Start: 2023-04-15 07:02:50 GMT [stretch] Package: parsnp Version: 1.2+dfsg-3 Installed-Size: 909 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libgomp1 (>= 4.9), libmuscle-3.7-1, libstdc++6 (>= 5.2), python:any (>= 2.7), python-numpy, fasttree, mummer, phipack Recommends: python-dendropy Description: rapid core genome multi-alignment Homepage: http://harvest.readthedocs.org/en/latest/content/parsnp.html Description-md5: e2e6d59e8a521577f278267009bb94b4 Section: science Priority: optional Filename: pool/main/p/parsnp/parsnp_1.2+dfsg-3_amd64.deb Size: 528254 MD5sum: f943f22eec9bac6fc0c2e774ea658fb5 SHA256: edf52b86999c748c0531567102d33db171e7a6acf401cf9b441faf565b965a37 [buster] Package: parsnp Version: 1.2+dfsg-5 Installed-Size: 913 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.27), libgcc1 (>= 1:3.0), libgomp1 (>= 4.9), libmuscle1 (>= 3.7+4565), libstdc++6 (>= 5.2), python:any, python-numpy, fasttree, mummer, phipack Recommends: python-dendropy Description: rapid core genome multi-alignment Homepage: http://harvest.readthedocs.org/en/latest/content/parsnp.html Description-md5: e2e6d59e8a521577f278267009bb94b4 Section: science Priority: optional Filename: pool/main/p/parsnp/parsnp_1.2+dfsg-5_amd64.deb Size: 528596 MD5sum: 99dcb6548c26d28cdea7dd999fe2db17 SHA256: 25f4ae322a760d6dfc435c45007534adddf2509300476bc6c1466c477c49625d 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 parsnp=1.2+dfsg-5 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 parsnp=1.2+dfsg-5 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpbnc9zbuc 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpbnc9zbuc 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/proc'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/proc'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/pts'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/pts'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/ptmx'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/ptmx'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/console'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/console'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/shm'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/shm'] 0m1.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.3s DEBUG: Created policy-rc.d and chmodded it. 0m1.3s DEBUG: Created resolv.conf. 0m1.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpbnc9zbuc/tmp/scripts/ 0m1.3s INFO: Running scripts post_chroot_unpack 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', 'update'] 0m2.1s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', 'update'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.0s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.0s INFO: Running scripts post_setup 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_setup_dummy_users'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_setup_dummy_users'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_setup_forbid_home'] 0m3.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_setup_forbid_home'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.4s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_setup_zz_backports'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_setup_zz_backports'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster-rcmd/reference-chroot-metadata.dat 0m3.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m3.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m3.7s INFO: Running scripts is_testable 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/is_testable_uninstallable'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/is_testable_uninstallable'] 0m3.7s INFO: Running scripts pre_test 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_test_exceptions'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_test_exceptions'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_test_root_password'] 0m3.7s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_test_root_password'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'show', '--no-all-versions', 'parsnp'] 0m3.9s DUMP: Package: parsnp Version: 1.2+dfsg-3 Installed-Size: 909 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libgomp1 (>= 4.9), libmuscle-3.7-1, libstdc++6 (>= 5.2), python:any (>= 2.7), python-numpy, fasttree, mummer, phipack Recommends: python-dendropy Description-en: rapid core genome multi-alignment Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction. Description-md5: e2e6d59e8a521577f278267009bb94b4 Homepage: http://harvest.readthedocs.org/en/latest/content/parsnp.html Section: science Priority: optional Filename: pool/main/p/parsnp/parsnp_1.2+dfsg-3_amd64.deb Size: 528254 MD5sum: f943f22eec9bac6fc0c2e774ea658fb5 SHA256: edf52b86999c748c0531567102d33db171e7a6acf401cf9b441faf565b965a37 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'show', '--no-all-versions', 'parsnp'] 0m3.9s INFO: apt-cache knows about the following packages: parsnp 0m3.9s INFO: Running scripts pre_install 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_database-server'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_database-server'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_exceptions'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_exceptions'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_extras'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_extras'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'policy'] 0m4.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'policy'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'policy', 'parsnp'] 0m4.0s DUMP: parsnp: Installed: (none) Candidate: 1.2+dfsg-3 Version table: 1.2+dfsg-3 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'policy', 'parsnp'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', '-y', 'install', 'parsnp'] 0m12.6s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bzip2 fasttree file gawk libblas-common libblas3 libexpat1 libffi6 libgdbm3 libgfortran3 libgmp10 libgomp1 liblapack3 libmagic-mgc libmagic1 libmpfr4 libmuscle-3.7-1 libperl5.24 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libsigsegv2 libsqlite3-0 libssl1.1 mime-support mummer netbase perl perl-modules-5.24 phipack python python-dendropy python-minimal python-numpy python-pkg-resources python2.7 python2.7-minimal readline-common rename xz-utils Suggested packages: bzip2-doc gawk-doc perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make python-doc python-tk gcc gfortran python-dev python-nose python-numpy-dbg python-numpy-doc python-setuptools python2.7-doc binutils binfmt-support readline-doc The following NEW packages will be installed: bzip2 fasttree file gawk libblas-common libblas3 libexpat1 libffi6 libgdbm3 libgfortran3 libgmp10 libgomp1 liblapack3 libmagic-mgc libmagic1 libmpfr4 libmuscle-3.7-1 libperl5.24 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libsigsegv2 libsqlite3-0 libssl1.1 mime-support mummer netbase parsnp perl perl-modules-5.24 phipack python python-dendropy python-minimal python-numpy python-pkg-resources python2.7 python2.7-minimal readline-common rename xz-utils 0 upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 29.3 MB of archives. After this operation, 166 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 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libmpfr4 amd64 3.1.5-1 [556 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 gawk amd64 1:4.1.4+dfsg-1 [571 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 netbase all 5.4 [19.1 kB] Get:24 http://deb.debian.org/debian stretch/main amd64 bzip2 amd64 1.0.6-8.1 [47.5 kB] Get:25 http://deb.debian.org/debian stretch/main amd64 libmagic-mgc amd64 1:5.30-1+deb9u3 [222 kB] Get:26 http://deb.debian.org/debian stretch/main amd64 libmagic1 amd64 1:5.30-1+deb9u3 [111 kB] Get:27 http://deb.debian.org/debian stretch/main amd64 file amd64 1:5.30-1+deb9u3 [64.2 kB] Get:28 http://deb.debian.org/debian stretch/main amd64 xz-utils amd64 5.2.2-1.2+b1 [266 kB] Get:29 http://deb.debian.org/debian stretch/main amd64 libblas-common amd64 3.7.0-2 [14.2 kB] Get:30 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:31 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libblas3 amd64 3.7.0-2 [155 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 liblapack3 amd64 3.7.0-2 [2141 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 libmuscle-3.7-1 amd64 3.7+4565-2 [252 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 mummer amd64 3.23+dfsg-2 [809 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 python-numpy amd64 1:1.12.1-3 [1936 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 fasttree amd64 2.1.9-1 [132 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 phipack amd64 0.0.20160614-2 [50.6 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 parsnp amd64 1.2+dfsg-3 [528 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 python-pkg-resources all 33.1.1-1 [166 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 python-dendropy all 4.2.0+dfsg-1 [7496 kB] Get:43 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 29.3 MB in 0s (47.0 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 python-numpy. Preparing to unpack .../15-python-numpy_1%3a1.12.1-3_amd64.deb ... Unpacking python-numpy (1:1.12.1-3) ... Selecting previously unselected package fasttree. Preparing to unpack .../16-fasttree_2.1.9-1_amd64.deb ... Unpacking fasttree (2.1.9-1) ... Selecting previously unselected package phipack. Preparing to unpack .../17-phipack_0.0.20160614-2_amd64.deb ... Unpacking phipack (0.0.20160614-2) ... Selecting previously unselected package parsnp. Preparing to unpack .../18-parsnp_1.2+dfsg-3_amd64.deb ... Unpacking parsnp (1.2+dfsg-3) ... Selecting previously unselected package python-pkg-resources. Preparing to unpack .../19-python-pkg-resources_33.1.1-1_all.deb ... Unpacking python-pkg-resources (33.1.1-1) ... Selecting previously unselected package python-dendropy. Preparing to unpack .../20-python-dendropy_4.2.0+dfsg-1_all.deb ... Unpacking python-dendropy (4.2.0+dfsg-1) ... Selecting previously unselected package rename. Preparing to unpack .../21-rename_0.20-4_all.deb ... Unpacking rename (0.20-4) ... Setting up libquadmath0:amd64 (6.3.0-18+deb9u1) ... Setting up libgomp1:amd64 (6.3.0-18+deb9u1) ... 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 libexpat1:amd64 (2.2.0-2+deb9u3) ... Setting up mime-support (3.60) ... Setting up libblas-common (3.7.0-2) ... Setting up phipack (0.0.20160614-2) ... Setting up libgfortran3:amd64 (6.3.0-18+deb9u1) ... Setting up gawk (1:4.1.4+dfsg-1) ... 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 perl (5.24.1-3+deb9u7) ... update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode 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 libssl1.1:amd64 (1.1.0l-1~deb9u1) ... 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 libmuscle-3.7-1 (3.7+4565-2) ... 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 netbase (5.4) ... Setting up rename (0.20-4) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up mummer (3.23+dfsg-2) ... Setting up liblapack3 (3.7.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up file (1:5.30-1+deb9u3) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up python (2.7.13-2) ... Setting up python-pkg-resources (33.1.1-1) ... Setting up python-numpy (1:1.12.1-3) ... Setting up parsnp (1.2+dfsg-3) ... Setting up python-dendropy (4.2.0+dfsg-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', '-y', 'install', 'parsnp'] 0m12.6s INFO: Running scripts post_install 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_install_exceptions'] 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_install_exceptions'] 0m12.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m13.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m13.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpbnc9zbuc to buster 0m13.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m13.3s INFO: Running scripts pre_distupgrade 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', 'update'] 0m16.7s 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 2s (5382 kB/s) Reading package lists... 0m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', 'update'] 0m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', '-y', 'upgrade'] 0m21.6s 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 gawk gpgv libapt-pkg5.0 libblas3 libblkid1 libc-bin libc6 libcomerr2 libexpat1 libfdisk1 libgcc1 libgomp1 libgpg-error0 liblapack3 libmount1 libncursesw5 libpam-modules libpam-modules-bin libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++6 libsystemd0 libtinfo5 libudev1 libuuid1 login mount ncurses-base ncurses-bin parsnp perl perl-base python python-minimal python-numpy python2.7 python2.7-minimal rename util-linux The following packages will be upgraded: adduser base-files base-passwd bsdutils bzip2 debconf debian-archive-keyring debianutils diffutils fasttree file findutils grep gzip hostname init-system-helpers libacl1 libattr1 libaudit-common libaudit1 libbz2-1.0 libcap-ng0 libdb5.3 libdebconfclient0 libffi6 libgcrypt20 libgmp10 liblz4-1 liblzma5 libmagic-mgc libmagic1 libpam-runtime libpam0g libpcre3 libselinux1 libsemanage-common libsemanage1 libsepol1 libsigsegv2 mime-support multiarch-support mummer netbase passwd phipack python-dendropy python-pkg-resources readline-common sed sensible-utils sysvinit-utils tar xz-utils zlib1g 54 upgraded, 0 newly installed, 0 to remove and 53 not upgraded. Need to get 10.3 MB of archives. After this operation, 65.2 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 fasttree amd64 2.1.10-2 [176 kB] Get:47 http://deb.debian.org/debian buster/main amd64 libffi6 amd64 3.2.1-9 [20.8 kB] Get:48 http://deb.debian.org/debian buster/main amd64 libgmp10 amd64 2:6.1.2+dfsg-4+deb10u1 [251 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:50 http://deb.debian.org/debian buster/main amd64 multiarch-support amd64 2.28-10+deb10u1 [216 kB] Get:51 http://deb.debian.org/debian buster/main amd64 mummer amd64 3.23+dfsg-4 [809 kB] Get:52 http://deb.debian.org/debian buster/main amd64 phipack amd64 0.0.20160614-3 [50.9 kB] Get:53 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get:54 http://deb.debian.org/debian buster/main amd64 python-dendropy all 4.4.0-1 [265 kB] debconf: delaying package configuration, since apt-utils is not installed 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Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-buster-security-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-security-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-jessie-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-jessie-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-jessie-stable.gpg ... (Reading database ... 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Preparing to unpack .../11-multiarch-support_2.28-10+deb10u1_amd64.deb ... Unpacking multiarch-support (2.28-10+deb10u1) over (2.24-11+deb9u4) ... Preparing to unpack .../12-mummer_3.23+dfsg-4_amd64.deb ... Unpacking mummer (3.23+dfsg-4) over (3.23+dfsg-2) ... Preparing to unpack .../13-phipack_0.0.20160614-3_amd64.deb ... Unpacking phipack (0.0.20160614-3) over (0.0.20160614-2) ... Preparing to unpack .../14-python-pkg-resources_40.8.0-1_all.deb ... Unpacking python-pkg-resources (40.8.0-1) over (33.1.1-1) ... Preparing to unpack .../15-python-dendropy_4.4.0-1_all.deb ... Unpacking python-dendropy (4.4.0-1) over (4.2.0+dfsg-1) ... Setting up readline-common (7.0-5) ... Setting up mime-support (3.62) ... Installing new version of config file /etc/mime.types ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up multiarch-support (2.28-10+deb10u1) ... Setting up phipack (0.0.20160614-3) ... Setting up mummer (3.23+dfsg-4) ... Setting up python-pkg-resources (40.8.0-1) ... 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 libgmp10:amd64 (2:6.1.2+dfsg-4+deb10u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up fasttree (2.1.10-2) ... Setting up xz-utils (5.2.4-1+deb10u1) ... Setting up libffi6:amd64 (3.2.1-9) ... Setting up netbase (5.6) ... Installing new version of config file /etc/services ... Setting up python-dendropy (4.4.0-1) ... Setting up file (1:5.35-4+deb10u2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m21.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', '-y', 'upgrade'] 0m21.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', '-yf', 'dist-upgrade'] 0m34.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libblas-common libgdbm3 libgfortran3 libmpfr4 libperl5.24 rename Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libmuscle-3.7-1 The following NEW packages will be installed: ca-certificates e2fsprogs-l10n fdisk gcc-8-base libcom-err2 libext2fs2 libgdbm-compat4 libgdbm6 libgfortran5 libgnutls30 libgpg-error-l10n libgpm2 libhogweed4 libidn2-0 libmpfr6 libmuscle1 libncursesw6 libnettle6 libp11-kit0 libperl5.28 libpython2-stdlib libseccomp2 libtasn1-6 libtinfo6 libunistring2 libzstd1 openssl perl-modules-5.28 python2 python2-minimal The following packages will be upgraded: apt bash coreutils dash dpkg e2fslibs e2fsprogs gawk gpgv libapt-pkg5.0 libblas3 libblkid1 libc-bin libc6 libcomerr2 libexpat1 libfdisk1 libgcc1 libgomp1 libgpg-error0 liblapack3 libmount1 libncursesw5 libpam-modules libpam-modules-bin libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++6 libsystemd0 libtinfo5 libudev1 libuuid1 login mount ncurses-base ncurses-bin parsnp perl perl-base python python-minimal python-numpy python2.7 python2.7-minimal rename util-linux 53 upgraded, 30 newly installed, 1 to remove and 0 not upgraded. Need to get 47.1 MB of archives. After this operation, 72.2 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 libc6 amd64 2.28-10+deb10u1 [2863 kB] Get:2 http://deb.debian.org/debian buster/main amd64 libc-bin amd64 2.28-10+deb10u1 [795 kB] Get:3 http://deb.debian.org/debian buster/main amd64 gcc-8-base amd64 8.3.0-6 [191 kB] Get:4 http://deb.debian.org/debian buster/main amd64 libgcc1 amd64 1:8.3.0-6 [40.6 kB] Get:5 http://deb.debian.org/debian buster/main amd64 libtinfo6 amd64 6.1+20181013-2+deb10u2 [325 kB] Get:6 http://deb.debian.org/debian buster/main amd64 bash amd64 5.0-4 [1378 kB] Get:7 http://deb.debian.org/debian buster/main amd64 coreutils amd64 8.30-3 [2708 kB] Get:8 http://deb.debian.org/debian buster/main amd64 libzstd1 amd64 1.3.8+dfsg-3+deb10u2 [237 kB] Get:9 http://deb.debian.org/debian buster/main amd64 libnettle6 amd64 3.4.1-1+deb10u1 [215 kB] Get:10 http://deb.debian.org/debian buster/main amd64 libhogweed4 amd64 3.4.1-1+deb10u1 [141 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libunistring2 amd64 0.9.10-1 [381 kB] Get:12 http://deb.debian.org/debian buster/main amd64 libidn2-0 amd64 2.0.5-1+deb10u1 [76.7 kB] Get:13 http://deb.debian.org/debian buster/main amd64 libp11-kit0 amd64 0.23.15-2+deb10u1 [316 kB] Get:14 http://deb.debian.org/debian buster/main amd64 libtasn1-6 amd64 4.13-3 [51.9 kB] Get:15 http://deb.debian.org/debian buster/main amd64 libgnutls30 amd64 3.6.7-4+deb10u8 [1126 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libseccomp2 amd64 2.3.3-4 [41.4 kB] Get:17 http://deb.debian.org/debian buster/main amd64 libgpg-error0 amd64 1.35-1 [71.1 kB] Get:18 http://deb.debian.org/debian buster/main amd64 gpgv amd64 2.2.12-1+deb10u2 [584 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libstdc++6 amd64 8.3.0-6 [395 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libapt-pkg5.0 amd64 1.8.2.3 [967 kB] Get:21 http://deb.debian.org/debian buster/main amd64 apt amd64 1.8.2.3 [1418 kB] Get:22 http://deb.debian.org/debian buster/main amd64 libsystemd0 amd64 241-7~deb10u8 [331 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libudev1 amd64 241-7~deb10u8 [151 kB] Get:24 http://deb.debian.org/debian buster/main amd64 dpkg amd64 1.19.8 [2210 kB] Get:25 http://deb.debian.org/debian buster/main amd64 dash amd64 0.5.10.2-5 [112 kB] Get:26 http://deb.debian.org/debian buster/main amd64 libcom-err2 amd64 1.44.5-1+deb10u3 [68.4 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libcomerr2 amd64 1.44.5-1+deb10u3 [64.2 kB] Get:28 http://deb.debian.org/debian buster/main amd64 libext2fs2 amd64 1.44.5-1+deb10u3 [221 kB] Get:29 http://deb.debian.org/debian buster/main amd64 e2fslibs amd64 1.44.5-1+deb10u3 [64.2 kB] Get:30 http://deb.debian.org/debian buster/main amd64 e2fsprogs amd64 1.44.5-1+deb10u3 [576 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libuuid1 amd64 2.33.1-0.1 [78.3 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libblkid1 amd64 2.33.1-0.1 [195 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libsmartcols1 amd64 2.33.1-0.1 [150 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libfdisk1 amd64 2.33.1-0.1 [234 kB] Get:35 http://deb.debian.org/debian buster/main amd64 libncursesw6 amd64 6.1+20181013-2+deb10u2 [132 kB] Get:36 http://deb.debian.org/debian buster/main amd64 libmount1 amd64 2.33.1-0.1 [207 kB] Get:37 http://deb.debian.org/debian buster/main amd64 fdisk amd64 2.33.1-0.1 [179 kB] Get:38 http://deb.debian.org/debian buster/main amd64 login amd64 1:4.5-1.1 [751 kB] Get:39 http://deb.debian.org/debian buster/main amd64 util-linux amd64 2.33.1-0.1 [1062 kB] Get:40 http://deb.debian.org/debian buster/main amd64 mount amd64 2.33.1-0.1 [174 kB] Get:41 http://deb.debian.org/debian buster/main amd64 ncurses-bin amd64 6.1+20181013-2+deb10u2 [406 kB] Get:42 http://deb.debian.org/debian buster/main amd64 perl-modules-5.28 all 5.28.1-6+deb10u1 [2873 kB] Get:43 http://deb.debian.org/debian buster/main amd64 libgdbm6 amd64 1.18.1-4 [64.7 kB] Get:44 http://deb.debian.org/debian buster/main amd64 libgdbm-compat4 amd64 1.18.1-4 [44.1 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libperl5.28 amd64 5.28.1-6+deb10u1 [3894 kB] Get:46 http://deb.debian.org/debian buster/main amd64 perl amd64 5.28.1-6+deb10u1 [204 kB] Get:47 http://deb.debian.org/debian buster/main amd64 perl-base amd64 5.28.1-6+deb10u1 [1514 kB] Get:48 http://deb.debian.org/debian buster/main amd64 libtinfo5 amd64 6.1+20181013-2+deb10u2 [321 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libncursesw5 amd64 6.1+20181013-2+deb10u2 [118 kB] Get:50 http://deb.debian.org/debian buster/main amd64 ncurses-base all 6.1+20181013-2+deb10u2 [258 kB] Get:51 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB] Get:52 http://deb.debian.org/debian buster/main amd64 parsnp amd64 1.2+dfsg-5 [529 kB] Get:53 http://deb.debian.org/debian buster/main amd64 libmuscle1 amd64 3.7+4565-6 [255 kB] Get:54 http://deb.debian.org/debian buster/main amd64 libpam-modules-bin amd64 1.3.1-5 [107 kB] Get:55 http://deb.debian.org/debian buster/main amd64 libpam-modules amd64 1.3.1-5 [309 kB] Get:56 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u3 [1551 kB] Get:57 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get:58 http://deb.debian.org/debian buster/main amd64 libquadmath0 amd64 8.3.0-6 [133 kB] Get:59 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get:61 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get:62 http://deb.debian.org/debian buster/main amd64 python-numpy amd64 1:1.16.2-1 [2101 kB] Get:63 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get:64 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:66 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get:67 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get:68 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get:69 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get:70 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get:71 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:72 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:73 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:74 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:75 http://deb.debian.org/debian buster/main amd64 libmpfr6 amd64 4.0.2-1 [775 kB] Get:76 http://deb.debian.org/debian buster/main amd64 gawk amd64 1:4.2.1+dfsg-1 [660 kB] Get:77 http://deb.debian.org/debian buster/main amd64 libss2 amd64 1.44.5-1+deb10u3 [72.9 kB] Get:78 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1n-0+deb10u3 [855 kB] Get:79 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get:80 http://deb.debian.org/debian buster/main amd64 e2fsprogs-l10n all 1.44.5-1+deb10u3 [504 kB] Get:81 http://deb.debian.org/debian buster/main amd64 libgpg-error-l10n all 1.35-1 [97.6 kB] Get:82 http://deb.debian.org/debian buster/main amd64 libgpm2 amd64 1.20.7-5 [35.1 kB] Get:83 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 47.1 MB in 0s (99.7 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 ... 8227 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 ... 8237 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 ... 8238 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 libnettle6: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 ... 8252 files and directories currently installed.) Preparing to unpack .../libhogweed4_3.4.1-1+deb10u1_amd64.deb ... Unpacking libhogweed4:amd64 (3.4.1-1+deb10u1) ... Setting up libhogweed4:amd64 (3.4.1-1+deb10u1) ... 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 ... 8255 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 ... 8295 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.23.15-2+deb10u1_amd64.deb ... Unpacking libp11-kit0:amd64 (0.23.15-2+deb10u1) ... Setting up libp11-kit0:amd64 (0.23.15-2+deb10u1) ... Selecting previously unselected package libtasn1-6: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 ... 8303 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.13-3_amd64.deb ... Unpacking libtasn1-6:amd64 (4.13-3) ... Setting up libtasn1-6:amd64 (4.13-3) ... Selecting previously unselected package libgnutls30: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 ... 8355 files and directories currently installed.) Preparing to unpack .../libudev1_241-7~deb10u8_amd64.deb ... Unpacking libudev1:amd64 (241-7~deb10u8) over (232-25+deb9u12) ... Setting up libudev1:amd64 (241-7~deb10u8) ... (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 ... 8355 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.19.8_amd64.deb ... Unpacking dpkg (1.19.8) over (1.18.25) ... Setting up dpkg (1.19.8) ... Installing new version of config file /etc/alternatives/README ... Installing new version of config file /etc/cron.daily/dpkg ... Installing new version of config file /etc/logrotate.d/dpkg ... (Reading database ... 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Unpacking fdisk (2.33.1-0.1) ... Setting up fdisk (2.33.1-0.1) ... (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 ... 8369 files and directories currently installed.) Preparing to unpack .../login_1%3a4.5-1.1_amd64.deb ... Unpacking login (1:4.5-1.1) over (1:4.4-4.1) ... Setting up login (1:4.5-1.1) ... Installing new version of config file /etc/securetty ... (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 ... 8359 files and directories currently installed.) Preparing to unpack .../0-perl_5.28.1-6+deb10u1_amd64.deb ... Unpacking perl (5.28.1-6+deb10u1) over (5.24.1-3+deb9u7) ... Selecting previously unselected package perl-modules-5.28. Preparing to unpack .../1-perl-modules-5.28_5.28.1-6+deb10u1_all.deb ... Unpacking perl-modules-5.28 (5.28.1-6+deb10u1) ... Selecting previously unselected package libgdbm6:amd64. 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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 ... 10259 files and directories currently installed.) Preparing to unpack .../libncursesw5_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncursesw5:amd64 (6.1+20181013-2+deb10u2) over (6.0+20161126-1+deb9u2) ... Setting up libncursesw5: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 ... 10259 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.1+20181013-2+deb10u2_all.deb ... Unpacking ncurses-base (6.1+20181013-2+deb10u2) over (6.0+20161126-1+deb9u2) ... Setting up ncurses-base (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 ... 10261 files and directories currently installed.) Preparing to unpack .../libgomp1_8.3.0-6_amd64.deb ... Unpacking libgomp1:amd64 (8.3.0-6) over (6.3.0-18+deb9u1) ... Preparing to unpack .../parsnp_1.2+dfsg-5_amd64.deb ... Unpacking parsnp (1.2+dfsg-5) over (1.2+dfsg-3) ... (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 ... 10256 files and directories currently installed.) Preparing to unpack .../libmuscle1_3.7+4565-6_amd64.deb ... Unpacking libmuscle1 (3.7+4565-6) ... Preparing to unpack .../libpam-modules-bin_1.3.1-5_amd64.deb ... Unpacking libpam-modules-bin (1.3.1-5) over (1.1.8-3.6) ... Setting up libpam-modules-bin (1.3.1-5) ... (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 ... 10263 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.3.1-5_amd64.deb ... Unpacking libpam-modules:amd64 (1.3.1-5) over (1.1.8-3.6) ... Setting up libpam-modules:amd64 (1.3.1-5) ... Installing new version of config file /etc/security/access.conf ... Installing new version of config file /etc/security/limits.conf ... (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 ... 10264 files and directories currently installed.) Preparing to unpack .../00-libssl1.1_1.1.1n-0+deb10u3_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1n-0+deb10u3) over (1.1.0l-1~deb9u1) ... Preparing to unpack .../01-python2.7_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) over (2.7.13-2+deb9u3) ... Preparing to unpack .../02-libquadmath0_8.3.0-6_amd64.deb ... Unpacking libquadmath0:amd64 (8.3.0-6) over (6.3.0-18+deb9u1) ... 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Unpacking libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) over (2.7.13-2+deb9u3) ... Preparing to unpack .../11-python2.7-minimal_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) over (2.7.13-2+deb9u3) ... Preparing to unpack .../12-libpython2.7-minimal_2.7.16-2+deb10u1_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) over (2.7.13-2+deb9u3) ... Preparing to unpack .../13-python-minimal_2.7.16-1_amd64.deb ... Unpacking python-minimal (2.7.16-1) over (2.7.13-2) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../14-python2-minimal_2.7.16-1_amd64.deb ... Unpacking python2-minimal (2.7.16-1) ... Setting up libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... (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 ... 10325 files and directories currently installed.) Preparing to unpack .../python_2.7.16-1_amd64.deb ... Unpacking python (2.7.16-1) over (2.7.13-2) ... Preparing to unpack .../libpython-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.16-1) over (2.7.13-2) ... Selecting previously unselected package libpython2-stdlib:amd64. Preparing to unpack .../libpython2-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython2-stdlib:amd64 (2.7.16-1) ... Selecting previously unselected package python2. Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Selecting previously unselected package libmpfr6:amd64. Preparing to unpack .../libmpfr6_4.0.2-1_amd64.deb ... Unpacking libmpfr6:amd64 (4.0.2-1) ... Setting up libmpfr6:amd64 (4.0.2-1) ... Setting up libreadline7:amd64 (7.0-5) ... (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 ... 10326 files and directories currently installed.) Preparing to unpack .../gawk_1%3a4.2.1+dfsg-1_amd64.deb ... Unpacking gawk (1:4.2.1+dfsg-1) over (1:4.1.4+dfsg-1) ... Preparing to unpack .../libss2_1.44.5-1+deb10u3_amd64.deb ... Unpacking libss2:amd64 (1.44.5-1+deb10u3) over (1.43.4-2+deb9u1) ... Setting up libss2:amd64 (1.44.5-1+deb10u3) ... Selecting previously unselected package openssl. (Reading database ... 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Preparing to unpack .../2-e2fsprogs-l10n_1.44.5-1+deb10u3_all.deb ... Unpacking e2fsprogs-l10n (1.44.5-1+deb10u3) ... Selecting previously unselected package libgpg-error-l10n. Preparing to unpack .../3-libgpg-error-l10n_1.35-1_all.deb ... Unpacking libgpg-error-l10n (1.35-1) ... Selecting previously unselected package libgpm2:amd64. Preparing to unpack .../4-libgpm2_1.20.7-5_amd64.deb ... Unpacking libgpm2:amd64 (1.20.7-5) ... Preparing to unpack .../5-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 libexpat1:amd64 (2.2.6-2+deb10u4) ... 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 gawk (1:4.2.1+dfsg-1) ... Setting up libssl1.1:amd64 (1.1.1n-0+deb10u3) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Setting up libgomp1:amd64 (8.3.0-6) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up libquadmath0:amd64 (8.3.0-6) ... 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 openssl (1.1.1n-0+deb10u3) ... Setting up libgpg-error-l10n (1.35-1) ... Setting up libgdbm6:amd64 (1.18.1-4) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libmuscle1 (3.7+4565-6) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up python2 (2.7.16-1) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libpython-stdlib:amd64 (2.7.16-1) ... 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 python (2.7.16-1) ... 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 python-numpy (1:1.16.2-1) ... Setting up perl (5.28.1-6+deb10u1) ... Removing obsolete conffile /etc/perl/sitecustomize.pl ... Setting up parsnp (1.2+dfsg-5) ... Setting up rename (1.10-1) ... 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. 0m34.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', '-yf', 'dist-upgrade'] 0m34.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m36.4s DUMP: f6fc0f2636004ef589309651dfd778f4 - 0m36.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m36.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'show', '--no-all-versions', 'parsnp'] 0m36.6s DUMP: Package: parsnp Version: 1.2+dfsg-5 Installed-Size: 913 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.27), libgcc1 (>= 1:3.0), libgomp1 (>= 4.9), libmuscle1 (>= 3.7+4565), libstdc++6 (>= 5.2), python:any, python-numpy, fasttree, mummer, phipack Recommends: python-dendropy Description-en: rapid core genome multi-alignment Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction. Description-md5: e2e6d59e8a521577f278267009bb94b4 Homepage: http://harvest.readthedocs.org/en/latest/content/parsnp.html Section: science Priority: optional Filename: pool/main/p/parsnp/parsnp_1.2+dfsg-5_amd64.deb Size: 528596 MD5sum: 99dcb6548c26d28cdea7dd999fe2db17 SHA256: 25f4ae322a760d6dfc435c45007534adddf2509300476bc6c1466c477c49625d 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'show', '--no-all-versions', 'parsnp'] 0m36.6s INFO: apt-cache knows about the following packages: parsnp 0m36.6s INFO: Running scripts pre_install 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_database-server'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_database-server'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_exceptions'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_exceptions'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_extras'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_extras'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_foreign_architecture'] 0m36.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_foreign_architecture'] 0m36.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m36.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m36.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'policy'] 0m36.7s 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: 0m36.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'policy'] 0m36.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'policy', 'parsnp'] 0m36.7s DUMP: parsnp: Installed: 1.2+dfsg-5 Candidate: 1.2+dfsg-5 Version table: *** 1.2+dfsg-5 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m36.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'policy', 'parsnp'] 0m36.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', '-y', 'install', 'parsnp'] 0m37.0s DUMP: Reading package lists... Building dependency tree... Reading state information... parsnp is already the newest version (1.2+dfsg-5). The following packages were automatically installed and are no longer required: libblas-common libgdbm3 libgfortran3 libmpfr4 libperl5.24 rename Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', '-y', 'install', 'parsnp'] 0m37.0s INFO: Running scripts post_install 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_install_exceptions'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_install_exceptions'] 0m37.0s INFO: Running scripts post_distupgrade 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m37.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m37.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_distupgrade_exceptions'] 0m37.2s DUMP: Running pam-auth-update... 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_distupgrade_exceptions'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_distupgrade_zz_backports'] 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_distupgrade_zz_backports'] 0m37.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m37.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m37.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m38.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m38.2s INFO: Running scripts pre_install 0m38.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_database-server'] 0m38.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_database-server'] 0m38.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_exceptions'] 0m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_exceptions'] 0m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_extras'] 0m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_extras'] 0m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_foreign_architecture'] 0m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_foreign_architecture'] 0m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'policy'] 0m38.3s 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: 0m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'policy'] 0m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'policy', 'parsnp'] 0m38.4s DUMP: parsnp: Installed: 1.2+dfsg-5 Candidate: 1.2+dfsg-5 Version table: *** 1.2+dfsg-5 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m38.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-cache', 'policy', 'parsnp'] 0m38.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', '-y', 'install', 'parsnp=1.2+dfsg-5'] 0m38.6s DUMP: Reading package lists... Building dependency tree... Reading state information... parsnp is already the newest version (1.2+dfsg-5). The following packages were automatically installed and are no longer required: libblas-common libgdbm3 libgfortran3 libmpfr4 libperl5.24 rename Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', '-y', 'install', 'parsnp=1.2+dfsg-5'] 0m38.6s INFO: Running scripts post_install 0m38.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_install_exceptions'] 0m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_install_exceptions'] 0m38.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m39.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m39.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', '-ac', '--ignore-obsolete'] 0m40.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', '-ac', '--ignore-obsolete'] 0m40.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m40.9s DUMP: 0.15.6 0m40.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m40.9s INFO: Running adequate version 0.15.6 now. 0m40.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'parsnp'] 0m41.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'parsnp'] 0m41.0s INFO: Running scripts pre_remove 0m41.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m41.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m41.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m41.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m41.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_remove_exceptions'] 0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/pre_remove_exceptions'] 0m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m42.4s 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 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 gawk gawk 1:4.2.1+dfsg-1 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 gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed 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 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 libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed liblapack3:amd64 liblapack3 3.8.0-2 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 libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libmpfr4:amd64 libmpfr4 3.1.5-1 install ok installed libmpfr6:amd64 libmpfr6 4.0.2-1 install ok installed libmuscle1 libmuscle1 3.7+4565-6 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 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 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 libsigsegv2:amd64 libsigsegv2 2.12-2 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 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 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 mummer mummer 3.23+dfsg-4 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 parsnp parsnp 1.2+dfsg-5 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 phipack phipack 0.0.20160614-3 install ok installed python python 2.7.16-1 install ok installed python-dendropy python-dendropy 4.4.0-1 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-pkg-resources python-pkg-resources 40.8.0-1 install ok installed python2 python2 2.7.16-1 install ok installed python2-minimal python2-minimal 2.7.16-1 install ok installed python2.7 python2.7 2.7.16-2+deb10u1 install ok installed python2.7-minimal python2.7-minimal 2.7.16-2+deb10u1 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 0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', 'remove', 'bzip2', 'fasttree', 'file', 'gawk', 'libblas-common', 'libblas3:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmpfr4:amd64', 'libmpfr6:amd64', 'libmuscle1', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'mime-support', 'mummer', 'netbase', 'perl', 'perl-modules-5.24', 'perl-modules-5.28', 'phipack', 'python', 'python-dendropy', 'python-minimal', 'python-numpy', 'python-pkg-resources', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'rename', 'xz-utils', 'parsnp'] 0m43.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bzip2 fasttree file gawk libblas-common libblas3 libexpat1 libgdbm-compat4 libgdbm3 libgdbm6 libgfortran3 libgfortran5 libgomp1 liblapack3 libmagic-mgc libmagic1 libmpfr4 libmpfr6 libmuscle1 libperl5.24 libperl5.28 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libsigsegv2 libsqlite3-0 mime-support mummer netbase parsnp perl perl-modules-5.24 perl-modules-5.28 phipack python python-dendropy python-minimal python-numpy python-pkg-resources python2 python2-minimal python2.7 python2.7-minimal readline-common rename xz-utils 0 upgraded, 0 newly installed, 49 to remove and 0 not upgraded. After this operation, 147 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 ... 10707 files and directories currently installed.) Removing bzip2 (1.0.6-9.2~deb10u1) ... Removing parsnp (1.2+dfsg-5) ... Removing fasttree (2.1.10-2) ... Removing file (1:5.35-4+deb10u2) ... Removing mummer (3.23+dfsg-4) ... Removing gawk (1:4.2.1+dfsg-1) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing libblas-common (3.7.0-2) ... Removing python-numpy (1:1.16.2-1) ... Removing liblapack3:amd64 (3.8.0-2) ... Removing libblas3:amd64 (3.8.0-2) ... Removing python-dendropy (4.4.0-1) ... Removing python-pkg-resources (40.8.0-1) ... Removing python (2.7.16-1) ... Removing python2 (2.7.16-1) ... Removing python2.7 (2.7.16-2+deb10u1) ... Removing libpython-stdlib:amd64 (2.7.16-1) ... Removing rename (1.10-1) ... 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 libmuscle1 (3.7+4565-6) ... Removing libgomp1:amd64 (8.3.0-6) ... Removing libmagic1:amd64 (1:5.35-4+deb10u2) ... Removing libmagic-mgc (1:5.35-4+deb10u2) ... Removing libmpfr4:amd64 (3.1.5-1) ... Removing libmpfr6:amd64 (4.0.2-1) ... Removing libpython2-stdlib:amd64 (2.7.16-1) ... Removing python-minimal (2.7.16-1) ... Removing python2-minimal (2.7.16-1) ... Removing python2.7-minimal (2.7.16-2+deb10u1) ... Removing libquadmath0:amd64 (8.3.0-6) ... Removing libsigsegv2:amd64 (2.12-2) ... 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 phipack (0.0.20160614-3) ... Removing xz-utils (5.2.4-1+deb10u1) ... Removing libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Removing libexpat1:amd64 (2.2.6-2+deb10u4) ... 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 mime-support (3.62) ... Removing readline-common (7.0-5) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... 0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', 'remove', 'bzip2', 'fasttree', 'file', 'gawk', 'libblas-common', 'libblas3:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmpfr4:amd64', 'libmpfr6:amd64', 'libmuscle1', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'mime-support', 'mummer', 'netbase', 'perl', 'perl-modules-5.24', 'perl-modules-5.28', 'phipack', 'python', 'python-dendropy', 'python-minimal', 'python-numpy', 'python-pkg-resources', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'rename', 'xz-utils', 'parsnp'] 0m43.4s INFO: Running scripts post_remove 0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_remove_exceptions'] 0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_remove_exceptions'] 0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg', '--purge', 'bzip2', 'fasttree', 'file', 'gawk', 'libblas-common', 'libblas3:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmpfr4:amd64', 'libmpfr6:amd64', 'libmuscle1', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'mime-support', 'mummer', 'netbase', 'perl', 'perl-modules-5.24', 'perl-modules-5.28', 'phipack', 'python', 'python-dendropy', 'python-minimal', 'python-numpy', 'python-pkg-resources', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'rename', 'xz-utils'] 0m43.4s DUMP: dpkg: warning: ignoring request to remove bzip2 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 ... 5018 files and directories currently installed.) Purging configuration files for gawk (1:4.2.1+dfsg-1) ... 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 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 liblapack3 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 libmpfr4 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libmuscle1 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 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 libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline7 which isn't installed dpkg: warning: ignoring request to remove libsigsegv2 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed Purging configuration files for mime-support (3.62) ... dpkg: warning: ignoring request to remove mummer which isn't installed 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 dpkg: warning: ignoring request to remove phipack which isn't installed Purging configuration files for python (2.7.16-1) ... dpkg: warning: ignoring request to remove python-dendropy 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-pkg-resources 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 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 0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg', '--purge', 'bzip2', 'fasttree', 'file', 'gawk', 'libblas-common', 'libblas3:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmpfr4:amd64', 'libmpfr6:amd64', 'libmuscle1', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'mime-support', 'mummer', 'netbase', 'perl', 'perl-modules-5.24', 'perl-modules-5.28', 'phipack', 'python', 'python-dendropy', 'python-minimal', 'python-numpy', 'python-pkg-resources', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'rename', 'xz-utils'] 0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg', '--purge', 'parsnp'] 0m43.5s DUMP: dpkg: warning: ignoring request to remove parsnp which isn't installed 0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg', '--purge', 'parsnp'] 0m43.5s INFO: Running scripts post_purge 0m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_purge_exceptions'] 0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_purge_exceptions'] 0m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg', '--purge', '--pending'] 0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg', '--purge', '--pending'] 0m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg', '--remove', '--pending'] 0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg', '--remove', '--pending'] 0m43.5s INFO: Running scripts post_test 0m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_test_exceptions'] 0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'tmp/scripts/post_test_exceptions'] 0m43.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m43.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg-divert', '--list'] 0m43.8s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'dpkg-divert', '--list'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', 'clean'] 0m43.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc', 'apt-get', 'clean'] 0m43.9s DEBUG: Recording chroot state 0m44.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/shm'] 0m44.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/shm'] 0m44.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/console'] 0m44.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/console'] 0m44.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/ptmx'] 0m44.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/ptmx'] 0m44.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/pts'] 0m44.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/dev/pts'] 0m44.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/proc'] 0m44.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc/proc'] 0m44.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m45.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpbnc9zbuc'] 0m45.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpbnc9zbuc 0m45.0s INFO: PASS: Upgrading between Debian distributions. 0m45.0s INFO: PASS: All tests. 0m45.0s INFO: piuparts run ends. ret=0 End: 2023-04-15 07:03:36 GMT