Start: 2019-12-15 21:53:50 UTC [testing] Package: conservation-code Version: 20110309.0-7 Installed-Size: 113 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any, python-numpy Enhances: concavity Description: protein sequence conservation scoring tool Homepage: http://compbio.cs.princeton.edu/conservation/ Description-md5: 35f238c6a81ce482741e5d5359932062 Section: science Priority: optional Filename: pool/main/c/conservation-code/conservation-code_20110309.0-7_all.deb Size: 23680 MD5sum: cfca3960340f58bffb8f524a1ef01de6 SHA256: d11e0cde865b176818f4ed039bb9d9b6491fa35e803c355f83daf9ee30b48258 [sid] Package: conservation-code Version: 20110309.0-8 Installed-Size: 115 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3:any, python3-numpy Enhances: concavity Description: protein sequence conservation scoring tool Homepage: https://compbio.cs.princeton.edu/conservation/ Description-md5: 35f238c6a81ce482741e5d5359932062 Section: science Priority: optional Filename: pool/main/c/conservation-code/conservation-code_20110309.0-8_all.deb Size: 24112 MD5sum: 303e07420737374ec735caa28c48ca45 SHA256: 56776d84d34085340a341bff21ef15cf63322a17b9caef8cee96d027dd325879 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python2.7/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://mirror-ubc.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt conservation-code=20110309.0-8 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 1.0.2~201909101611~1.0.1-11-g98f8c745 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://mirror-ubc.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt conservation-code=20110309.0-8 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.19.0-6-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp21ljJ7 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp21ljJ7 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m4.7s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m4.7s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/proc'] 0m4.7s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/proc'] 0m4.7s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/pts'] 0m4.8s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/pts'] 0m4.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/ptmx'] 0m4.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/ptmx'] 0m4.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/console'] 0m4.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/console'] 0m4.8s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/shm'] 0m4.8s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/shm'] 0m4.8s DEBUG: sources.list: deb http://mirror-ubc.debian.org/debian/ bullseye main 0m4.8s DEBUG: Created policy-rc.d and chmodded it. 0m4.8s DEBUG: Created resolv.conf. 0m4.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp21ljJ7/tmp/scripts/ 0m4.8s INFO: Running scripts post_chroot_unpack 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', 'update'] 0m12.3s DUMP: Get:1 http://mirror-ubc.debian.org/debian bullseye InRelease [113 kB] Get:2 http://mirror-ubc.debian.org/debian bullseye/main amd64 Packages [7622 kB] Get:3 http://mirror-ubc.debian.org/debian bullseye/main Translation-en [5786 kB] Fetched 13.5 MB in 5s (2665 kB/s) Reading package lists... 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', 'update'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', '-yf', 'dist-upgrade'] 0m13.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: debianutils libtasn1-6 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 155 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian bullseye/main amd64 debianutils amd64 4.9.1 [101 kB] Get:2 http://mirror-ubc.debian.org/debian bullseye/main amd64 libtasn1-6 amd64 4.15.0-2 [53.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 155 kB in 0s (7006 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6532 files and directories currently installed.) Preparing to unpack .../debianutils_4.9.1_amd64.deb ... Unpacking debianutils (4.9.1) over (4.9) ... Setting up debianutils (4.9.1) ... (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 ... 6532 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.15.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.15.0-2) over (4.14-3) ... Setting up libtasn1-6:amd64 (4.15.0-2) ... Processing triggers for libc-bin (2.29-3) ... 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', '-yf', 'dist-upgrade'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m14.5s DUMP: 51f12cb64900537dde1da7719b91deea - 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m14.5s INFO: Running scripts post_setup 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_setup_dummy_users'] 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_setup_dummy_users'] 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_setup_forbid_home'] 0m16.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_setup_forbid_home'] 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m17.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_setup_minimize'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_setup_minimize'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_setup_squeeze-backports'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_setup_squeeze-backports'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_setup_zz_backports'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_setup_zz_backports'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m17.0s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.4 install ok installed base-files base-files 11 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-5 install ok installed bsdutils bsdutils 1:2.34-0.1 install ok installed coreutils coreutils 8.30-3+b1 install ok installed dash dash 0.5.10.2-6 install ok installed debconf debconf 1.5.73 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.9.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.7 install ok installed e2fsprogs e2fsprogs 1.45.4-1 install ok installed fdisk fdisk 2.34-0.1 install ok installed findutils findutils 4.7.0-1 install ok installed gcc-9-base:amd64 gcc-9-base 9.2.1-21 install ok installed gpgv gpgv 2.2.17-3 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+b1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.57 install ok installed libacl1:amd64 libacl1 2.2.53-5 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-5 install ok installed libaudit-common libaudit-common 1:2.8.5-2 install ok installed libaudit1:amd64 libaudit1 1:2.8.5-2+b1 install ok installed libblkid1:amd64 libblkid1 2.34-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-2 install ok installed libc-bin libc-bin 2.29-3 install ok installed libc6:amd64 libc6 2.29-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.1+b1 install ok installed libcom-err2:amd64 libcom-err2 1.45.4-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.250 install ok installed libext2fs2:amd64 libext2fs2 1.45.4-1 install ok installed libfdisk1:amd64 libfdisk1 2.34-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:9.2.1-21 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.5-3 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4 install ok installed libgnutls30:amd64 libgnutls30 3.6.10-5 install ok installed libgpg-error0:amd64 libgpg-error0 1.36-7 install ok installed libhogweed5:amd64 libhogweed5 3.5.1+really3.5.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.2.0-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.2-2 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+b1 install ok installed libmount1:amd64 libmount1 2.34-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20191019-1 install ok installed libnettle7:amd64 libnettle7 3.5.1+really3.5.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.18.1-2 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 libpcre2-8-0:amd64 libpcre2-8-0 10.34-7 install ok installed libpcre3:amd64 libpcre3 2:8.39-12+b1 install ok installed libseccomp2:amd64 libseccomp2 2.4.2-2 install ok installed libselinux1:amd64 libselinux1 2.9-3+b1 install ok installed libsemanage-common libsemanage-common 2.9-3 install ok installed libsemanage1:amd64 libsemanage1 2.9-3+b1 install ok installed libsepol1:amd64 libsepol1 2.9-2+b2 install ok installed libsmartcols1:amd64 libsmartcols1 2.34-0.1 install ok installed libss2:amd64 libss2 1.45.4-1 install ok installed libstdc++6:amd64 libstdc++6 9.2.1-21 install ok installed libsystemd0:amd64 libsystemd0 244-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.15.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.1+20191019-1 install ok installed libudev1:amd64 libudev1 244-3 install ok installed libunistring2:amd64 libunistring2 0.9.10-2 install ok installed libuuid1:amd64 libuuid1 2.34-0.1 install ok installed libzstd1:amd64 libzstd1 1.4.4+dfsg-1 install ok installed login login 1:4.7-2 install ok installed logsave logsave 1.45.4-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.34-0.1 install ok installed ncurses-base ncurses-base 6.1+20191019-1 install ok installed ncurses-bin ncurses-bin 6.1+20191019-1 install ok installed passwd passwd 1:4.7-2 install ok installed perl-base perl-base 5.30.0-9 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-1 install ok installed tar tar 1.30+dfsg-6+b1 install ok installed tzdata tzdata 2019c-3 install ok installed util-linux util-linux 2.34-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+b1 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m17.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m17.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 0m18.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 0m18.5s INFO: Running scripts is_testable 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/is_testable_uninstallable'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/is_testable_uninstallable'] 0m18.5s INFO: Running scripts pre_test 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_test_exceptions'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_test_exceptions'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_test_root_password'] 0m18.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_test_root_password'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'show', '--no-all-versions', 'conservation-code'] 0m18.9s DUMP: Package: conservation-code Version: 20110309.0-7 Installed-Size: 113 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any, python-numpy Enhances: concavity Description-en: protein sequence conservation scoring tool This package provides score_conservation(1), a tool to score protein sequence conservation. . The following conservation scoring methods are implemented: * sum of pairs * weighted sum of pairs * Shannon entropy * Shannon entropy with property groupings (Mirny and Shakhnovich 1995, Valdar and Thornton 2001) * relative entropy with property groupings (Williamson 1995) * von Neumann entropy (Caffrey et al 2004) * relative entropy (Samudrala and Wang 2006) * Jensen-Shannon divergence (Capra and Singh 2007) . A window-based extension that incorporates the estimated conservation of sequentially adjacent residues into the score for each column is also given. This window approach can be applied to any of the conservation scoring methods. . The program accepts alignments in the CLUSTAL and FASTA formats. . The sequence-specific output can be used as the conservation input for concavity. . Conservation is highly predictive in identifying catalytic sites and residues near bound ligands. Description-md5: 35f238c6a81ce482741e5d5359932062 Homepage: http://compbio.cs.princeton.edu/conservation/ Section: science Priority: optional Filename: pool/main/c/conservation-code/conservation-code_20110309.0-7_all.deb Size: 23680 MD5sum: cfca3960340f58bffb8f524a1ef01de6 SHA256: d11e0cde865b176818f4ed039bb9d9b6491fa35e803c355f83daf9ee30b48258 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'show', '--no-all-versions', 'conservation-code'] 0m18.9s INFO: apt-cache knows about the following packages: conservation-code 0m18.9s INFO: Running scripts pre_install 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_database-server'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_database-server'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_exceptions'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_exceptions'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_extras'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_extras'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'policy'] 0m19.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian bullseye/main amd64 Packages release o=Debian,a=testing,n=bullseye,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'policy'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'policy', 'conservation-code'] 0m19.1s DUMP: conservation-code: Installed: (none) Candidate: 20110309.0-7 Version table: 20110309.0-7 500 500 http://mirror-ubc.debian.org/debian bullseye/main amd64 Packages 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'policy', 'conservation-code'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', '-y', 'install', 'conservation-code'] 0m27.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libblas3 libexpat1 libgfortran5 liblapack3 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl1.1 mime-support python python-minimal python-numpy python-pkg-resources python2 python2-minimal python2.7 python2.7-minimal readline-common Suggested packages: python-doc python-tk gcc gfortran python-dev python-pytest python-numpy-dbg python-numpy-doc python-setuptools python2-doc python2.7-doc binutils binfmt-support readline-doc Recommended packages: bzip2 file xz-utils The following NEW packages will be installed: conservation-code libblas3 libexpat1 libgfortran5 liblapack3 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl1.1 mime-support python python-minimal python-numpy python-pkg-resources python2 python2-minimal python2.7 python2.7-minimal readline-common 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. Need to get 12.1 MB of archives. After this operation, 46.5 MB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython2.7-minimal amd64 2.7.17-1 [395 kB] Get:2 http://mirror-ubc.debian.org/debian bullseye/main amd64 python2.7-minimal amd64 2.7.17-1 [1363 kB] Get:3 http://mirror-ubc.debian.org/debian bullseye/main amd64 python2-minimal amd64 2.7.17-2 [41.4 kB] Get:4 http://mirror-ubc.debian.org/debian bullseye/main amd64 python-minimal amd64 2.7.17-2 [21.1 kB] Get:5 http://mirror-ubc.debian.org/debian bullseye/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB] Get:6 http://mirror-ubc.debian.org/debian bullseye/main amd64 mime-support all 3.64 [37.8 kB] Get:7 http://mirror-ubc.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:8 http://mirror-ubc.debian.org/debian bullseye/main amd64 readline-common all 8.0-3 [72.5 kB] Get:9 http://mirror-ubc.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.0-3 [160 kB] Get:10 http://mirror-ubc.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.30.1-1 [649 kB] Get:11 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython2.7-stdlib amd64 2.7.17-1 [1885 kB] Get:12 http://mirror-ubc.debian.org/debian bullseye/main amd64 python2.7 amd64 2.7.17-1 [309 kB] Get:13 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython2-stdlib amd64 2.7.17-2 [20.9 kB] Get:14 http://mirror-ubc.debian.org/debian bullseye/main amd64 libpython-stdlib amd64 2.7.17-2 [20.9 kB] Get:15 http://mirror-ubc.debian.org/debian bullseye/main amd64 python2 amd64 2.7.17-2 [41.7 kB] Get:16 http://mirror-ubc.debian.org/debian bullseye/main amd64 python amd64 2.7.17-2 [22.9 kB] Get:17 http://mirror-ubc.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-1 [153 kB] Get:18 http://mirror-ubc.debian.org/debian bullseye/main amd64 libquadmath0 amd64 9.2.1-21 [145 kB] Get:19 http://mirror-ubc.debian.org/debian bullseye/main amd64 libgfortran5 amd64 9.2.1-21 [634 kB] Get:20 http://mirror-ubc.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-1 [2168 kB] Get:21 http://mirror-ubc.debian.org/debian bullseye/main amd64 python-pkg-resources all 41.2.0-1 [183 kB] Get:22 http://mirror-ubc.debian.org/debian bullseye/main amd64 python-numpy amd64 1:1.16.5-1 [2153 kB] Get:23 http://mirror-ubc.debian.org/debian bullseye/main amd64 conservation-code all 20110309.0-7 [23.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.1 MB in 0s (37.1 MB/s) Selecting previously unselected package libpython2.7-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6534 files and directories currently installed.) Preparing to unpack .../00-libpython2.7-minimal_2.7.17-1_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.17-1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../01-python2.7-minimal_2.7.17-1_amd64.deb ... Unpacking python2.7-minimal (2.7.17-1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../02-python2-minimal_2.7.17-2_amd64.deb ... Unpacking python2-minimal (2.7.17-2) ... Selecting previously unselected package python-minimal. Preparing to unpack .../03-python-minimal_2.7.17-2_amd64.deb ... Unpacking python-minimal (2.7.17-2) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../04-libssl1.1_1.1.1d-2_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-2) ... Selecting previously unselected package mime-support. Preparing to unpack .../05-mime-support_3.64_all.deb ... Unpacking mime-support (3.64) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../06-libexpat1_2.2.9-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.9-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../07-readline-common_8.0-3_all.deb ... Unpacking readline-common (8.0-3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../08-libreadline8_8.0-3_amd64.deb ... Unpacking libreadline8:amd64 (8.0-3) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../09-libsqlite3-0_3.30.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.30.1-1) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Preparing to unpack .../10-libpython2.7-stdlib_2.7.17-1_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.17-1) ... Selecting previously unselected package python2.7. Preparing to unpack .../11-python2.7_2.7.17-1_amd64.deb ... Unpacking python2.7 (2.7.17-1) ... Selecting previously unselected package libpython2-stdlib:amd64. Preparing to unpack .../12-libpython2-stdlib_2.7.17-2_amd64.deb ... Unpacking libpython2-stdlib:amd64 (2.7.17-2) ... Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../13-libpython-stdlib_2.7.17-2_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.17-2) ... Setting up libpython2.7-minimal:amd64 (2.7.17-1) ... Setting up python2.7-minimal (2.7.17-1) ... Setting up python2-minimal (2.7.17-2) ... Selecting previously unselected package python2. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 7371 files and directories currently installed.) Preparing to unpack .../python2_2.7.17-2_amd64.deb ... Unpacking python2 (2.7.17-2) ... Setting up python-minimal (2.7.17-2) ... Selecting previously unselected package python. (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 ... 7404 files and directories currently installed.) Preparing to unpack .../0-python_2.7.17-2_amd64.deb ... Unpacking python (2.7.17-2) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../1-libblas3_3.9.0-1_amd64.deb ... Unpacking libblas3:amd64 (3.9.0-1) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../2-libquadmath0_9.2.1-21_amd64.deb ... Unpacking libquadmath0:amd64 (9.2.1-21) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../3-libgfortran5_9.2.1-21_amd64.deb ... Unpacking libgfortran5:amd64 (9.2.1-21) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../4-liblapack3_3.9.0-1_amd64.deb ... Unpacking liblapack3:amd64 (3.9.0-1) ... Selecting previously unselected package python-pkg-resources. Preparing to unpack .../5-python-pkg-resources_41.2.0-1_all.deb ... Unpacking python-pkg-resources (41.2.0-1) ... Selecting previously unselected package python-numpy. Preparing to unpack .../6-python-numpy_1%3a1.16.5-1_amd64.deb ... Unpacking python-numpy (1:1.16.5-1) ... Selecting previously unselected package conservation-code. Preparing to unpack .../7-conservation-code_20110309.0-7_all.deb ... Unpacking conservation-code (20110309.0-7) ... Setting up libexpat1:amd64 (2.2.9-1) ... Setting up mime-support (3.64) ... Setting up libssl1.1:amd64 (1.1.1d-2) ... Setting up libsqlite3-0:amd64 (3.30.1-1) ... Setting up libblas3:amd64 (3.9.0-1) ... 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 libquadmath0:amd64 (9.2.1-21) ... Setting up libgfortran5:amd64 (9.2.1-21) ... Setting up readline-common (8.0-3) ... Setting up liblapack3:amd64 (3.9.0-1) ... 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 libreadline8:amd64 (8.0-3) ... Setting up libpython2.7-stdlib:amd64 (2.7.17-1) ... Setting up python2.7 (2.7.17-1) ... Setting up libpython2-stdlib:amd64 (2.7.17-2) ... Setting up python2 (2.7.17-2) ... Setting up libpython-stdlib:amd64 (2.7.17-2) ... Setting up python (2.7.17-2) ... Setting up python-pkg-resources (41.2.0-1) ... Setting up python-numpy (1:1.16.5-1) ... Setting up conservation-code (20110309.0-7) ... Processing triggers for libc-bin (2.29-3) ... 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', '-y', 'install', 'conservation-code'] 0m27.9s INFO: Running scripts post_install 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_install_exceptions'] 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_install_exceptions'] 0m27.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 0m28.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 0m28.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp21ljJ7 to sid 0m28.5s DEBUG: sources.list: deb http://mirror-ubc.debian.org/debian/ sid main 0m28.5s INFO: Running scripts pre_distupgrade 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_distupgrade_exceptions'] 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_distupgrade_exceptions'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', 'update'] 0m36.0s DUMP: Get:1 http://mirror-ubc.debian.org/debian sid InRelease [142 kB] Get:2 http://mirror-ubc.debian.org/debian sid/main amd64 Packages [8204 kB] Get:3 http://mirror-ubc.debian.org/debian sid/main Translation-en [6163 kB] Fetched 14.5 MB in 6s (2430 kB/s) Reading package lists... 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', 'update'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', '-yf', 'dist-upgrade'] 0m55.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python python-minimal python-numpy python-pkg-resources python2 python2-minimal python2.7 python2.7-minimal Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libcrypt1 libmpdec2 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.8-minimal libpython3.8-stdlib python3 python3-minimal python3-numpy python3-pkg-resources python3.7 python3.7-minimal python3.8 python3.8-minimal The following packages will be upgraded: conservation-code libc-bin libc6 libgnutls30 libselinux1 libsemanage-common libsemanage1 libsepol1 python-numpy python-pkg-resources 10 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. Need to get 23.5 MB of archives. After this operation, 77.5 MB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.10-5 [84.8 kB] Get:2 http://mirror-ubc.debian.org/debian sid/main amd64 libc6 amd64 2.29-6 [2806 kB] Get:3 http://mirror-ubc.debian.org/debian sid/main amd64 libc-bin amd64 2.29-6 [806 kB] Get:4 http://mirror-ubc.debian.org/debian sid/main amd64 libpython3.7-minimal amd64 3.7.5-2 [590 kB] Get:5 http://mirror-ubc.debian.org/debian sid/main amd64 python3.7-minimal amd64 3.7.5-2 [1812 kB] Get:6 http://mirror-ubc.debian.org/debian sid/main amd64 python3-minimal amd64 3.7.5-3 [36.8 kB] Get:7 http://mirror-ubc.debian.org/debian sid/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:8 http://mirror-ubc.debian.org/debian sid/main amd64 libpython3.7-stdlib amd64 3.7.5-2 [1732 kB] Get:9 http://mirror-ubc.debian.org/debian sid/main amd64 python3.7 amd64 3.7.5-2 [347 kB] Get:10 http://mirror-ubc.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.7.5-3 [20.2 kB] Get:11 http://mirror-ubc.debian.org/debian sid/main amd64 python3 amd64 3.7.5-3 [62.1 kB] Get:12 http://mirror-ubc.debian.org/debian sid/main amd64 libpython3.8-minimal amd64 3.8.1~rc1-1 [749 kB] Get:13 http://mirror-ubc.debian.org/debian sid/main amd64 python3.8-minimal amd64 3.8.1~rc1-1 [1939 kB] Get:14 http://mirror-ubc.debian.org/debian sid/main amd64 libgnutls30 amd64 3.6.11.1-2 [1181 kB] Get:15 http://mirror-ubc.debian.org/debian sid/main amd64 libselinux1 amd64 3.0-1 [86.6 kB] Get:16 http://mirror-ubc.debian.org/debian sid/main amd64 libsepol1 amd64 3.0-1 [262 kB] Get:17 http://mirror-ubc.debian.org/debian sid/main amd64 libsemanage-common all 3.0-1 [20.9 kB] Get:18 http://mirror-ubc.debian.org/debian sid/main amd64 libsemanage1 amd64 3.0-1 [96.8 kB] Get:19 http://mirror-ubc.debian.org/debian sid/main amd64 libpython3.8-stdlib amd64 3.8.1~rc1-1 [1666 kB] Get:20 http://mirror-ubc.debian.org/debian sid/main amd64 python3.8 amd64 3.8.1~rc1-1 [405 kB] Get:21 http://mirror-ubc.debian.org/debian sid/main amd64 python3-pkg-resources all 41.4.0-1 [154 kB] Get:22 http://mirror-ubc.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.17.4-4 [6150 kB] Get:23 http://mirror-ubc.debian.org/debian sid/main amd64 conservation-code all 20110309.0-8 [24.1 kB] Get:24 http://mirror-ubc.debian.org/debian sid/main amd64 python-pkg-resources all 41.4.0-1 [183 kB] Get:25 http://mirror-ubc.debian.org/debian sid/main amd64 python-numpy amd64 1:1.16.5-2 [2155 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 23.5 MB in 1s (37.5 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 7936 files and directories currently installed.) Preparing to unpack .../libc6_2.29-6_amd64.deb ... Unpacking libc6:amd64 (2.29-6) over (2.29-3) ... Selecting previously unselected package libcrypt1:amd64. Preparing to unpack .../libcrypt1_1%3a4.4.10-5_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.10-5) ... Setting up libcrypt1:amd64 (1:4.4.10-5) ... Setting up libc6:amd64 (2.29-6) ... (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 ... 7940 files and directories currently installed.) Preparing to unpack .../libc-bin_2.29-6_amd64.deb ... Unpacking libc-bin (2.29-6) over (2.29-3) ... Setting up libc-bin (2.29-6) ... Selecting previously unselected package libpython3.7-minimal:amd64. (Reading database ... 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Selecting previously unselected package python3-minimal. (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 ... 8180 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.7.5-3_amd64.deb ... Unpacking python3-minimal (3.7.5-3) ... Selecting previously unselected package libmpdec2:amd64. Preparing to unpack .../libmpdec2_2.4.2-2_amd64.deb ... Unpacking libmpdec2:amd64 (2.4.2-2) ... Selecting previously unselected package libpython3.7-stdlib:amd64. Preparing to unpack .../libpython3.7-stdlib_3.7.5-2_amd64.deb ... Unpacking libpython3.7-stdlib:amd64 (3.7.5-2) ... Selecting previously unselected package python3.7. Preparing to unpack .../python3.7_3.7.5-2_amd64.deb ... Unpacking python3.7 (3.7.5-2) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../libpython3-stdlib_3.7.5-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.7.5-3) ... Setting up python3-minimal (3.7.5-3) ... Selecting previously unselected package python3. (Reading database ... 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Unpacking python3-pkg-resources (41.4.0-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../3-python3-numpy_1%3a1.17.4-4_amd64.deb ... Unpacking python3-numpy (1:1.17.4-4) ... Preparing to unpack .../4-conservation-code_20110309.0-8_all.deb ... Unpacking conservation-code (20110309.0-8) over (20110309.0-7) ... Preparing to unpack .../5-python-pkg-resources_41.4.0-1_all.deb ... Unpacking python-pkg-resources (41.4.0-1) over (41.2.0-1) ... Preparing to unpack .../6-python-numpy_1%3a1.16.5-2_amd64.deb ... Unpacking python-numpy (1:1.16.5-2) over (1:1.16.5-1) ... Setting up libpython3.8-minimal:amd64 (3.8.1~rc1-1) ... Setting up python-pkg-resources (41.4.0-1) ... Setting up python3.8-minimal (3.8.1~rc1-1) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libpython3.8-stdlib:amd64 (3.8.1~rc1-1) ... Setting up python3.8 (3.8.1~rc1-1) ... Setting up libpython3.7-stdlib:amd64 (3.7.5-2) ... Setting up python-numpy (1:1.16.5-2) ... Setting up libpython3-stdlib:amd64 (3.7.5-3) ... Setting up python3.7 (3.7.5-2) ... Setting up python3 (3.7.5-3) ... Setting up python3-pkg-resources (41.4.0-1) ... Setting up python3-numpy (1:1.17.4-4) ... Setting up conservation-code (20110309.0-8) ... Processing triggers for libc-bin (2.29-6) ... Processing triggers for mime-support (3.64) ... 0m55.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', '-yf', 'dist-upgrade'] 0m55.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m56.4s DUMP: cc93b71ca0b80bbc8ab4d181938f83f3 - 0m56.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m56.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'show', '--no-all-versions', 'conservation-code'] 0m56.8s DUMP: Package: conservation-code Version: 20110309.0-8 Installed-Size: 115 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3:any, python3-numpy Enhances: concavity Description-en: protein sequence conservation scoring tool This package provides score_conservation(1), a tool to score protein sequence conservation. . The following conservation scoring methods are implemented: * sum of pairs * weighted sum of pairs * Shannon entropy * Shannon entropy with property groupings (Mirny and Shakhnovich 1995, Valdar and Thornton 2001) * relative entropy with property groupings (Williamson 1995) * von Neumann entropy (Caffrey et al 2004) * relative entropy (Samudrala and Wang 2006) * Jensen-Shannon divergence (Capra and Singh 2007) . A window-based extension that incorporates the estimated conservation of sequentially adjacent residues into the score for each column is also given. This window approach can be applied to any of the conservation scoring methods. . The program accepts alignments in the CLUSTAL and FASTA formats. . The sequence-specific output can be used as the conservation input for concavity. . Conservation is highly predictive in identifying catalytic sites and residues near bound ligands. Description-md5: 35f238c6a81ce482741e5d5359932062 Homepage: https://compbio.cs.princeton.edu/conservation/ Section: science Priority: optional Filename: pool/main/c/conservation-code/conservation-code_20110309.0-8_all.deb Size: 24112 MD5sum: 303e07420737374ec735caa28c48ca45 SHA256: 56776d84d34085340a341bff21ef15cf63322a17b9caef8cee96d027dd325879 0m56.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'show', '--no-all-versions', 'conservation-code'] 0m56.8s INFO: apt-cache knows about the following packages: conservation-code 0m56.8s INFO: Running scripts pre_install 0m56.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_database-server'] 0m56.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_database-server'] 0m56.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_exceptions'] 0m56.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_exceptions'] 0m56.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_extras'] 0m56.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_extras'] 0m56.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_foreign_architecture'] 0m56.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_foreign_architecture'] 0m56.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m56.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m56.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'policy'] 0m57.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 0m57.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'policy'] 0m57.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'policy', 'conservation-code'] 0m57.1s DUMP: conservation-code: Installed: 20110309.0-8 Candidate: 20110309.0-8 Version table: *** 20110309.0-8 500 500 http://mirror-ubc.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m57.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'policy', 'conservation-code'] 0m57.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', '-y', 'install', 'conservation-code'] 0m57.6s DUMP: Reading package lists... Building dependency tree... Reading state information... conservation-code is already the newest version (20110309.0-8). The following packages were automatically installed and are no longer required: libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python python-minimal python-numpy python-pkg-resources python2 python2-minimal python2.7 python2.7-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', '-y', 'install', 'conservation-code'] 0m57.6s INFO: Running scripts post_install 0m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_install_exceptions'] 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_install_exceptions'] 0m57.6s INFO: Running scripts post_distupgrade 0m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_distupgrade_exceptions'] 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_distupgrade_exceptions'] 0m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_distupgrade_zz_backports'] 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_distupgrade_zz_backports'] 0m57.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 0m59.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 0m59.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 1m0.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 1m0.0s INFO: Running scripts pre_install 1m0.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_database-server'] 1m0.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_database-server'] 1m0.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_exceptions'] 1m0.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_exceptions'] 1m0.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_extras'] 1m0.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_extras'] 1m0.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_foreign_architecture'] 1m0.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_foreign_architecture'] 1m0.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m0.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m0.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'policy'] 1m0.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'policy'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'policy', 'conservation-code'] 1m0.3s DUMP: conservation-code: Installed: 20110309.0-8 Candidate: 20110309.0-8 Version table: *** 20110309.0-8 500 500 http://mirror-ubc.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-cache', 'policy', 'conservation-code'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', '-y', 'install', 'conservation-code=20110309.0-8'] 1m1.0s DUMP: Reading package lists... Building dependency tree... Reading state information... conservation-code is already the newest version (20110309.0-8). The following packages were automatically installed and are no longer required: libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python python-minimal python-numpy python-pkg-resources python2 python2-minimal python2.7 python2.7-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', '-y', 'install', 'conservation-code=20110309.0-8'] 1m1.0s INFO: Running scripts post_install 1m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_install_exceptions'] 1m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_install_exceptions'] 1m1.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 1m1.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 1m2.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', '-ac', '--ignore-obsolete'] 1m4.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', '-ac', '--ignore-obsolete'] 1m4.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m4.6s DUMP: 0.15.2 1m4.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m4.6s INFO: Running adequate version 0.15.2 now. 1m4.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'conservation-code'] 1m4.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'conservation-code'] 1m4.8s INFO: Running scripts pre_remove 1m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_remove_exceptions'] 1m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/pre_remove_exceptions'] 1m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m7.2s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.4 install ok installed base-files base-files 11 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-5 install ok installed bsdutils bsdutils 1:2.34-0.1 install ok installed conservation-code conservation-code 20110309.0-8 install ok installed coreutils coreutils 8.30-3+b1 install ok installed dash dash 0.5.10.2-6 install ok installed debconf debconf 1.5.73 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.9.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.7 install ok installed e2fsprogs e2fsprogs 1.45.4-1 install ok installed fdisk fdisk 2.34-0.1 install ok installed findutils findutils 4.7.0-1 install ok installed gcc-9-base:amd64 gcc-9-base 9.2.1-21 install ok installed gpgv gpgv 2.2.17-3 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+b1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.57 install ok installed libacl1:amd64 libacl1 2.2.53-5 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-5 install ok installed libaudit-common libaudit-common 1:2.8.5-2 install ok installed libaudit1:amd64 libaudit1 1:2.8.5-2+b1 install ok installed libblas3:amd64 libblas3 3.9.0-1 install ok installed libblkid1:amd64 libblkid1 2.34-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-2 install ok installed libc-bin libc-bin 2.29-6 install ok installed libc6:amd64 libc6 2.29-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.1+b1 install ok installed libcom-err2:amd64 libcom-err2 1.45.4-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.10-5 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.250 install ok installed libexpat1:amd64 libexpat1 2.2.9-1 install ok installed libext2fs2:amd64 libext2fs2 1.45.4-1 install ok installed libfdisk1:amd64 libfdisk1 2.34-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:9.2.1-21 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.5-3 install ok installed libgfortran5:amd64 libgfortran5 9.2.1-21 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4 install ok installed libgnutls30:amd64 libgnutls30 3.6.11.1-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.36-7 install ok installed libhogweed5:amd64 libhogweed5 3.5.1+really3.5.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.2.0-2 install ok installed liblapack3:amd64 liblapack3 3.9.0-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.2-2 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+b1 install ok installed libmount1:amd64 libmount1 2.34-0.1 install ok installed libmpdec2:amd64 libmpdec2 2.4.2-2 install ok installed libncursesw6:amd64 libncursesw6 6.1+20191019-1 install ok installed libnettle7:amd64 libnettle7 3.5.1+really3.5.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.18.1-2 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 libpcre2-8-0:amd64 libpcre2-8-0 10.34-7 install ok installed libpcre3:amd64 libpcre3 2:8.39-12+b1 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.17-2 install ok installed libpython2-stdlib:amd64 libpython2-stdlib 2.7.17-2 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.17-1 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.17-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.7.5-3 install ok installed libpython3.7-minimal:amd64 libpython3.7-minimal 3.7.5-2 install ok installed libpython3.7-stdlib:amd64 libpython3.7-stdlib 3.7.5-2 install ok installed libpython3.8-minimal:amd64 libpython3.8-minimal 3.8.1~rc1-1 install ok installed libpython3.8-stdlib:amd64 libpython3.8-stdlib 3.8.1~rc1-1 install ok installed libquadmath0:amd64 libquadmath0 9.2.1-21 install ok installed libreadline8:amd64 libreadline8 8.0-3 install ok installed libseccomp2:amd64 libseccomp2 2.4.2-2 install ok installed libselinux1:amd64 libselinux1 3.0-1 install ok installed libsemanage-common libsemanage-common 3.0-1 install ok installed libsemanage1:amd64 libsemanage1 3.0-1 install ok installed libsepol1:amd64 libsepol1 3.0-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.34-0.1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.30.1-1 install ok installed libss2:amd64 libss2 1.45.4-1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1d-2 install ok installed libstdc++6:amd64 libstdc++6 9.2.1-21 install ok installed libsystemd0:amd64 libsystemd0 244-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.15.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.1+20191019-1 install ok installed libudev1:amd64 libudev1 244-3 install ok installed libunistring2:amd64 libunistring2 0.9.10-2 install ok installed libuuid1:amd64 libuuid1 2.34-0.1 install ok installed libzstd1:amd64 libzstd1 1.4.4+dfsg-1 install ok installed login login 1:4.7-2 install ok installed logsave logsave 1.45.4-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mime-support mime-support 3.64 install ok installed mount mount 2.34-0.1 install ok installed ncurses-base ncurses-base 6.1+20191019-1 install ok installed ncurses-bin ncurses-bin 6.1+20191019-1 install ok installed passwd passwd 1:4.7-2 install ok installed perl-base perl-base 5.30.0-9 install ok installed python python 2.7.17-2 install ok installed python-minimal python-minimal 2.7.17-2 install ok installed python-numpy python-numpy 1:1.16.5-2 install ok installed python-pkg-resources python-pkg-resources 41.4.0-1 install ok installed python2 python2 2.7.17-2 install ok installed python2-minimal python2-minimal 2.7.17-2 install ok installed python2.7 python2.7 2.7.17-1 install ok installed python2.7-minimal python2.7-minimal 2.7.17-1 install ok installed python3 python3 3.7.5-3 install ok installed python3-minimal python3-minimal 3.7.5-3 install ok installed python3-numpy python3-numpy 1:1.17.4-4 install ok installed python3-pkg-resources python3-pkg-resources 41.4.0-1 install ok installed python3.7 python3.7 3.7.5-2 install ok installed python3.7-minimal python3.7-minimal 3.7.5-2 install ok installed python3.8 python3.8 3.8.1~rc1-1 install ok installed python3.8-minimal python3.8-minimal 3.8.1~rc1-1 install ok installed readline-common readline-common 8.0-3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-1 install ok installed tar tar 1.30+dfsg-6+b1 install ok installed tzdata tzdata 2019c-3 install ok installed util-linux util-linux 2.34-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+b1 1m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', 'remove', 'python-pkg-resources', 'libpython-stdlib:amd64', 'python2-minimal', 'libblas3:amd64', 'libpython2.7-minimal:amd64', 'libpython3-stdlib:amd64', 'libgfortran5:amd64', 'libpython2-stdlib:amd64', 'libpython3.7-stdlib:amd64', 'libssl1.1:amd64', 'libquadmath0:amd64', 'python2.7', 'libreadline8:amd64', 'libpython3.8-stdlib:amd64', 'libpython3.8-minimal:amd64', 'libsqlite3-0:amd64', 'libpython3.7-minimal:amd64', 'python3-pkg-resources', 'python', 'python-numpy', 'libexpat1:amd64', 'liblapack3:amd64', 'python3-minimal', 'python3.7', 'libmpdec2:amd64', 'readline-common', 'mime-support', 'python3.7-minimal', 'python-minimal', 'python2', 'python3.8-minimal', 'libpython2.7-stdlib:amd64', 'python2.7-minimal', 'python3.8', 'python3-numpy', 'python3', 'conservation-code'] 1m12.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: conservation-code libblas3 libexpat1 libgfortran5 liblapack3 libmpdec2 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.8-minimal libpython3.8-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl1.1 mime-support python python-minimal python-numpy python-pkg-resources python2 python2-minimal python2.7 python2.7-minimal python3 python3-minimal python3-numpy python3-pkg-resources python3.7 python3.7-minimal python3.8 python3.8-minimal readline-common 0 upgraded, 0 newly installed, 37 to remove and 0 not upgraded. After this operation, 124 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 ... 9820 files and directories currently installed.) Removing conservation-code (20110309.0-8) ... Removing python-numpy (1:1.16.5-2) ... Removing python3-numpy (1:1.17.4-4) ... Removing liblapack3:amd64 (3.9.0-1) ... Removing libblas3:amd64 (3.9.0-1) ... Removing python3.8 (3.8.1~rc1-1) ... Removing python3.8-minimal (3.8.1~rc1-1) ... Removing python3-pkg-resources (41.4.0-1) ... Removing python3 (3.7.5-3) ... Removing python3-minimal (3.7.5-3) ... Removing libgfortran5:amd64 (9.2.1-21) ... Removing libpython3.8-stdlib:amd64 (3.8.1~rc1-1) ... Removing python3.7 (3.7.5-2) ... Removing python (2.7.17-2) ... Removing libpython-stdlib:amd64 (2.7.17-2) ... Removing python-pkg-resources (41.4.0-1) ... Removing python2 (2.7.17-2) ... Removing libpython2-stdlib:amd64 (2.7.17-2) ... Removing python2.7 (2.7.17-1) ... Removing libpython2.7-stdlib:amd64 (2.7.17-1) ... Removing python-minimal (2.7.17-2) ... Removing libpython3-stdlib:amd64 (3.7.5-3) ... Removing libpython3.8-minimal:amd64 (3.8.1~rc1-1) ... find: '/usr/lib/python3': No such file or directory Removing libquadmath0:amd64 (9.2.1-21) ... Removing python2-minimal (2.7.17-2) ... Removing python3.7-minimal (3.7.5-2) ... Removing libexpat1:amd64 (2.2.9-1) ... Removing libpython3.7-stdlib:amd64 (3.7.5-2) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec2:amd64 (2.4.2-2) ... Removing python2.7-minimal (2.7.17-1) ... Removing libpython2.7-minimal:amd64 (2.7.17-1) ... find: '/usr/lib/python2.7': No such file or directory Removing libpython3.7-minimal:amd64 (3.7.5-2) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.0-3) ... Removing libsqlite3-0:amd64 (3.30.1-1) ... Removing libssl1.1:amd64 (1.1.1d-2) ... Removing mime-support (3.64) ... Removing readline-common (8.0-3) ... Processing triggers for libc-bin (2.29-6) ... 1m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', 'remove', 'python-pkg-resources', 'libpython-stdlib:amd64', 'python2-minimal', 'libblas3:amd64', 'libpython2.7-minimal:amd64', 'libpython3-stdlib:amd64', 'libgfortran5:amd64', 'libpython2-stdlib:amd64', 'libpython3.7-stdlib:amd64', 'libssl1.1:amd64', 'libquadmath0:amd64', 'python2.7', 'libreadline8:amd64', 'libpython3.8-stdlib:amd64', 'libpython3.8-minimal:amd64', 'libsqlite3-0:amd64', 'libpython3.7-minimal:amd64', 'python3-pkg-resources', 'python', 'python-numpy', 'libexpat1:amd64', 'liblapack3:amd64', 'python3-minimal', 'python3.7', 'libmpdec2:amd64', 'readline-common', 'mime-support', 'python3.7-minimal', 'python-minimal', 'python2', 'python3.8-minimal', 'libpython2.7-stdlib:amd64', 'python2.7-minimal', 'python3.8', 'python3-numpy', 'python3', 'conservation-code'] 1m12.8s INFO: Running scripts post_remove 1m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_remove_exceptions'] 1m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_remove_exceptions'] 1m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg', '--purge', 'python-pkg-resources', 'libpython-stdlib:amd64', 'python2-minimal', 'libblas3:amd64', 'libpython2.7-minimal:amd64', 'libpython3-stdlib:amd64', 'libgfortran5:amd64', 'libpython2-stdlib:amd64', 'libpython3.7-stdlib:amd64', 'libssl1.1:amd64', 'libquadmath0:amd64', 'python2.7', 'libreadline8:amd64', 'libpython3.8-stdlib:amd64', 'libpython3.8-minimal:amd64', 'libsqlite3-0:amd64', 'libpython3.7-minimal:amd64', 'python3-pkg-resources', 'python', 'python-numpy', 'libexpat1:amd64', 'liblapack3:amd64', 'python3-minimal', 'python3.7', 'libmpdec2:amd64', 'readline-common', 'mime-support', 'python3.7-minimal', 'python-minimal', 'python2', 'python3.8-minimal', 'libpython2.7-stdlib:amd64', 'python2.7-minimal', 'python3.8', 'python3-numpy', 'python3'] 1m13.0s DUMP: dpkg: warning: ignoring request to remove python-pkg-resources which isn't installed dpkg: warning: ignoring request to remove libpython-stdlib which isn't installed dpkg: warning: ignoring request to remove python2-minimal which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed (Reading database ... 6543 files and directories currently installed.) Purging configuration files for libpython2.7-minimal:amd64 (2.7.17-1) ... dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libpython2-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.7-stdlib which isn't installed Purging configuration files for libssl1.1:amd64 (1.1.1d-2) ... dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libpython3.8-stdlib which isn't installed Purging configuration files for libpython3.8-minimal:amd64 (3.8.1~rc1-1) ... dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed Purging configuration files for libpython3.7-minimal:amd64 (3.7.5-2) ... dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed Purging configuration files for python (2.7.17-2) ... dpkg: warning: ignoring request to remove python-numpy which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.7 which isn't installed dpkg: warning: ignoring request to remove libmpdec2 which isn't installed Purging configuration files for readline-common (8.0-3) ... Purging configuration files for mime-support (3.64) ... Purging configuration files for python3.7-minimal (3.7.5-2) ... dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python2 which isn't installed Purging configuration files for python3.8-minimal (3.8.1~rc1-1) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed Purging configuration files for python2.7-minimal (2.7.17-1) ... dpkg: warning: ignoring request to remove python3.8 which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed Purging configuration files for python3 (3.7.5-3) ... 1m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg', '--purge', 'python-pkg-resources', 'libpython-stdlib:amd64', 'python2-minimal', 'libblas3:amd64', 'libpython2.7-minimal:amd64', 'libpython3-stdlib:amd64', 'libgfortran5:amd64', 'libpython2-stdlib:amd64', 'libpython3.7-stdlib:amd64', 'libssl1.1:amd64', 'libquadmath0:amd64', 'python2.7', 'libreadline8:amd64', 'libpython3.8-stdlib:amd64', 'libpython3.8-minimal:amd64', 'libsqlite3-0:amd64', 'libpython3.7-minimal:amd64', 'python3-pkg-resources', 'python', 'python-numpy', 'libexpat1:amd64', 'liblapack3:amd64', 'python3-minimal', 'python3.7', 'libmpdec2:amd64', 'readline-common', 'mime-support', 'python3.7-minimal', 'python-minimal', 'python2', 'python3.8-minimal', 'libpython2.7-stdlib:amd64', 'python2.7-minimal', 'python3.8', 'python3-numpy', 'python3'] 1m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg', '--purge', 'conservation-code'] 1m13.1s DUMP: dpkg: warning: ignoring request to remove conservation-code which isn't installed 1m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg', '--purge', 'conservation-code'] 1m13.1s INFO: Running scripts post_purge 1m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_purge_exceptions'] 1m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_purge_exceptions'] 1m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg', '--purge', '--pending'] 1m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg', '--purge', '--pending'] 1m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg', '--remove', '--pending'] 1m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg', '--remove', '--pending'] 1m13.2s INFO: Running scripts post_test 1m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_test_exceptions'] 1m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'tmp/scripts/post_test_exceptions'] 1m13.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 1m13.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 1m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg-divert', '--list'] 1m13.7s 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 1m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'dpkg-divert', '--list'] 1m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', 'clean'] 1m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp21ljJ7', 'apt-get', 'clean'] 1m13.8s DEBUG: Recording chroot state 1m15.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/shm'] 1m15.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/shm'] 1m15.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/console'] 1m15.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/console'] 1m15.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/ptmx'] 1m15.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/ptmx'] 1m15.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/pts'] 1m15.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/dev/pts'] 1m15.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/proc'] 1m15.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp21ljJ7/proc'] 1m15.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 1m16.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp21ljJ7'] 1m16.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp21ljJ7 1m16.1s INFO: PASS: Upgrading between Debian distributions. 1m16.1s INFO: PASS: All tests. 1m16.1s INFO: piuparts run ends. ret=0 End: 2019-12-15 21:55:07 UTC