~deb10u1 [48.4 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libbz2-1.0 amd64 1.0.6-9.2~deb10u1 [45.3 kB] Get:28 http://deb.debian.org/debian buster/main amd64 passwd amd64 1:4.5-1.1 [1005 kB] Get:29 http://deb.debian.org/debian buster/main amd64 adduser all 3.118 [240 kB] Get:30 http://deb.debian.org/debian buster/main amd64 debian-archive-keyring all 2019.1+deb10u1 [93.5 kB] Get:31 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libattr1 amd64 1:2.4.48-4 [21.3 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libacl1 amd64 2.2.53-4 [30.4 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.5 [683 kB] Get:35 http://deb.debian.org/debian buster/main amd64 libgcrypt20 amd64 1.8.4-5+deb10u1 [556 kB] Get:36 http://deb.debian.org/debian buster/main amd64 liblz4-1 amd64 1.8.3-1+deb10u1 [53.3 kB] Get:37 http://deb.debian.org/debian buster/main amd64 liblzma5 amd64 5.2.4-1+deb10u1 [153 kB] Get:38 http://deb.debian.org/debian buster/main amd64 zlib1g amd64 1:1.2.11.dfsg-1+deb10u1 [90.8 kB] Get:39 http://deb.debian.org/debian buster/main amd64 netbase all 5.6 [19.4 kB] Get:40 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:41 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get:42 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get:43 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get:44 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:45 http://deb.debian.org/debian buster/main amd64 xz-utils amd64 5.2.4-1+deb10u1 [183 kB] Get:46 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] Get:47 http://deb.debian.org/debian buster/main amd64 fasttree amd64 2.1.10-2 [176 kB] Get:48 http://deb.debian.org/debian buster/main amd64 gsfonts all 1:8.11+urwcyr1.0.7~pre44-4.4 [3125 kB] Get:49 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get:50 http://deb.debian.org/debian buster/main amd64 python3-dendropy all 4.4.0-1 [265 kB] Get:51 http://deb.debian.org/debian buster/main amd64 python3-nose all 1.3.7-4 [132 kB] Get:52 http://deb.debian.org/debian buster/main amd64 raxml amd64 8.2.12+dfsg-1 [1275 kB] Get:53 http://deb.debian.org/debian buster/main amd64 gubbins amd64 2.3.4-1 [48.5 kB] Get:54 http://deb.debian.org/debian buster/main amd64 libart-2.0-2 amd64 2.3.21-4 [66.8 kB] Get:55 http://deb.debian.org/debian buster/main amd64 libffi6 amd64 3.2.1-9 [20.8 kB] Get:56 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get:57 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u3 [380 kB] Get:58 http://deb.debian.org/debian buster/main amd64 libgmp10 amd64 2:6.1.2+dfsg-4+deb10u1 [251 kB] Get:59 http://deb.debian.org/debian buster/main amd64 libhogweed4 amd64 3.4.1-1+deb10u1 [141 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libnettle6 amd64 3.4.1-1+deb10u1 [215 kB] Get:61 http://deb.debian.org/debian buster/main amd64 libidn11 amd64 1.33-2.2 [116 kB] Get:62 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get:63 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get:64 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libtasn1-6 amd64 4.13-3 [51.9 kB] Get:66 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get:67 http://deb.debian.org/debian buster/main amd64 libwebpdemux2 amd64 0.6.1-2+deb10u1 [87.6 kB] Get:68 http://deb.debian.org/debian buster/main amd64 multiarch-support amd64 2.28-10+deb10u1 [216 kB] Get:69 http://deb.debian.org/debian buster/main amd64 ncbi-data all 6.1.20170106+dfsg1-0+deb10u2 [3552 kB] Get:70 http://deb.debian.org/debian buster/main amd64 python-renderpm amd64 3.5.13-1+deb10u1 [76.6 kB] Get:71 http://deb.debian.org/debian buster/main amd64 python-reportlab-accel amd64 3.5.13-1+deb10u1 [39.8 kB] Get:72 http://deb.debian.org/debian buster/main amd64 python-reportlab all 3.5.13-1+deb10u1 [545 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.3 MB in 0s (20.9 MB/s) (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 ... 13807 files and directories currently installed.) Preparing to unpack .../libpam0g_1.3.1-5_amd64.deb ... Unpacking libpam0g:amd64 (1.3.1-5) over (1.1.8-3.6) ... Setting up libpam0g:amd64 (1.3.1-5) ... Checking for services that may need to be restarted...Checking init scripts... Nothing to restart. (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 ... 13807 files and directories currently installed.) Preparing to unpack .../libselinux1_2.8-1+b1_amd64.deb ... Unpacking libselinux1:amd64 (2.8-1+b1) over (2.6-3+b3) ... Setting up libselinux1:amd64 (2.8-1+b1) ... (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 ... 13805 files and directories currently installed.) Preparing to unpack .../libsemanage-common_2.8-2_all.deb ... Unpacking libsemanage-common (2.8-2) over (2.6-2) ... Setting up libsemanage-common (2.8-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13804 files and directories currently installed.) Preparing to unpack .../libsemanage1_2.8-2_amd64.deb ... Unpacking libsemanage1:amd64 (2.8-2) over (2.6-2) ... Setting up libsemanage1:amd64 (2.8-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13803 files and directories currently installed.) Preparing to unpack .../bzip2_1.0.6-9.2~deb10u1_amd64.deb ... Unpacking bzip2 (1.0.6-9.2~deb10u1) over (1.0.6-8.1) ... Preparing to unpack .../libbz2-1.0_1.0.6-9.2~deb10u1_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.6-9.2~deb10u1) over (1.0.6-8.1) ... Setting up libbz2-1.0:amd64 (1.0.6-9.2~deb10u1) ... (Reading database ... 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Preparing to unpack .../33-python-reportlab_3.5.13-1+deb10u1_all.deb ... Unpacking python-reportlab (3.5.13-1+deb10u1) over (3.3.0-2+deb9u1) ... Setting up libart-2.0-2:amd64 (2.3.21-4) ... Setting up readline-common (7.0-5) ... Setting up libnettle6:amd64 (3.4.1-1+deb10u1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Setting up mime-support (3.62) ... Installing new version of config file /etc/mime.types ... Setting up gsfonts (1:8.11+urwcyr1.0.7~pre44-4.4) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up python-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Setting up liblcms2-2:amd64 (2.9-3) ... Setting up python-reportlab (3.5.13-1+deb10u1) ... Setting up multiarch-support (2.28-10+deb10u1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up libfreetype6:amd64 (2.9.1-3+deb10u3) ... Setting up libtasn1-6:amd64 (4.13-3) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up bzip2 (1.0.6-9.2~deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up raxml (8.2.12+dfsg-1) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-4+deb10u1) ... Setting up ncbi-data (6.1.20170106+dfsg1-0+deb10u2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up fasttree (2.1.10-2) ... Setting up python3-nose (1.3.7-4) ... Setting up xz-utils (5.2.4-1+deb10u1) ... Setting up python-renderpm:amd64 (3.5.13-1+deb10u1) ... Setting up libffi6:amd64 (3.2.1-9) ... Setting up python3-dendropy (4.4.0-1) ... Setting up dh-python (3.20190308) ... Setting up libidn11:amd64 (1.33-2.2) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up netbase (5.6) ... Installing new version of config file /etc/services ... Setting up libwebp6:amd64 (0.6.1-2+deb10u1) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libhogweed4:amd64 (3.4.1-1+deb10u1) ... Setting up gubbins (2.3.4-1) ... Setting up libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m52.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', '-y', 'upgrade'] 0m52.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', '-yf', 'dist-upgrade'] 1m27.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: dh-python libart-2.0-2 libblas-common libgdbm3 libgfortran3 libidn11 libperl5.24 libpython3.5-minimal libpython3.5-stdlib libwebpmux2 python3-distutils python3-lib2to3 python3.5 python3.5-minimal rename Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: ca-certificates e2fsprogs-l10n fdisk gcc-8-base libcom-err2 libext2fs2 libgdbm-compat4 libgdbm6 libgfortran5 libgpg-error-l10n libgpm2 libidn2-0 libimagequant0 liblmdb0 libmbedcrypto3 libmbedtls12 libmbedx509-0 libncursesw6 libperl5.28 libpython2-stdlib libpython3.7-minimal libpython3.7-stdlib libseccomp2 libtinfo6 libunistring2 libwebpmux3 libzstd1 openssl perl-modules-5.28 python-olefile python-pkg-resources python2 python2-minimal python3-distutils python3-lib2to3 python3-olefile python3.7 python3.7-minimal The following packages will be upgraded: apt bash coreutils dash dpkg e2fslibs e2fsprogs gpgv libapt-pkg5.0 libblas3 libblkid1 libc-bin libc6 libcomerr2 libexpat1 libfdisk1 libgcc1 libgnutls30 libgomp1 libgpg-error0 liblapack3 libmount1 libncursesw5 libp11-kit0 libpam-modules libpam-modules-bin libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libquadmath0 libreadline7 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++6 libsystemd0 libtiff5 libtinfo5 libudev1 libuuid1 login mount ncbi-blast+ ncurses-base ncurses-bin perl perl-base python python-biopython python-biopython-doc python-minimal python-numpy python-pil python2.7 python2.7-minimal python3 python3-biopython python3-minimal python3-numpy python3-pil python3-renderpm python3-reportlab python3-reportlab-accel rename util-linux 67 upgraded, 38 newly installed, 0 to remove and 0 not upgraded. Need to get 81.5 MB of archives. After this operation, 105 MB of additional disk space will be used. 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[316 kB] Get:12 http://deb.debian.org/debian buster/main amd64 libgnutls30 amd64 3.6.7-4+deb10u8 [1126 kB] Get:13 http://deb.debian.org/debian buster/main amd64 libseccomp2 amd64 2.3.3-4 [41.4 kB] Get:14 http://deb.debian.org/debian buster/main amd64 libgpg-error0 amd64 1.35-1 [71.1 kB] Get:15 http://deb.debian.org/debian buster/main amd64 gpgv amd64 2.2.12-1+deb10u2 [584 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libstdc++6 amd64 8.3.0-6 [395 kB] Get:17 http://deb.debian.org/debian buster/main amd64 libapt-pkg5.0 amd64 1.8.2.3 [967 kB] Get:18 http://deb.debian.org/debian buster/main amd64 apt amd64 1.8.2.3 [1418 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libsystemd0 amd64 241-7~deb10u8 [331 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libudev1 amd64 241-7~deb10u8 [151 kB] Get:21 http://deb.debian.org/debian buster/main amd64 dpkg amd64 1.19.8 [2210 kB] Get:22 http://deb.debian.org/debian buster/main amd64 dash amd64 0.5.10.2-5 [112 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libcom-err2 amd64 1.44.5-1+deb10u3 [68.4 kB] Get:24 http://deb.debian.org/debian buster/main amd64 libcomerr2 amd64 1.44.5-1+deb10u3 [64.2 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libext2fs2 amd64 1.44.5-1+deb10u3 [221 kB] Get:26 http://deb.debian.org/debian buster/main amd64 e2fslibs amd64 1.44.5-1+deb10u3 [64.2 kB] Get:27 http://deb.debian.org/debian buster/main amd64 e2fsprogs amd64 1.44.5-1+deb10u3 [576 kB] Get:28 http://deb.debian.org/debian buster/main amd64 libuuid1 amd64 2.33.1-0.1 [78.3 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libblkid1 amd64 2.33.1-0.1 [195 kB] Get:30 http://deb.debian.org/debian buster/main amd64 libsmartcols1 amd64 2.33.1-0.1 [150 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libfdisk1 amd64 2.33.1-0.1 [234 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libncursesw6 amd64 6.1+20181013-2+deb10u2 [132 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libmount1 amd64 2.33.1-0.1 [207 kB] Get:34 http://deb.debian.org/debian buster/main amd64 fdisk amd64 2.33.1-0.1 [179 kB] Get:35 http://deb.debian.org/debian buster/main amd64 login amd64 1:4.5-1.1 [751 kB] Get:36 http://deb.debian.org/debian buster/main amd64 util-linux amd64 2.33.1-0.1 [1062 kB] Get:37 http://deb.debian.org/debian buster/main amd64 mount amd64 2.33.1-0.1 [174 kB] Get:38 http://deb.debian.org/debian buster/main amd64 ncurses-bin amd64 6.1+20181013-2+deb10u2 [406 kB] Get:39 http://deb.debian.org/debian buster/main amd64 perl-modules-5.28 all 5.28.1-6+deb10u1 [2873 kB] Get:40 http://deb.debian.org/debian buster/main amd64 libgdbm6 amd64 1.18.1-4 [64.7 kB] Get:41 http://deb.debian.org/debian buster/main amd64 libgdbm-compat4 amd64 1.18.1-4 [44.1 kB] Get:42 http://deb.debian.org/debian buster/main amd64 libperl5.28 amd64 5.28.1-6+deb10u1 [3894 kB] Get:43 http://deb.debian.org/debian buster/main amd64 perl amd64 5.28.1-6+deb10u1 [204 kB] Get:44 http://deb.debian.org/debian buster/main amd64 perl-base amd64 5.28.1-6+deb10u1 [1514 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libtinfo5 amd64 6.1+20181013-2+deb10u2 [321 kB] Get:46 http://deb.debian.org/debian buster/main amd64 libncursesw5 amd64 6.1+20181013-2+deb10u2 [118 kB] Get:47 http://deb.debian.org/debian buster/main amd64 ncurses-base all 6.1+20181013-2+deb10u2 [258 kB] Get:48 http://deb.debian.org/debian buster/main amd64 libpam-modules-bin amd64 1.3.1-5 [107 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libpam-modules amd64 1.3.1-5 [309 kB] Get:50 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u3 [1551 kB] Get:51 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get:52 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get:53 http://deb.debian.org/debian buster/main amd64 libquadmath0 amd64 8.3.0-6 [133 kB] Get:54 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get:55 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get:56 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get:57 http://deb.debian.org/debian buster/main amd64 python-numpy amd64 1:1.16.2-1 [2101 kB] Get:58 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get:59 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:61 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get:62 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get:63 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get:64 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get:65 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get:66 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:67 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:68 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:69 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:70 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get:71 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get:72 http://deb.debian.org/debian buster/main amd64 python3-renderpm amd64 3.5.13-1+deb10u1 [76.8 kB] Get:73 http://deb.debian.org/debian buster/main amd64 python3-biopython amd64 1.73+dfsg-1 [1287 kB] Get:74 http://deb.debian.org/debian buster/main amd64 python3-reportlab-accel amd64 3.5.13-1+deb10u1 [35.3 kB] Get:75 http://deb.debian.org/debian buster/main amd64 python3-numpy amd64 1:1.16.2-1 [2119 kB] Get:76 http://deb.debian.org/debian buster/main amd64 python3-pil amd64 5.4.1-2+deb10u3 [395 kB] Get:77 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get:78 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get:79 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get:80 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get:81 http://deb.debian.org/debian buster/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get:82 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u4 [271 kB] Get:83 http://deb.debian.org/debian buster/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u1 [97.8 kB] Get:84 http://deb.debian.org/debian buster/main amd64 python3-reportlab all 3.5.13-1+deb10u1 [541 kB] Get:85 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get:86 http://deb.debian.org/debian buster/main amd64 libss2 amd64 1.44.5-1+deb10u3 [72.9 kB] Get:87 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1n-0+deb10u3 [855 kB] Get:88 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get:89 http://deb.debian.org/debian buster/main amd64 e2fsprogs-l10n all 1.44.5-1+deb10u3 [504 kB] Get:90 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB] Get:91 http://deb.debian.org/debian buster/main amd64 libgpg-error-l10n all 1.35-1 [97.6 kB] Get:92 http://deb.debian.org/debian buster/main amd64 libgpm2 amd64 1.20.7-5 [35.1 kB] Get:93 http://deb.debian.org/debian buster/main amd64 liblmdb0 amd64 0.9.22-1 [45.0 kB] Get:94 http://deb.debian.org/debian buster/main amd64 libmbedcrypto3 amd64 2.16.0-1 [209 kB] Get:95 http://deb.debian.org/debian buster/main amd64 libmbedx509-0 amd64 2.16.0-1 [91.4 kB] Get:96 http://deb.debian.org/debian buster/main amd64 libmbedtls12 amd64 2.16.0-1 [130 kB] Get:97 http://deb.debian.org/debian buster/main amd64 ncbi-blast+ amd64 2.8.1-1+deb10u1 [10.9 MB] Get:98 http://deb.debian.org/debian buster/main amd64 python-biopython amd64 1.73+dfsg-1 [1334 kB] Get:99 http://deb.debian.org/debian buster/main amd64 python-biopython-doc all 1.73+dfsg-1 [14.1 MB] Get:100 http://deb.debian.org/debian buster/main amd64 python-olefile all 0.46-1 [35.9 kB] Get:101 http://deb.debian.org/debian buster/main amd64 python-pil amd64 5.4.1-2+deb10u3 [395 kB] Get:102 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get:103 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get:104 http://deb.debian.org/debian buster/main amd64 python3-olefile all 0.46-1 [35.9 kB] Get:105 http://deb.debian.org/debian buster/main amd64 rename all 1.10-1 [17.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 81.5 MB in 4s (19.3 MB/s) (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 ... 13243 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libtinfo6:amd64 (6.1+20181013-2+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 ... 13253 files and directories currently installed.) Preparing to unpack .../archives/bash_5.0-4_amd64.deb ... Unpacking bash (5.0-4) over (4.4-5) ... Setting up bash (5.0-4) ... Installing new version of config file /etc/bash.bashrc ... Installing new version of config file /etc/skel/.profile ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (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 ... 13254 files and directories currently installed.) Preparing to unpack .../libzstd1_1.3.8+dfsg-3+deb10u2_amd64.deb ... Unpacking libzstd1:amd64 (1.3.8+dfsg-3+deb10u2) ... Setting up libzstd1:amd64 (1.3.8+dfsg-3+deb10u2) ... Selecting previously unselected package libunistring2: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 ... 13260 files and directories currently installed.) Preparing to unpack .../libunistring2_0.9.10-1_amd64.deb ... Unpacking libunistring2:amd64 (0.9.10-1) ... Setting up libunistring2:amd64 (0.9.10-1) ... Selecting previously unselected package libidn2-0:amd64. (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 ... 13300 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.7-4+deb10u8_amd64.deb ... Unpacking libgnutls30:amd64 (3.6.7-4+deb10u8) over (3.5.8-5+deb9u5) ... Setting up libgnutls30:amd64 (3.6.7-4+deb10u8) ... Selecting previously unselected package libseccomp2:amd64. (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 ... 15556 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.7.3-1_amd64.deb ... Unpacking python3-minimal (3.7.3-1) over (3.5.3-1) ... Setting up python3-minimal (3.7.3-1) ... (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 ... 15556 files and directories currently installed.) Preparing to unpack .../0-python3_3.7.3-1_amd64.deb ... Unpacking python3 (3.7.3-1) over (3.5.3-1) ... Selecting previously unselected package libpython3.7-stdlib:amd64. Preparing to unpack .../1-libpython3.7-stdlib_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package python3.7. 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Unpacking python-olefile (0.46-1) ... Preparing to unpack .../14-python-pil_5.4.1-2+deb10u3_amd64.deb ... Unpacking python-pil:amd64 (5.4.1-2+deb10u3) over (4.0.0-4+deb9u1) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../15-python3-lib2to3_3.7.3-1_all.deb ... Unpacking python3-lib2to3 (3.7.3-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../16-python3-distutils_3.7.3-1_all.deb ... Unpacking python3-distutils (3.7.3-1) ... Selecting previously unselected package python3-olefile. Preparing to unpack .../17-python3-olefile_0.46-1_all.deb ... Unpacking python3-olefile (0.46-1) ... Preparing to unpack .../18-rename_1.10-1_all.deb ... Unpacking rename (1.10-1) over (0.20-4) ... Setting up perl-modules-5.28 (5.28.1-6+deb10u1) ... Setting up liblmdb0:amd64 (0.9.22-1) ... Setting up apt (1.8.2.3) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt-compat ... Setting up libgpm2:amd64 (1.20.7-5) ... Setting up e2fslibs:amd64 (1.44.5-1+deb10u3) ... Setting up e2fsprogs-l10n (1.44.5-1+deb10u3) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Setting up libgomp1:amd64 (8.3.0-6) ... Setting up libquadmath0:amd64 (8.3.0-6) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up util-linux (2.33.1-0.1) ... update-alternatives: warning: alternative /usr/bin/pg (part of link group pager) doesn't exist; removing from list of alternatives Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up mount (2.33.1-0.1) ... Setting up libcomerr2:amd64 (1.44.5-1+deb10u3) ... Setting up python-biopython-doc (1.73+dfsg-1) ... Setting up libmbedcrypto3:amd64 (2.16.0-1) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Setting up openssl (1.1.1n-0+deb10u3) ... Setting up libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Setting up libgpg-error-l10n (1.35-1) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libgdbm6:amd64 (1.18.1-4) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libmbedx509-0:amd64 (2.16.0-1) ... Setting up libmbedtls12:amd64 (2.16.0-1) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. 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 libgdbm-compat4:amd64 (1.18.1-4) ... Setting up libperl5.28:amd64 (5.28.1-6+deb10u1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3.7 (3.7.3-2+deb10u3) ... 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 python3 (3.7.3-1) ... Setting up python2 (2.7.16-1) ... Setting up python3-pil:amd64 (5.4.1-2+deb10u3) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up perl (5.28.1-6+deb10u1) ... Removing obsolete conffile /etc/perl/sitecustomize.pl ... Setting up python3-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Setting up python3-numpy (1:1.16.2-1) ... Setting up python3-reportlab (3.5.13-1+deb10u1) ... Setting up python3-biopython (1.73+dfsg-1) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python (2.7.16-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up python3-renderpm:amd64 (3.5.13-1+deb10u1) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up python3-olefile (0.46-1) ... Setting up rename (1.10-1) ... Setting up python-pil:amd64 (5.4.1-2+deb10u3) ... Setting up ncbi-blast+ (2.8.1-1+deb10u1) ... Setting up python-olefile (0.46-1) ... Setting up python-numpy (1:1.16.2-1) ... Setting up python-biopython (1.73+dfsg-1) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... Processing triggers for mime-support (3.62) ... Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 1m27.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', '-yf', 'dist-upgrade'] 1m27.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m28.9s DUMP: f6fc0f2636004ef589309651dfd778f4 - 1m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'show', '--no-all-versions', 'gubbins'] 1m29.2s DUMP: Package: gubbins Version: 2.3.4-1 Installed-Size: 187 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), zlib1g (>= 1:1.1.4), python3-biopython, python3-dendropy, python3-nose, python3-reportlab, python3:any, python3, fasttree, raxml (>= 8) Description-en: phylogenetic analysis of genome sequences Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. . Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences. Description-md5: cc258d495d1b902fa507e53b5cc3902e Homepage: https://sanger-pathogens.github.io/gubbins/ Section: science Priority: optional Filename: pool/main/g/gubbins/gubbins_2.3.4-1_amd64.deb Size: 48528 MD5sum: 46836e385ecc89d2dfcccd092f3cbdeb SHA256: 3587556fb6ef7f72a6856b7b9a96b0e0517b3e41351d2172dd1483d160bc33da 1m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'show', '--no-all-versions', 'gubbins'] 1m29.2s INFO: apt-cache knows about the following packages: gubbins 1m29.2s INFO: Running scripts pre_install 1m29.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_database-server'] 1m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_database-server'] 1m29.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_exceptions'] 1m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_exceptions'] 1m29.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_extras'] 1m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_extras'] 1m29.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_foreign_architecture'] 1m29.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_foreign_architecture'] 1m29.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m29.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m29.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'policy'] 1m29.3s 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=oldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m29.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'policy'] 1m29.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'policy', 'gubbins'] 1m29.4s DUMP: gubbins: Installed: 2.3.4-1 Candidate: 2.3.4-1 Version table: *** 2.3.4-1 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 1m29.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'policy', 'gubbins'] 1m29.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', '-y', 'install', 'gubbins'] 1m29.9s DUMP: Reading package lists... Building dependency tree... Reading state information... gubbins is already the newest version (2.3.4-1). The following packages were automatically installed and are no longer required: dh-python libart-2.0-2 libblas-common libgdbm3 libgfortran3 libidn11 libperl5.24 libpython3.5-minimal libpython3.5-stdlib libwebpmux2 python3-distutils python3-lib2to3 python3.5 python3.5-minimal rename Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', '-y', 'install', 'gubbins'] 1m29.9s INFO: Running scripts post_install 1m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_install_exceptions'] 1m30.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_install_exceptions'] 1m30.0s INFO: Running scripts post_distupgrade 1m30.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m30.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m30.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_distupgrade_exceptions'] 1m30.1s DUMP: Running pam-auth-update... 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_distupgrade_exceptions'] 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_distupgrade_zz_backports'] 1m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_distupgrade_zz_backports'] 1m30.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 1m31.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 1m31.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 1m31.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 1m31.7s INFO: Running scripts pre_install 1m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_database-server'] 1m31.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_database-server'] 1m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_exceptions'] 1m31.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_exceptions'] 1m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_extras'] 1m31.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_extras'] 1m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_foreign_architecture'] 1m31.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_foreign_architecture'] 1m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'policy'] 1m31.8s 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=oldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'policy'] 1m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'policy', 'gubbins'] 1m31.8s DUMP: gubbins: Installed: 2.3.4-1 Candidate: 2.3.4-1 Version table: *** 2.3.4-1 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 1m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-cache', 'policy', 'gubbins'] 1m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', '-y', 'install', 'gubbins=2.3.4-1'] 1m32.3s DUMP: Reading package lists... Building dependency tree... Reading state information... gubbins is already the newest version (2.3.4-1). The following packages were automatically installed and are no longer required: dh-python libart-2.0-2 libblas-common libgdbm3 libgfortran3 libidn11 libperl5.24 libpython3.5-minimal libpython3.5-stdlib libwebpmux2 python3-distutils python3-lib2to3 python3.5 python3.5-minimal rename Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m32.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', '-y', 'install', 'gubbins=2.3.4-1'] 1m32.3s INFO: Running scripts post_install 1m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_install_exceptions'] 1m32.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_install_exceptions'] 1m32.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 1m33.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 1m34.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', '-ac', '--ignore-obsolete'] 1m37.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', '-ac', '--ignore-obsolete'] 1m37.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m37.0s DUMP: 0.15.6 1m37.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m37.0s INFO: Running adequate version 0.15.6 now. 1m37.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'gubbins'] 1m37.4s DUMP: gubbins: undefined-symbol /usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 => gzclose gubbins: undefined-symbol /usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 => gzread gubbins: undefined-symbol /usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 => gzopen 1m37.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'gubbins'] 1m37.4s ERROR: WARN: Inadequate results from running adequate! gubbins: undefined-symbol /usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 => gzclose gubbins: undefined-symbol /usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 => gzread gubbins: undefined-symbol /usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 => gzopen 1m37.4s ERROR: WARN: Running adequate resulted in inadequate tags found: undefined-symbol 1m37.4s INFO: Running scripts pre_remove 1m37.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m37.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m37.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m37.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m37.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m40.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m40.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m41.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m41.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m41.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m41.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_remove_exceptions'] 1m41.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/pre_remove_exceptions'] 1m41.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m41.1s 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 bzip2 bzip2 1.0.6-9.2~deb10u1 install ok installed ca-certificates ca-certificates 20200601~deb10u2 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 dh-python dh-python 3.20190308 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fslibs:amd64 e2fslibs 1.44.5-1+deb10u3 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed e2fsprogs-l10n e2fsprogs-l10n 1.44.5-1+deb10u3 install ok installed fasttree fasttree 2.1.10-2 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed file file 1:5.35-4+deb10u2 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 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 gsfonts gsfonts 1:8.11+urwcyr1.0.7~pre44-4.4 install ok installed gubbins gubbins 2.3.4-1 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 libart-2.0-2:amd64 libart-2.0-2 2.3.21-4 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 libblas-common libblas-common 3.7.0-2 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~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 libcomerr2:amd64 libcomerr2 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 libexpat1:amd64 libexpat1 2.2.6-2+deb10u4 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 libgdbm-compat4:amd64 libgdbm-compat4 1.18.1-4 install ok installed libgdbm3:amd64 libgdbm3 1.8.3-14 install ok installed libgdbm6:amd64 libgdbm6 1.18.1-4 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 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+deb10u8 install ok installed libgomp1:amd64 libgomp1 8.3.0-6 install ok installed libgpg-error-l10n libgpg-error-l10n 1.35-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libgpm2:amd64 libgpm2 1.20.7-5 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libidn11:amd64 libidn11 1.33-2.2 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 liblapack3:amd64 liblapack3 3.8.0-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.9-3 install ok installed liblmdb0:amd64 liblmdb0 0.9.22-1 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 libmagic-mgc libmagic-mgc 1:5.35-4+deb10u2 install ok installed libmagic1:amd64 libmagic1 1:5.35-4+deb10u2 install ok installed libmbedcrypto3:amd64 libmbedcrypto3 2.16.0-1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.0-1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.0-1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libmpdec2:amd64 libmpdec2 2.4.2-2 install ok installed libncursesw5:amd64 libncursesw5 6.1+20181013-2+deb10u2 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 libperl5.24:amd64 libperl5.24 5.24.1-3+deb9u7 install ok installed libperl5.28:amd64 libperl5.28 5.28.1-6+deb10u1 install ok installed libpng16-16:amd64 libpng16-16 1.6.36-6 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+deb10u1 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.16-2+deb10u1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.7.3-1 install ok installed libpython3.5-minimal:amd64 libpython3.5-minimal 3.5.3-1+deb9u1 install ok installed libpython3.5-stdlib:amd64 libpython3.5-stdlib 3.5.3-1+deb9u1 install ok installed libpython3.7-minimal:amd64 libpython3.7-minimal 3.7.3-2+deb10u3 install ok installed libpython3.7-stdlib:amd64 libpython3.7-stdlib 3.7.3-2+deb10u3 install ok installed libquadmath0:amd64 libquadmath0 8.3.0-6 install ok installed libreadline7:amd64 libreadline7 7.0-5 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+deb10u1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libssl1.1:amd64 libssl1.1 1.1.1n-0+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 libtiff5:amd64 libtiff5 4.1.0+git191117-2~deb10u4 install ok installed libtinfo5:amd64 libtinfo5 6.1+20181013-2+deb10u2 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 libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2+deb10u1 install ok installed libwebpdemux2:amd64 libwebpdemux2 0.6.1-2+deb10u1 install ok installed libwebpmux2:amd64 libwebpmux2 0.5.2-1 install ok installed libwebpmux3:amd64 libwebpmux3 0.6.1-2+deb10u1 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 multiarch-support multiarch-support 2.28-10+deb10u1 install ok installed ncbi-blast+ ncbi-blast+ 2.8.1-1+deb10u1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-0+deb10u2 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 netbase netbase 5.6 install ok installed openssl openssl 1.1.1n-0+deb10u3 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl perl 5.28.1-6+deb10u1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed perl-modules-5.24 perl-modules-5.24 5.24.1-3+deb9u7 install ok installed perl-modules-5.28 perl-modules-5.28 5.28.1-6+deb10u1 install ok installed python python 2.7.16-1 install ok installed python-biopython python-biopython 1.73+dfsg-1 install ok installed python-biopython-doc python-biopython-doc 1.73+dfsg-1 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-olefile python-olefile 0.46-1 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-renderpm:amd64 python-renderpm 3.5.13-1+deb10u1 install ok installed python-reportlab python-reportlab 3.5.13-1+deb10u1 install ok installed python-reportlab-accel:amd64 python-reportlab-accel 3.5.13-1+deb10u1 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+deb10u1 install ok installed python2.7-minimal python2.7-minimal 2.7.16-2+deb10u1 install ok installed python3 python3 3.7.3-1 install ok installed python3-biopython python3-biopython 1.73+dfsg-1 install ok installed python3-dendropy python3-dendropy 4.4.0-1 install ok installed python3-distutils python3-distutils 3.7.3-1 install ok installed python3-lib2to3 python3-lib2to3 3.7.3-1 install ok installed python3-minimal python3-minimal 3.7.3-1 install ok installed python3-nose python3-nose 1.3.7-4 install ok installed python3-numpy python3-numpy 1:1.16.2-1 install ok installed python3-olefile python3-olefile 0.46-1 install ok installed python3-pil:amd64 python3-pil 5.4.1-2+deb10u3 install ok installed python3-pkg-resources python3-pkg-resources 40.8.0-1 install ok installed python3-renderpm:amd64 python3-renderpm 3.5.13-1+deb10u1 install ok installed python3-reportlab python3-reportlab 3.5.13-1+deb10u1 install ok installed python3-reportlab-accel:amd64 python3-reportlab-accel 3.5.13-1+deb10u1 install ok installed python3.5 python3.5 3.5.3-1+deb9u1 install ok installed python3.5-minimal python3.5-minimal 3.5.3-1+deb9u1 install ok installed python3.7 python3.7 3.7.3-2+deb10u3 install ok installed python3.7-minimal python3.7-minimal 3.7.3-2+deb10u3 install ok installed raxml raxml 8.2.12+dfsg-1 install ok installed readline-common readline-common 7.0-5 install ok installed rename rename 1.10-1 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.12 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed xz-utils xz-utils 5.2.4-1+deb10u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 1m41.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m41.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', 'remove', 'bzip2', 'dh-python', 'fasttree', 'file', 'gsfonts', 'libart-2.0-2:amd64', 'libblas-common', 'libblas3:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblmdb0:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec2:amd64', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpng16-16:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.5-minimal:amd64', 'libpython3.5-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'libsqlite3-0:amd64', 'libtiff5:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux2:amd64', 'libwebpmux3:amd64', 'mime-support', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'perl', 'perl-modules-5.24', 'perl-modules-5.28', 'python', 'python-biopython', 'python-biopython-doc', 'python-minimal', 'python-numpy', 'python-olefile', 'python-pil:amd64', 'python-pkg-resources', 'python-renderpm:amd64', 'python-reportlab', 'python-reportlab-accel:amd64', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-biopython', 'python3-dendropy', 'python3-distutils', 'python3-lib2to3', 'python3-minimal', 'python3-nose', 'python3-numpy', 'python3-olefile', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.5', 'python3.5-minimal', 'python3.7', 'python3.7-minimal', 'raxml', 'readline-common', 'rename', 'xz-utils', 'gubbins'] 1m45.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bzip2 dh-python fasttree file gsfonts gubbins libart-2.0-2 libblas-common libblas3 libexpat1 libfreetype6 libgdbm-compat4 libgdbm3 libgdbm6 libgfortran3 libgfortran5 libgomp1 libidn11 libimagequant0 libjbig0 libjpeg62-turbo liblapack3 liblcms2-2 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec2 libperl5.24 libperl5.28 libpng16-16 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline7 libsqlite3-0 libtiff5 libwebp6 libwebpdemux2 libwebpmux2 libwebpmux3 mime-support ncbi-blast+ ncbi-data netbase perl perl-modules-5.24 perl-modules-5.28 python python-biopython python-biopython-doc python-minimal python-numpy python-olefile python-pil python-pkg-resources python-renderpm python-reportlab python-reportlab-accel python2 python2-minimal python2.7 python2.7-minimal python3 python3-biopython python3-dendropy python3-distutils python3-lib2to3 python3-minimal python3-nose python3-numpy python3-olefile python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3.5 python3.5-minimal python3.7 python3.7-minimal raxml readline-common rename xz-utils 0 upgraded, 0 newly installed, 94 to remove and 0 not upgraded. After this operation, 333 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 ... 16588 files and directories currently installed.) Removing bzip2 (1.0.6-9.2~deb10u1) ... Removing dh-python (3.20190308) ... Removing gubbins (2.3.4-1) ... Removing fasttree (2.1.10-2) ... Removing file (1:5.35-4+deb10u2) ... Removing python3-renderpm:amd64 (3.5.13-1+deb10u1) ... Removing python-renderpm:amd64 (3.5.13-1+deb10u1) ... Removing gsfonts (1:8.11+urwcyr1.0.7~pre44-4.4) ... Removing libart-2.0-2:amd64 (2.3.21-4) ... Removing libblas-common (3.7.0-2) ... Removing python3-biopython (1.73+dfsg-1) ... Removing python3-numpy (1:1.16.2-1) ... 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 python3.5 (3.5.3-1+deb9u1) ... Removing python3.5-minimal (3.5.3-1+deb9u1) ... Removing python3-distutils (3.7.3-1) ... Removing python3-dendropy (4.4.0-1) ... Removing python3-reportlab (3.5.13-1+deb10u1) ... Removing python3-pil:amd64 (5.4.1-2+deb10u3) ... Removing rename (1.10-1) ... Removing ncbi-blast+ (2.8.1-1+deb10u1) ... Removing perl (5.28.1-6+deb10u1) ... Removing libperl5.28:amd64 (5.28.1-6+deb10u1) ... Removing libgdbm-compat4:amd64 (1.18.1-4) ... Removing libperl5.24:amd64 (5.24.1-3+deb9u7) ... Removing libgdbm3:amd64 (1.8.3-14) ... Removing libgdbm6:amd64 (1.18.1-4) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libgfortran5:amd64 (8.3.0-6) ... Removing libgomp1:amd64 (8.3.0-6) ... Removing libidn11:amd64 (1.33-2.2) ... Removing python-reportlab (3.5.13-1+deb10u1) ... Removing python-pil:amd64 (5.4.1-2+deb10u3) ... Removing libimagequant0:amd64 (2.12.2-1.1) ... Removing libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Removing liblcms2-2:amd64 (2.9-3) ... Removing liblmdb0:amd64 (0.9.22-1) ... Removing libmagic1:amd64 (1:5.35-4+deb10u2) ... Removing libmagic-mgc (1:5.35-4+deb10u2) ... Removing libmbedtls12:amd64 (2.16.0-1) ... Removing libmbedx509-0:amd64 (2.16.0-1) ... Removing libmbedcrypto3:amd64 (2.16.0-1) ... Removing libpython3.5-stdlib:amd64 (3.5.3-1+deb9u1) ... Removing python-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Removing python-pkg-resources (40.8.0-1) ... Removing python-olefile (0.46-1) ... Removing python (2.7.16-1) ... Removing libpython-stdlib:amd64 (2.7.16-1) ... Removing python2 (2.7.16-1) ... Removing libpython2-stdlib:amd64 (2.7.16-1) ... Removing python2.7 (2.7.16-2+deb10u1) ... Removing libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Removing python-minimal (2.7.16-1) ... Removing libpython3.5-minimal:amd64 (3.5.3-1+deb9u1) ... Removing libquadmath0:amd64 (8.3.0-6) ... Removing libwebpmux2:amd64 (0.5.2-1) ... Removing libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Removing libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Removing ncbi-data (6.1.20170106+dfsg1-0+deb10u2) ... Removing netbase (5.6) ... Removing perl-modules-5.24 (5.24.1-3+deb9u7) ... Removing perl-modules-5.28 (5.28.1-6+deb10u1) ... Removing python-biopython-doc (1.73+dfsg-1) ... Removing python2-minimal (2.7.16-1) ... Removing python3-lib2to3 (3.7.3-1) ... Removing python3-nose (1.3.7-4) ... Removing python3-olefile (0.46-1) ... Removing python3-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Removing raxml (8.2.12+dfsg-1) ... Removing xz-utils (5.2.4-1+deb10u1) ... Removing python3-pkg-resources (40.8.0-1) ... Removing python3 (3.7.3-1) ... Removing python3.7 (3.7.3-2+deb10u3) ... Removing libfreetype6:amd64 (2.9.1-3+deb10u3) ... Removing libpython3-stdlib:amd64 (3.7.3-1) ... Removing libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec2:amd64 (2.4.2-2) ... Removing libpng16-16:amd64 (1.6.36-6) ... Removing python2.7-minimal (2.7.16-2+deb10u1) ... Removing libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... find: '/usr/lib/python2.7': No such file or directory Removing libreadline7:amd64 (7.0-5) ... Removing libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Removing libwebp6:amd64 (0.6.1-2+deb10u1) ... Removing mime-support (3.62) ... Removing python3-minimal (3.7.3-1) ... Removing readline-common (7.0-5) ... Removing python3.7-minimal (3.7.3-2+deb10u3) ... Removing libexpat1:amd64 (2.2.6-2+deb10u4) ... Removing libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... find: '/usr/lib/python3': No such file or directory Processing triggers for libc-bin (2.28-10+deb10u1) ... 1m45.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', 'remove', 'bzip2', 'dh-python', 'fasttree', 'file', 'gsfonts', 'libart-2.0-2:amd64', 'libblas-common', 'libblas3:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblmdb0:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec2:amd64', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpng16-16:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.5-minimal:amd64', 'libpython3.5-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'libsqlite3-0:amd64', 'libtiff5:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux2:amd64', 'libwebpmux3:amd64', 'mime-support', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'perl', 'perl-modules-5.24', 'perl-modules-5.28', 'python', 'python-biopython', 'python-biopython-doc', 'python-minimal', 'python-numpy', 'python-olefile', 'python-pil:amd64', 'python-pkg-resources', 'python-renderpm:amd64', 'python-reportlab', 'python-reportlab-accel:amd64', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-biopython', 'python3-dendropy', 'python3-distutils', 'python3-lib2to3', 'python3-minimal', 'python3-nose', 'python3-numpy', 'python3-olefile', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.5', 'python3.5-minimal', 'python3.7', 'python3.7-minimal', 'raxml', 'readline-common', 'rename', 'xz-utils', 'gubbins'] 1m45.5s INFO: Running scripts post_remove 1m45.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_remove_exceptions'] 1m45.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_remove_exceptions'] 1m45.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg', '--purge', 'bzip2', 'dh-python', 'fasttree', 'file', 'gsfonts', 'libart-2.0-2:amd64', 'libblas-common', 'libblas3:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblmdb0:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec2:amd64', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpng16-16:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.5-minimal:amd64', 'libpython3.5-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'libsqlite3-0:amd64', 'libtiff5:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux2:amd64', 'libwebpmux3:amd64', 'mime-support', 'ncbi-blast+', 'ncbi-data', 'netbase', 'perl', 'perl-modules-5.24', 'perl-modules-5.28', 'python', 'python-biopython', 'python-biopython-doc', 'python-minimal', 'python-numpy', 'python-olefile', 'python-pil:amd64', 'python-pkg-resources', 'python-renderpm:amd64', 'python-reportlab', 'python-reportlab-accel:amd64', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-biopython', 'python3-dendropy', 'python3-distutils', 'python3-lib2to3', 'python3-minimal', 'python3-nose', 'python3-numpy', 'python3-olefile', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.5', 'python3.5-minimal', 'python3.7', 'python3.7-minimal', 'raxml', 'readline-common', 'rename', 'xz-utils'] 1m45.6s DUMP: dpkg: warning: ignoring request to remove bzip2 which isn't installed dpkg: warning: ignoring request to remove dh-python which isn't installed dpkg: warning: ignoring request to remove fasttree which isn't installed dpkg: warning: ignoring request to remove file which isn't installed (Reading database ... 5026 files and directories currently installed.) Purging configuration files for gsfonts (1:8.11+urwcyr1.0.7~pre44-4.4) ... dpkg: warning: ignoring request to remove libart-2.0-2 which isn't installed dpkg: warning: ignoring request to remove libblas-common which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm3 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgfortran3 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 dpkg: warning: ignoring request to remove libidn11 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 liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove libmagic-mgc which isn't installed Purging configuration files for libmagic1:amd64 (1:5.35-4+deb10u2) ... dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed dpkg: warning: ignoring request to remove libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libmpdec2 which isn't installed dpkg: warning: ignoring request to remove libperl5.24 which isn't installed dpkg: warning: ignoring request to remove libperl5.28 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 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+deb10u1) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.5-minimal:amd64 (3.5.3-1+deb9u1) ... dpkg: warning: ignoring request to remove libpython3.5-stdlib which isn't installed Purging configuration files for libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... dpkg: warning: ignoring request to remove libpython3.7-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 libsqlite3-0 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 libwebpmux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed Purging configuration files for mime-support (3.62) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-0+deb10u2) ... Purging configuration files for netbase (5.6) ... Purging configuration files for perl (5.28.1-6+deb10u1) ... dpkg: warning: ignoring request to remove perl-modules-5.24 which isn't installed dpkg: warning: ignoring request to remove perl-modules-5.28 which isn't installed Purging configuration files for python (2.7.16-1) ... dpkg: warning: ignoring request to remove python-biopython which isn't installed dpkg: warning: ignoring request to remove python-biopython-doc which isn't installed 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-olefile 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-renderpm 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 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+deb10u1) ... Purging configuration files for python3 (3.7.3-1) ... dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-dendropy which isn't installed dpkg: warning: ignoring request to remove python3-distutils which isn't installed dpkg: warning: ignoring request to remove python3-lib2to3 which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-nose which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-olefile which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-renderpm which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-reportlab-accel which isn't installed dpkg: warning: ignoring request to remove python3.5 which isn't installed Purging configuration files for python3.5-minimal (3.5.3-1+deb9u1) ... dpkg: warning: ignoring request to remove python3.7 which isn't installed Purging configuration files for python3.7-minimal (3.7.3-2+deb10u3) ... dpkg: warning: ignoring request to remove raxml which isn't installed Purging configuration files for readline-common (7.0-5) ... dpkg: warning: ignoring request to remove rename which isn't installed dpkg: warning: ignoring request to remove xz-utils which isn't installed 1m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg', '--purge', 'bzip2', 'dh-python', 'fasttree', 'file', 'gsfonts', 'libart-2.0-2:amd64', 'libblas-common', 'libblas3:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblmdb0:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec2:amd64', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpng16-16:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.5-minimal:amd64', 'libpython3.5-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'libsqlite3-0:amd64', 'libtiff5:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux2:amd64', 'libwebpmux3:amd64', 'mime-support', 'ncbi-blast+', 'ncbi-data', 'netbase', 'perl', 'perl-modules-5.24', 'perl-modules-5.28', 'python', 'python-biopython', 'python-biopython-doc', 'python-minimal', 'python-numpy', 'python-olefile', 'python-pil:amd64', 'python-pkg-resources', 'python-renderpm:amd64', 'python-reportlab', 'python-reportlab-accel:amd64', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-biopython', 'python3-dendropy', 'python3-distutils', 'python3-lib2to3', 'python3-minimal', 'python3-nose', 'python3-numpy', 'python3-olefile', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.5', 'python3.5-minimal', 'python3.7', 'python3.7-minimal', 'raxml', 'readline-common', 'rename', 'xz-utils'] 1m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg', '--purge', 'gubbins'] 1m45.6s DUMP: dpkg: warning: ignoring request to remove gubbins which isn't installed 1m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg', '--purge', 'gubbins'] 1m45.6s INFO: Running scripts post_purge 1m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_purge_exceptions'] 1m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_purge_exceptions'] 1m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg', '--purge', '--pending'] 1m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg', '--purge', '--pending'] 1m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg', '--remove', '--pending'] 1m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg', '--remove', '--pending'] 1m45.6s INFO: Running scripts post_test 1m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_test_exceptions'] 1m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'tmp/scripts/post_test_exceptions'] 1m45.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 1m46.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 1m46.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg-divert', '--list'] 1m46.0s 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 1m46.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'dpkg-divert', '--list'] 1m46.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', 'clean'] 1m46.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56', 'apt-get', 'clean'] 1m46.0s DEBUG: Recording chroot state 1m47.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/shm'] 1m47.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/shm'] 1m47.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/console'] 1m47.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/console'] 1m47.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/ptmx'] 1m47.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/ptmx'] 1m47.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/pts'] 1m47.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/dev/pts'] 1m47.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/proc'] 1m47.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56/proc'] 1m47.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 1m47.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp8jjk8g56'] 1m47.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp8jjk8g56 1m47.2s INFO: PASS: Upgrading between Debian distributions. 1m47.2s INFO: PASS: All tests. 1m47.2s INFO: piuparts run ends. ret=0 End: 2023-04-16 18:19:54 GMT