Start: 2025-05-07 15:27:58 GMT [testing] Package: voronota Version: 1.29.4307+ds-1 Installed-Size: 13978 Maintainer: Debian Science Maintainers Architecture: amd64 Depends: bsdextrautils, libc6 (>= 2.34), libgcc-s1 (>= 3.4), libstdc++6 (>= 14) Description: Voronoi diagram-based tool to find atom contacts Homepage: https://bitbucket.org/kliment/voronota Description-md5: 406a01a6edd5b72aa5a80fb00f49f33e Section: science Priority: optional Filename: pool/main/v/voronota/voronota_1.29.4307+ds-1_amd64.deb Size: 2649776 MD5sum: 7491a073f9a0fc4a942db9ec154c4eb5 SHA256: 879236dd0d10df9a89769d61f44a562194a7d026f1740131a7a3f2b2e6d5b776 [sid] Package: voronota Version: 1.29.4307+ds-2 Installed-Size: 14511 Maintainer: Debian Science Maintainers Architecture: amd64 Depends: bsdextrautils, libc6 (>= 2.34), libgcc-s1 (>= 3.4), libgomp1 (>= 4.9), libstdc++6 (>= 14) Description: Voronoi diagram-based tool to find atom contacts Homepage: https://bitbucket.org/kliment/voronota Description-md5: 406a01a6edd5b72aa5a80fb00f49f33e Section: science Priority: optional Filename: pool/main/v/voronota/voronota_1.29.4307+ds-2_amd64.deb Size: 2779836 MD5sum: 8d1f70095c9ca4d5aa7acbcf2f11284e SHA256: f4efa25afeea5b8157c6e27b2f06f723db6ec2fe563146643ac144267dde5b9a Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt voronota=1.29.4307+ds-2 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 1.5.2~202503162239~1.5.1-10-g345d5865 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt voronota=1.29.4307+ds-2 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-34-amd64 #1 SMP Debian 5.10.234-1 (2025-02-24) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpjx37gn69 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpjx37gn69 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpjx37gn69/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', 'update'] 0m1.5s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [175 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9682 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6493 kB] Fetched 16.4 MB in 1s (19.4 MB/s) Reading package lists... 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', 'update'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: apt libapt-pkg7.0 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2565 kB of archives. After this operation, 8192 B of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libapt-pkg7.0 amd64 3.0.1 [1113 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 apt amd64 3.0.1 [1452 kB] Fetched 2565 kB in 0s (30.7 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 ... 4936 files and directories currently installed.) Preparing to unpack .../libapt-pkg7.0_3.0.1_amd64.deb ... Unpacking libapt-pkg7.0:amd64 (3.0.1) over (3.0.0) ... Setting up libapt-pkg7.0:amd64 (3.0.1) ... (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 ... 4936 files and directories currently installed.) Preparing to unpack .../archives/apt_3.0.1_amd64.deb ... Unpacking apt (3.0.1) over (3.0.0) ... Setting up apt (3.0.1) ... Processing triggers for libc-bin (2.41-7) ... 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.9s DUMP: 891620a096a738ce410c1ba7f36e0e04 - 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.9s INFO: Running scripts post_setup 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_setup_dummy_users'] 0m3.3s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_setup_dummy_users'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_setup_forbid_home'] 0m3.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_setup_forbid_home'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.3s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_setup_minimize'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_setup_minimize'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_setup_zz_backports'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_setup_zz_backports'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.3s DUMP: install ok installed apt apt 3.0.1 install ok installed base-files base-files 13.7 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2 install ok installed bsdutils bsdutils 1:2.41-4 install ok installed coreutils coreutils 9.7-2 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.22 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.18 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.1 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-4 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-7 install ok installed libc6:amd64 libc6 2.41-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-7 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-4 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-4 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-4 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-3 install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.5-2 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.5-2 install ok installed libuuid1:amd64 libuuid1 2.41-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-4 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-4 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-3 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-1 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-2 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.41-4 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m3.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m3.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m3.5s INFO: Running scripts is_testable 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s INFO: Running scripts pre_test 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_test_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_test_exceptions'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_test_root_password'] 0m3.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_test_root_password'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'show', '--no-all-versions', 'voronota'] 0m3.7s DUMP: Package: voronota Version: 1.29.4307+ds-1 Installed-Size: 13978 Maintainer: Debian Science Maintainers Architecture: amd64 Depends: bsdextrautils, libc6 (>= 2.34), libgcc-s1 (>= 3.4), libstdc++6 (>= 14) Description-en: Voronoi diagram-based tool to find atom contacts The analysis of macromolecular structures often requires a comprehensive definition of atomic neighborhoods. Such a definition can be based on the Voronoi diagram of balls, where each ball represents an atom of some van der Waals radius. Voronota is a software tool for finding all the vertices of the Voronoi diagram of balls. Such vertices correspond to the centers of the empty tangent spheres defined by quadruples of balls. Voronota is especially suitable for processing three-dimensional structures of biological macromolecules such as proteins and RNA. . Since version 1.2 Voronota also uses the Voronoi vertices to construct inter-atom contact surfaces and solvent accessible surfaces. Voronota provides tools to query contacts, generate contacts graphics, compare contacts and evaluate quality of protein structural models using contacts. Description-md5: 406a01a6edd5b72aa5a80fb00f49f33e Homepage: https://bitbucket.org/kliment/voronota Section: science Priority: optional Filename: pool/main/v/voronota/voronota_1.29.4307+ds-1_amd64.deb Size: 2649776 MD5sum: 7491a073f9a0fc4a942db9ec154c4eb5 SHA256: 879236dd0d10df9a89769d61f44a562194a7d026f1740131a7a3f2b2e6d5b776 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'show', '--no-all-versions', 'voronota'] 0m3.7s INFO: apt-cache knows about the following packages: voronota 0m3.7s INFO: Running scripts pre_install 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'policy'] 0m3.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'policy'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'policy', 'voronota'] 0m3.7s DUMP: voronota: Installed: (none) Candidate: 1.29.4307+ds-1 Version table: 1.29.4307+ds-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'policy', 'voronota'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', '-y', 'install', 'voronota'] 0m4.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: bsdextrautils The following NEW packages will be installed: bsdextrautils voronota 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 2744 kB of archives. After this operation, 14.7 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-4 [94.6 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 voronota amd64 1.29.4307+ds-1 [2650 kB] Fetched 2744 kB in 0s (7177 kB/s) Selecting previously unselected package bsdextrautils. (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 ... 4940 files and directories currently installed.) Preparing to unpack .../bsdextrautils_2.41-4_amd64.deb ... Unpacking bsdextrautils (2.41-4) ... Selecting previously unselected package voronota. Preparing to unpack .../voronota_1.29.4307+ds-1_amd64.deb ... Unpacking voronota (1.29.4307+ds-1) ... Setting up bsdextrautils (2.41-4) ... Setting up voronota (1.29.4307+ds-1) ... 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', '-y', 'install', 'voronota'] 0m4.6s INFO: Running scripts post_install 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_install_exceptions'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_install_exceptions'] 0m4.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m4.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m4.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpjx37gn69 to sid 0m4.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m4.8s INFO: Running scripts pre_distupgrade 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_distupgrade_exceptions'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_distupgrade_exceptions'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', 'update'] 0m6.7s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7406 kB] Fetched 17.7 MB in 1s (12.2 MB/s) Reading package lists... 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', 'update'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', '-yf', 'dist-upgrade'] 0m7.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libgomp1 The following packages will be upgraded: libsqlite3-0 tzdata voronota 3 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 4090 kB of archives. After this operation, 924 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.46.1-4 [913 kB] Get:2 http://deb.debian.org/debian sid/main amd64 tzdata all 2025b-3 [260 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:4 http://deb.debian.org/debian sid/main amd64 voronota amd64 1.29.4307+ds-2 [2780 kB] Preconfiguring packages ... Fetched 4090 kB in 0s (46.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4986 files and directories currently installed.) Preparing to unpack .../libsqlite3-0_3.46.1-4_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-4) over (3.46.1-3) ... Setting up libsqlite3-0:amd64 (3.46.1-4) ... (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 ... 4986 files and directories currently installed.) Preparing to unpack .../tzdata_2025b-3_all.deb ... Unpacking tzdata (2025b-3) over (2025b-2) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../libgomp1_14.2.0-19_amd64.deb ... Unpacking libgomp1:amd64 (14.2.0-19) ... Preparing to unpack .../voronota_1.29.4307+ds-2_amd64.deb ... Unpacking voronota (1.29.4307+ds-2) over (1.29.4307+ds-1) ... Setting up libgomp1:amd64 (14.2.0-19) ... Setting up tzdata (2025b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Wed May 7 15:28:06 UTC 2025. Universal Time is now: Wed May 7 15:28:06 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up voronota (1.29.4307+ds-2) ... Processing triggers for libc-bin (2.41-7) ... 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', '-yf', 'dist-upgrade'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.8s DUMP: 2a72e336ef3e6b981d2647d71e4782fd - 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'show', '--no-all-versions', 'voronota'] 0m7.9s DUMP: Package: voronota Version: 1.29.4307+ds-2 Installed-Size: 14511 Maintainer: Debian Science Maintainers Architecture: amd64 Depends: bsdextrautils, libc6 (>= 2.34), libgcc-s1 (>= 3.4), libgomp1 (>= 4.9), libstdc++6 (>= 14) Description-en: Voronoi diagram-based tool to find atom contacts The analysis of macromolecular structures often requires a comprehensive definition of atomic neighborhoods. Such a definition can be based on the Voronoi diagram of balls, where each ball represents an atom of some van der Waals radius. Voronota is a software tool for finding all the vertices of the Voronoi diagram of balls. Such vertices correspond to the centers of the empty tangent spheres defined by quadruples of balls. Voronota is especially suitable for processing three-dimensional structures of biological macromolecules such as proteins and RNA. . Since version 1.2 Voronota also uses the Voronoi vertices to construct inter-atom contact surfaces and solvent accessible surfaces. Voronota provides tools to query contacts, generate contacts graphics, compare contacts and evaluate quality of protein structural models using contacts. Description-md5: 406a01a6edd5b72aa5a80fb00f49f33e Homepage: https://bitbucket.org/kliment/voronota Section: science Priority: optional Filename: pool/main/v/voronota/voronota_1.29.4307+ds-2_amd64.deb Size: 2779836 MD5sum: 8d1f70095c9ca4d5aa7acbcf2f11284e SHA256: f4efa25afeea5b8157c6e27b2f06f723db6ec2fe563146643ac144267dde5b9a 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'show', '--no-all-versions', 'voronota'] 0m7.9s INFO: apt-cache knows about the following packages: voronota 0m7.9s INFO: Running scripts pre_install 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_database-server'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_database-server'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_exceptions'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_exceptions'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_extras'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_extras'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'policy'] 0m8.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'policy'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'policy', 'voronota'] 0m8.0s DUMP: voronota: Installed: 1.29.4307+ds-2 Candidate: 1.29.4307+ds-2 Version table: *** 1.29.4307+ds-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'policy', 'voronota'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', '-y', 'install', 'voronota'] 0m8.2s DUMP: Reading package lists... Building dependency tree... Reading state information... voronota is already the newest version (1.29.4307+ds-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', '-y', 'install', 'voronota'] 0m8.2s INFO: Running scripts post_install 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_install_exceptions'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_install_exceptions'] 0m8.2s INFO: Running scripts post_distupgrade 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_distupgrade_exceptions'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_distupgrade_exceptions'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_distupgrade_zz_backports'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_distupgrade_zz_backports'] 0m8.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m8.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m8.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m8.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m8.6s INFO: Running scripts pre_install 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_database-server'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_database-server'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_exceptions'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_exceptions'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_extras'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_extras'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'policy'] 0m8.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'policy'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'policy', 'voronota'] 0m8.7s DUMP: voronota: Installed: 1.29.4307+ds-2 Candidate: 1.29.4307+ds-2 Version table: *** 1.29.4307+ds-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-cache', 'policy', 'voronota'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', '-y', 'install', 'voronota=1.29.4307+ds-2'] 0m8.9s DUMP: Reading package lists... Building dependency tree... Reading state information... voronota is already the newest version (1.29.4307+ds-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', '-y', 'install', 'voronota=1.29.4307+ds-2'] 0m8.9s INFO: Running scripts post_install 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_install_exceptions'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_install_exceptions'] 0m8.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m9.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m9.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', '-ac', '--ignore-obsolete'] 0m9.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', '-ac', '--ignore-obsolete'] 0m9.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m9.7s DUMP: 0.15.6 0m9.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m9.7s INFO: Running adequate version 0.15.6 now. 0m9.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'voronota'] 0m9.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'voronota'] 0m9.7s INFO: Running scripts pre_remove 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_remove_exceptions'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/pre_remove_exceptions'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.0s DUMP: install ok installed apt apt 3.0.1 install ok installed base-files base-files 13.7 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2 install ok installed bsdextrautils bsdextrautils 2.41-4 install ok installed bsdutils bsdutils 1:2.41-4 install ok installed coreutils coreutils 9.7-2 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.22 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.18 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.1 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-4 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-7 install ok installed libc6:amd64 libc6 2.41-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-7 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgomp1:amd64 libgomp1 14.2.0-19 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-4 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-4 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-4 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-4 install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.5-2 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.5-2 install ok installed libuuid1:amd64 libuuid1 2.41-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-4 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-4 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-3 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-1 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-3 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.41-4 install ok installed voronota voronota 1.29.4307+ds-2 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', 'remove', '--allow-remove-essential', 'bsdextrautils', 'libgomp1:amd64', 'voronota'] 0m10.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bsdextrautils libgomp1 voronota 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. After this operation, 15.6 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 ... 5004 files and directories currently installed.) Removing voronota (1.29.4307+ds-2) ... Removing bsdextrautils (2.41-4) ... Removing libgomp1:amd64 (14.2.0-19) ... Processing triggers for libc-bin (2.41-7) ... 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', 'remove', '--allow-remove-essential', 'bsdextrautils', 'libgomp1:amd64', 'voronota'] 0m10.4s INFO: Running scripts post_remove 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_remove_exceptions'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_remove_exceptions'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg', '--purge', 'bsdextrautils', 'libgomp1:amd64'] 0m10.4s DUMP: dpkg: warning: ignoring request to remove bsdextrautils which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg', '--purge', 'bsdextrautils', 'libgomp1:amd64'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg', '--purge', 'voronota'] 0m10.4s DUMP: dpkg: warning: ignoring request to remove voronota which isn't installed 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg', '--purge', 'voronota'] 0m10.4s INFO: Running scripts post_purge 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_purge_exceptions'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_purge_exceptions'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg', '--purge', '--pending'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg', '--purge', '--pending'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg', '--remove', '--pending'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg', '--remove', '--pending'] 0m10.4s INFO: Running scripts post_test 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_test_exceptions'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'tmp/scripts/post_test_exceptions'] 0m10.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m10.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg-divert', '--list'] 0m10.6s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'dpkg-divert', '--list'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', 'clean'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpjx37gn69', 'apt-get', 'clean'] 0m10.6s DEBUG: Recording chroot state 0m11.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/shm'] 0m11.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/shm'] 0m11.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/console'] 0m11.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/console'] 0m11.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/ptmx'] 0m11.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/ptmx'] 0m11.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/pts'] 0m11.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/dev/pts'] 0m11.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/proc'] 0m11.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpjx37gn69/proc'] 0m11.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m11.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpjx37gn69'] 0m11.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpjx37gn69 0m11.3s INFO: PASS: Upgrading between Debian distributions. 0m11.3s INFO: PASS: All tests. 0m11.3s INFO: piuparts run ends. ret=0 End: 2025-05-07 15:28:09 GMT