Start: 2025-08-12 00:23:28 GMT [trixie] Package: pftools Version: 3.2.12-1 Installed-Size: 52597 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.33), libgfortran5 (>= 8), libpcre2-8-0 (>= 10.22), libfile-slurp-perl Description: build and search protein and DNA generalized profiles Homepage: https://github.com/sib-swiss/pftools3 Description-md5: 4e95fd2926a532a35d8b09eb65b029b1 Section: science Priority: optional Filename: pool/main/p/pftools/pftools_3.2.12-1_amd64.deb Size: 24782188 MD5sum: 5c0c7ae7cafa197667aeb59eeeed848f SHA256: 55b4bb153a63706f16e3150bfba2e85e8deac5f90bada8da879df7cd80ffd63c [trixie-next] Package: pftools Version: 3.2.12-1 Installed-Size: 52597 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.33), libgfortran5 (>= 8), libpcre2-8-0 (>= 10.22), libfile-slurp-perl Description: build and search protein and DNA generalized profiles Homepage: https://github.com/sib-swiss/pftools3 Description-md5: 4e95fd2926a532a35d8b09eb65b029b1 Section: science Priority: optional Filename: pool/main/p/pftools/pftools_3.2.12-1_amd64.deb Size: 24782188 MD5sum: 5c0c7ae7cafa197667aeb59eeeed848f SHA256: 55b4bb153a63706f16e3150bfba2e85e8deac5f90bada8da879df7cd80ffd63c 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 trixie -d trixie-next -B /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat --apt pftools=3.2.12-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.6.1~202508101417~1.6.0-7-g17c4ea32 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 trixie -d trixie-next -B /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat --apt pftools=3.2.12-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpl6hqojp4 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpl6hqojp4 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpl6hqojp4/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', 'update'] 0m1.8s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [138 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9668 kB] Fetched 9805 kB in 1s (13.4 MB/s) Reading package lists... 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', 'update'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s DUMP: 8fc0def95551deb38dc214d6c9cce720 - 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s INFO: Running scripts post_setup 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s 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 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s 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' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.6s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 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 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 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 3.0.3 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 2.41-5 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 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 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 0.280 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 2.41-5 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 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 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 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libuuid1:amd64 libuuid1 2.41-5 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+really2.41-5 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 2.41-5 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 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 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-4 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.6s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat 0m3.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m3.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m3.9s INFO: Running scripts is_testable 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/is_testable_uninstallable'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/is_testable_uninstallable'] 0m3.9s INFO: Running scripts pre_test 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_test_exceptions'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_test_exceptions'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_test_root_password'] 0m4.0s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_test_root_password'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'show', '--no-all-versions', 'pftools'] 0m4.2s DUMP: Package: pftools Version: 3.2.12-1 Installed-Size: 52597 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.33), libgfortran5 (>= 8), libpcre2-8-0 (>= 10.22), libfile-slurp-perl Description-en: build and search protein and DNA generalized profiles The pftools package contains all the software necessary to build protein and DNA generalized profiles and use them to scan and align sequences, and search databases. . File formats used by the pftools * Generalized profiles format and syntax. * The multiple sequence alignment format (PSA). * The extended header multiple sequence alignment format (XPSA). . Programs to build generalized profiles pfmake Build a profile from a multiple sequence alignment. pfscale Fit parameters of an extreme-value distribution to a profile score list. pfw Weight sequences of a multiple sequence alignment to correct for sampling bias. . Programs to search with generalized profiles pfsearch / pfsearchV3 Search a protein or DNA sequence library for sequence segments matching a profile (V3 is the new version of this tool). pfscan Scan a protein or DNA sequence with a profile library . Conversion programs psa2msa Reformat PSA file to Pearson/Fasta multiple sequence alignment file. ptof Convert a protein profile into a frame-search profile to search DNA sequences. To be used with 2ft. 2ft Converts both strands of DNA into so-called interleaved frame-translated DNA sequences to search with protein profiles. To be used with ptof. 6ft Translates all six reading frames of a double-stranded DNA sequence into individual protein sequences. pfgtop Convert a profile in GCG format into PROSITE format. pfhtop Convert a HMMER1 ASCII-formatted HMM into an equivalent PROSITE profile. ptoh Converts a generalized profile into an approximately equivalent HMM profile in HMMER1 format (can be read by the hmmconvert program from the HMMER2 package). Description-md5: 4e95fd2926a532a35d8b09eb65b029b1 Homepage: https://github.com/sib-swiss/pftools3 Section: science Priority: optional Filename: pool/main/p/pftools/pftools_3.2.12-1_amd64.deb Size: 24782188 MD5sum: 5c0c7ae7cafa197667aeb59eeeed848f SHA256: 55b4bb153a63706f16e3150bfba2e85e8deac5f90bada8da879df7cd80ffd63c 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'show', '--no-all-versions', 'pftools'] 0m4.2s INFO: apt-cache knows about the following packages: pftools 0m4.2s INFO: Running scripts pre_install 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_database-server'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_database-server'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_exceptions'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_exceptions'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_extras'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_extras'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'policy'] 0m4.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'policy'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'policy', 'pftools'] 0m4.3s DUMP: pftools: Installed: (none) Candidate: 3.2.12-1 Version table: 3.2.12-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'policy', 'pftools'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', '-y', 'install', 'pftools'] 0m6.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libfile-slurp-perl libgdbm-compat4t64 libgdbm6t64 libgfortran5 libperl5.40 perl perl-modules-5.40 Suggested packages: gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl Recommended packages: netbase The following NEW packages will be installed: libfile-slurp-perl libgdbm-compat4t64 libgdbm6t64 libgfortran5 libperl5.40 perl perl-modules-5.40 pftools 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. Need to get 33.4 MB of archives. After this operation, 109 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.1-6 [3019 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.1-6 [4341 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.1-6 [267 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libfile-slurp-perl all 9999.32-2 [26.7 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 pftools amd64 3.2.12-1 [24.8 MB] Fetched 33.4 MB in 0s (127 MB/s) Selecting previously unselected package perl-modules-5.40. (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 ... 4938 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.40_5.40.1-6_all.deb ... Unpacking perl-modules-5.40 (5.40.1-6) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../1-libgdbm6t64_1.24-2_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.24-2) ... Selecting previously unselected package libgdbm-compat4t64:amd64. Preparing to unpack .../2-libgdbm-compat4t64_1.24-2_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.24-2) ... Selecting previously unselected package libperl5.40:amd64. Preparing to unpack .../3-libperl5.40_5.40.1-6_amd64.deb ... Unpacking libperl5.40:amd64 (5.40.1-6) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.40.1-6_amd64.deb ... Unpacking perl (5.40.1-6) ... Selecting previously unselected package libfile-slurp-perl. Preparing to unpack .../5-libfile-slurp-perl_9999.32-2_all.deb ... Unpacking libfile-slurp-perl (9999.32-2) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../6-libgfortran5_14.2.0-19_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-19) ... Selecting previously unselected package pftools. Preparing to unpack .../7-pftools_3.2.12-1_amd64.deb ... Unpacking pftools (3.2.12-1) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up perl-modules-5.40 (5.40.1-6) ... Setting up libperl5.40:amd64 (5.40.1-6) ... Setting up perl (5.40.1-6) ... Setting up libfile-slurp-perl (9999.32-2) ... Setting up pftools (3.2.12-1) ... Processing triggers for libc-bin (2.41-12) ... 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', '-y', 'install', 'pftools'] 0m6.7s INFO: Running scripts post_install 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_install_exceptions'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_install_exceptions'] 0m6.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m7.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m7.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpl6hqojp4 to trixie-next 0m7.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main deb http://security.debian.org trixie-security main deb http://deb.debian.org/debian/ trixie-updates main deb http://deb.debian.org/debian/ trixie-proposed-updates main 0m7.1s INFO: Running scripts pre_distupgrade 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_distupgrade_exceptions'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_distupgrade_exceptions'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', 'update'] 0m7.9s DUMP: Hit:1 http://deb.debian.org/debian trixie InRelease Get:2 http://security.debian.org trixie-security InRelease [43.4 kB] Get:3 http://deb.debian.org/debian trixie-updates InRelease [47.1 kB] Get:4 http://deb.debian.org/debian trixie-proposed-updates InRelease [55.8 kB] Get:5 http://security.debian.org trixie-security/main amd64 Packages [5304 B] Get:6 http://deb.debian.org/debian trixie-updates/main amd64 Packages [2432 B] Get:7 http://security.debian.org trixie-security/main Translation-en [6724 B] Get:8 http://deb.debian.org/debian trixie-updates/main Translation-en [396 B] Get:9 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages [7300 B] Get:10 http://deb.debian.org/debian trixie-proposed-updates/main Translation-en [3288 B] Fetched 172 kB in 0s (1510 kB/s) Reading package lists... 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', 'update'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', '-yf', 'dist-upgrade'] 0m8.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', '-yf', 'dist-upgrade'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.9s DUMP: 5c6a884f0339ba51c78a9d3f50b19f1b - 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'show', '--no-all-versions', 'pftools'] 0m9.2s DUMP: Package: pftools Version: 3.2.12-1 Installed-Size: 52597 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.33), libgfortran5 (>= 8), libpcre2-8-0 (>= 10.22), libfile-slurp-perl Description-en: build and search protein and DNA generalized profiles The pftools package contains all the software necessary to build protein and DNA generalized profiles and use them to scan and align sequences, and search databases. . File formats used by the pftools * Generalized profiles format and syntax. * The multiple sequence alignment format (PSA). * The extended header multiple sequence alignment format (XPSA). . Programs to build generalized profiles pfmake Build a profile from a multiple sequence alignment. pfscale Fit parameters of an extreme-value distribution to a profile score list. pfw Weight sequences of a multiple sequence alignment to correct for sampling bias. . Programs to search with generalized profiles pfsearch / pfsearchV3 Search a protein or DNA sequence library for sequence segments matching a profile (V3 is the new version of this tool). pfscan Scan a protein or DNA sequence with a profile library . Conversion programs psa2msa Reformat PSA file to Pearson/Fasta multiple sequence alignment file. ptof Convert a protein profile into a frame-search profile to search DNA sequences. To be used with 2ft. 2ft Converts both strands of DNA into so-called interleaved frame-translated DNA sequences to search with protein profiles. To be used with ptof. 6ft Translates all six reading frames of a double-stranded DNA sequence into individual protein sequences. pfgtop Convert a profile in GCG format into PROSITE format. pfhtop Convert a HMMER1 ASCII-formatted HMM into an equivalent PROSITE profile. ptoh Converts a generalized profile into an approximately equivalent HMM profile in HMMER1 format (can be read by the hmmconvert program from the HMMER2 package). Description-md5: 4e95fd2926a532a35d8b09eb65b029b1 Homepage: https://github.com/sib-swiss/pftools3 Section: science Priority: optional Filename: pool/main/p/pftools/pftools_3.2.12-1_amd64.deb Size: 24782188 MD5sum: 5c0c7ae7cafa197667aeb59eeeed848f SHA256: 55b4bb153a63706f16e3150bfba2e85e8deac5f90bada8da879df7cd80ffd63c 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'show', '--no-all-versions', 'pftools'] 0m9.2s INFO: apt-cache knows about the following packages: pftools 0m9.2s INFO: Running scripts pre_install 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_database-server'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_database-server'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_exceptions'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_exceptions'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_extras'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_extras'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'policy'] 0m9.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages release v=13-updates,o=Debian,a=proposed-updates,n=trixie-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian trixie-updates/main amd64 Packages release v=13-updates,o=Debian,a=stable-updates,n=trixie-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org trixie-security/main amd64 Packages release v=13,o=Debian,a=stable-security,n=trixie-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'policy'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'policy', 'pftools'] 0m9.3s DUMP: pftools: Installed: 3.2.12-1 Candidate: 3.2.12-1 Version table: *** 3.2.12-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'policy', 'pftools'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', '-y', 'install', 'pftools'] 0m9.8s DUMP: Reading package lists... Building dependency tree... Reading state information... pftools is already the newest version (3.2.12-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', '-y', 'install', 'pftools'] 0m9.8s INFO: Running scripts post_install 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_install_exceptions'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_install_exceptions'] 0m9.8s INFO: Running scripts post_distupgrade 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_distupgrade_exceptions'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_distupgrade_exceptions'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_distupgrade_zz_backports'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_distupgrade_zz_backports'] 0m9.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m10.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m10.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m10.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m10.6s INFO: Running scripts pre_install 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_database-server'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_database-server'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_exceptions'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_exceptions'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_extras'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_extras'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'policy'] 0m10.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages release v=13-updates,o=Debian,a=proposed-updates,n=trixie-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian trixie-updates/main amd64 Packages release v=13-updates,o=Debian,a=stable-updates,n=trixie-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org trixie-security/main amd64 Packages release v=13,o=Debian,a=stable-security,n=trixie-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'policy'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'policy', 'pftools'] 0m10.7s DUMP: pftools: Installed: 3.2.12-1 Candidate: 3.2.12-1 Version table: *** 3.2.12-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-cache', 'policy', 'pftools'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', '-y', 'install', 'pftools=3.2.12-1'] 0m11.1s DUMP: Reading package lists... Building dependency tree... Reading state information... pftools is already the newest version (3.2.12-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', '-y', 'install', 'pftools=3.2.12-1'] 0m11.1s INFO: Running scripts post_install 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_install_exceptions'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_install_exceptions'] 0m11.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m11.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m11.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', '-ac', '--ignore-obsolete'] 0m12.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', '-ac', '--ignore-obsolete'] 0m12.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m12.6s DUMP: 0.15.9~deb12u1 0m12.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m12.6s INFO: Running adequate version 0.15.9~deb12u1 now. 0m12.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'pftools'] 0m12.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'pftools'] 0m12.9s INFO: Running scripts pre_remove 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_remove_exceptions'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/pre_remove_exceptions'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m13.5s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 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 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 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 3.0.3 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 2.41-5 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 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 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 0.280 install ok installed libfile-slurp-perl libfile-slurp-perl 9999.32-2 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgfortran5:amd64 libgfortran5 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 2.41-5 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 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libperl5.40:amd64 libperl5.40 5.40.1-6 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 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libuuid1:amd64 libuuid1 2.41-5 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+really2.41-5 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 2.41-5 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 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl perl 5.40.1-6 install ok installed perl-base perl-base 5.40.1-6 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.1-6 install ok installed pftools pftools 3.2.12-1 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 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-4 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', 'remove', '--allow-remove-essential', 'libfile-slurp-perl', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libperl5.40:amd64', 'perl', 'perl-modules-5.40', 'pftools'] 0m14.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libfile-slurp-perl libgdbm-compat4t64 libgdbm6t64 libgfortran5 libperl5.40 perl perl-modules-5.40 pftools 0 upgraded, 0 newly installed, 8 to remove and 0 not upgraded. After this operation, 109 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 ... 7256 files and directories currently installed.) Removing pftools (3.2.12-1) ... Removing libfile-slurp-perl (9999.32-2) ... Removing perl (5.40.1-6) ... Removing libperl5.40:amd64 (5.40.1-6) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgfortran5:amd64 (14.2.0-19) ... Removing perl-modules-5.40 (5.40.1-6) ... Processing triggers for libc-bin (2.41-12) ... 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', 'remove', '--allow-remove-essential', 'libfile-slurp-perl', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libperl5.40:amd64', 'perl', 'perl-modules-5.40', 'pftools'] 0m14.4s INFO: Running scripts post_remove 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_remove_exceptions'] 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_remove_exceptions'] 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg', '--purge', 'libfile-slurp-perl', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libperl5.40:amd64', 'perl', 'perl-modules-5.40'] 0m14.4s DUMP: dpkg: warning: ignoring request to remove libfile-slurp-perl which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed (Reading database ... 4941 files and directories currently installed.) Purging configuration files for perl (5.40.1-6) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg', '--purge', 'libfile-slurp-perl', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libperl5.40:amd64', 'perl', 'perl-modules-5.40'] 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg', '--purge', 'pftools'] 0m14.5s DUMP: dpkg: warning: ignoring request to remove pftools which isn't installed 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg', '--purge', 'pftools'] 0m14.5s INFO: Running scripts post_purge 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_purge_exceptions'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_purge_exceptions'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg', '--purge', '--pending'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg', '--purge', '--pending'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg', '--remove', '--pending'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg', '--remove', '--pending'] 0m14.5s INFO: Running scripts post_test 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_test_exceptions'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'tmp/scripts/post_test_exceptions'] 0m14.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m14.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg-divert', '--list'] 0m14.9s 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 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'dpkg-divert', '--list'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', 'clean'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4', 'apt-get', 'clean'] 0m14.9s DEBUG: Recording chroot state 0m15.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/shm'] 0m15.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/shm'] 0m15.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/console'] 0m15.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/console'] 0m15.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/ptmx'] 0m15.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/ptmx'] 0m15.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/pts'] 0m15.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/dev/pts'] 0m15.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/proc'] 0m15.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4/proc'] 0m15.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m16.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpl6hqojp4'] 0m16.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpl6hqojp4 0m16.0s INFO: PASS: Upgrading between Debian distributions. 0m16.0s INFO: PASS: All tests. 0m16.0s INFO: piuparts run ends. ret=0 End: 2025-08-12 00:23:44 GMT