Start: 2022-03-26 23:50:42 GMT [testing] Package: pftools Source: pftools (3.2.11-2) Version: 3.2.11-2+b1 Installed-Size: 52623 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.33), libgfortran5 (>= 8), 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_3.2.11-2+b1_amd64.deb Size: 24774428 MD5sum: 7fae413d3e340e3fcac064673cde9e79 SHA256: d3a4c8d2fb9e8a8539db041a2c21cf5f9ba2e03fd659b86675fa6f53ad53d1ad [sid] 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/sbin/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/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/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 1.1.4 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt pftools=3.2.12-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.19.0-20-amd64 #1 SMP Debian 4.19.235-1 (2022-03-17) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpqrybm0nj 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpqrybm0nj 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m1.8s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/proc'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/proc'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/pts'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/pts'] 0m1.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/ptmx'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/ptmx'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/console'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/console'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/shm'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/shm'] 0m1.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m1.9s DEBUG: Created policy-rc.d and chmodded it. 0m1.9s DEBUG: Created resolv.conf. 0m1.9s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpqrybm0nj/tmp/scripts/ 0m1.9s INFO: Running scripts post_chroot_unpack 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', 'update'] 0m4.3s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [130 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8359 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5717 kB] Fetched 14.2 MB in 2s (7743 kB/s) Reading package lists... 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', 'update'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', '-yf', 'dist-upgrade'] 0m6.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: adduser apt gcc-12-base libapt-pkg6.0 libgcc-s1 libstdc++6 libzstd1 tzdata 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 4238 kB of archives. After this operation, 93.2 kB disk space will be freed. Get:1 http://deb.debian.org/debian bookworm/main amd64 gcc-12-base amd64 12-20220319-1 [206 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libgcc-s1 amd64 12-20220319-1 [50.2 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libstdc++6 amd64 12-20220319-1 [617 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libzstd1 amd64 1.4.9+dfsg-1 [324 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libapt-pkg6.0 amd64 2.4.3 [1028 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 adduser all 3.121 [224 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 apt amd64 2.4.3 [1496 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2022a-1 [292 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 4238 kB in 0s (57.2 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 ... 6687 files and directories currently installed.) Preparing to unpack .../gcc-12-base_12-20220319-1_amd64.deb ... Unpacking gcc-12-base:amd64 (12-20220319-1) over (12-20220313-1) ... Setting up gcc-12-base:amd64 (12-20220319-1) ... (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 ... 6687 files and directories currently installed.) Preparing to unpack .../libgcc-s1_12-20220319-1_amd64.deb ... Unpacking libgcc-s1:amd64 (12-20220319-1) over (12-20220313-1) ... Setting up libgcc-s1:amd64 (12-20220319-1) ... (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 ... 6687 files and directories currently installed.) Preparing to unpack .../libstdc++6_12-20220319-1_amd64.deb ... Unpacking libstdc++6:amd64 (12-20220319-1) over (12-20220313-1) ... Setting up libstdc++6:amd64 (12-20220319-1) ... (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 ... 6687 files and directories currently installed.) Preparing to unpack .../libzstd1_1.4.9+dfsg-1_amd64.deb ... Unpacking libzstd1:amd64 (1.4.9+dfsg-1) over (1.4.8+dfsg-3) ... Setting up libzstd1:amd64 (1.4.9+dfsg-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 ... 6687 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.4.3_amd64.deb ... Unpacking libapt-pkg6.0:amd64 (2.4.3) over (2.4.2) ... Setting up libapt-pkg6.0:amd64 (2.4.3) ... (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 ... 6687 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.121_all.deb ... Unpacking adduser (3.121) over (3.120) ... Setting up adduser (3.121) ... Installing new version of config file /etc/deluser.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6687 files and directories currently installed.) Preparing to unpack .../archives/apt_2.4.3_amd64.deb ... Unpacking apt (2.4.3) over (2.4.2) ... Setting up apt (2.4.3) ... (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 ... 6687 files and directories currently installed.) Preparing to unpack .../tzdata_2022a-1_all.deb ... Unpacking tzdata (2022a-1) over (2021e-1) ... Setting up tzdata (2022a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Mar 26 23:50:48 UTC 2022. Universal Time is now: Sat Mar 26 23:50:48 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Processing triggers for libc-bin (2.33-7) ... 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', '-yf', 'dist-upgrade'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.9s DUMP: 98a3fbe03e237a4890804426b8bed6e5 - 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.9s INFO: Running scripts post_setup 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_setup_dummy_users'] 0m7.8s DUMP: useradd warning: dummy1000's uid 1000 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1001's uid 1001 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1002's uid 1002 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1003's uid 1003 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1004's uid 1004 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1005's uid 1005 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1006's uid 1006 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1007's uid 1007 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1008's uid 1008 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1009's uid 1009 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1010's uid 1010 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_setup_dummy_users'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_setup_forbid_home'] 0m7.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_setup_forbid_home'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_setup_minimize'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_setup_minimize'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_setup_zz_backports'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_setup_zz_backports'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.8s DUMP: install ok installed adduser adduser 3.121 install ok installed apt apt 2.4.3 install ok installed base-files base-files 12.2 install ok installed base-passwd base-passwd 3.5.52 install ok installed bash bash 5.1-6 install ok installed bsdutils bsdutils 1:2.37.3-1+b1 install ok installed coreutils coreutils 8.32-4.1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-8 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.1 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.21.2 install ok installed e2fsprogs e2fsprogs 1.46.5-2 install ok installed findutils findutils 4.9.0-2 install ok installed gcc-12-base:amd64 gcc-12-base 12-20220319-1 install ok installed gpgv gpgv 2.2.27-3+b1 install ok installed grep grep 3.7-1 install ok installed gzip gzip 1.10-4 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.62 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.4.3 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1+b1 install ok installed libblkid1:amd64 libblkid1 2.37.3-1+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5 install ok installed libc-bin libc-bin 2.33-7 install ok installed libc6:amd64 libc6 2.33-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.5-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.27-1.1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.261 install ok installed libext2fs2:amd64 libext2fs2 1.46.5-2 install ok installed libffi8:amd64 libffi8 3.4.2-4 install ok installed libgcc-s1:amd64 libgcc-s1 12-20220319-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.9.4-5 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-3 install ok installed libgnutls30:amd64 libgnutls30 3.7.3-4+b1 install ok installed libgpg-error0:amd64 libgpg-error0 1.43-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.19.2-2+b1 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.2-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.19.2-2+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.19.2-2+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.19.2-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2 install ok installed libmount1:amd64 libmount1 2.37.3-1+b1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.0-6 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-11 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-11 install ok installed libpam-runtime libpam-runtime 1.4.0-11 install ok installed libpam0g:amd64 libpam0g 1.4.0-11 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.39-3 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.3-2 install ok installed libselinux1:amd64 libselinux1 3.3-1+b2 install ok installed libsemanage-common libsemanage-common 3.3-1 install ok installed libsemanage2:amd64 libsemanage2 3.3-1+b2 install ok installed libsepol2:amd64 libsepol2 3.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.37.3-1+b1 install ok installed libss2:amd64 libss2 1.46.5-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1n-1 install ok installed libstdc++6:amd64 libstdc++6 12-20220319-1 install ok installed libsystemd0:amd64 libsystemd0 250.4-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.18.0-4 install ok installed libtinfo6:amd64 libtinfo6 6.3-2 install ok installed libtirpc-common libtirpc-common 1.3.2-2 install ok installed libtirpc3:amd64 libtirpc3 1.3.2-2 install ok installed libudev1:amd64 libudev1 250.4-1 install ok installed libunistring2:amd64 libunistring2 1.0-1 install ok installed libuuid1:amd64 libuuid1 2.37.3-1+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.4.9+dfsg-1 install ok installed login login 1:4.11.1+dfsg1-2 install ok installed logsave logsave 1.46.5-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-3+b1 install ok installed mount mount 2.37.3-1+b1 install ok installed ncurses-base ncurses-base 6.3-2 install ok installed ncurses-bin ncurses-bin 6.3-2 install ok installed passwd passwd 1:4.11.1+dfsg1-2 install ok installed perl-base perl-base 5.34.0-3 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.01-1 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022a-1 install ok installed util-linux util-linux 2.37.3-1+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m7.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m8.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m8.1s INFO: Running scripts is_testable 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/is_testable_uninstallable'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/is_testable_uninstallable'] 0m8.2s INFO: Running scripts pre_test 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_test_exceptions'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_test_exceptions'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_test_root_password'] 0m8.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_test_root_password'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'show', '--no-all-versions', 'pftools'] 0m8.4s DUMP: Package: pftools Source: pftools (3.2.11-2) Version: 3.2.11-2+b1 Installed-Size: 52623 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.33), libgfortran5 (>= 8), 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_3.2.11-2+b1_amd64.deb Size: 24774428 MD5sum: 7fae413d3e340e3fcac064673cde9e79 SHA256: d3a4c8d2fb9e8a8539db041a2c21cf5f9ba2e03fd659b86675fa6f53ad53d1ad 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'show', '--no-all-versions', 'pftools'] 0m8.4s INFO: apt-cache knows about the following packages: pftools 0m8.4s INFO: Running scripts pre_install 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_database-server'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_database-server'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_exceptions'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_exceptions'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_extras'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_extras'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'policy'] 0m8.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'policy'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'policy', 'pftools'] 0m8.5s DUMP: pftools: Installed: (none) Candidate: 3.2.11-2+b1 Version table: 3.2.11-2+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'policy', 'pftools'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', '-y', 'install', 'pftools'] 0m12.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfile-slurp-perl libgdbm-compat4 libgdbm6 libgfortran5 libperl5.34 libquadmath0 perl perl-modules-5.34 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-compat4 libgdbm6 libgfortran5 libperl5.34 libquadmath0 perl perl-modules-5.34 pftools 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 33.2 MB of archives. After this operation, 106 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.34 all 5.34.0-3 [2850 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-1 [82.9 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-1 [58.6 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libperl5.34 amd64 5.34.0-3 [4208 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.34.0-3 [297 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libfile-slurp-perl all 9999.32-1 [28.1 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12-20220319-1 [145 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12-20220319-1 [792 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 pftools amd64 3.2.11-2+b1 [24.8 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 33.2 MB in 0s (109 MB/s) Selecting previously unselected package perl-modules-5.34. (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 ... 6689 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.34_5.34.0-3_all.deb ... Unpacking perl-modules-5.34 (5.34.0-3) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.23-1_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-1) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.23-1_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-1) ... Selecting previously unselected package libperl5.34:amd64. Preparing to unpack .../3-libperl5.34_5.34.0-3_amd64.deb ... Unpacking libperl5.34:amd64 (5.34.0-3) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.34.0-3_amd64.deb ... Unpacking perl (5.34.0-3) ... Selecting previously unselected package libfile-slurp-perl. Preparing to unpack .../5-libfile-slurp-perl_9999.32-1_all.deb ... Unpacking libfile-slurp-perl (9999.32-1) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../6-libquadmath0_12-20220319-1_amd64.deb ... Unpacking libquadmath0:amd64 (12-20220319-1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../7-libgfortran5_12-20220319-1_amd64.deb ... Unpacking libgfortran5:amd64 (12-20220319-1) ... Selecting previously unselected package pftools. Preparing to unpack .../8-pftools_3.2.11-2+b1_amd64.deb ... Unpacking pftools (3.2.11-2+b1) ... Setting up perl-modules-5.34 (5.34.0-3) ... Setting up libquadmath0:amd64 (12-20220319-1) ... Setting up libgfortran5:amd64 (12-20220319-1) ... Setting up libgdbm6:amd64 (1.23-1) ... Setting up libgdbm-compat4:amd64 (1.23-1) ... Setting up libperl5.34:amd64 (5.34.0-3) ... Setting up perl (5.34.0-3) ... Setting up libfile-slurp-perl (9999.32-1) ... Setting up pftools (3.2.11-2+b1) ... Processing triggers for libc-bin (2.33-7) ... 0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', '-y', 'install', 'pftools'] 0m12.4s INFO: Running scripts post_install 0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_install_exceptions'] 0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_install_exceptions'] 0m12.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m12.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m12.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpqrybm0nj to sid 0m12.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m12.7s INFO: Running scripts pre_distupgrade 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_distupgrade_exceptions'] 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_distupgrade_exceptions'] 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', 'update'] 0m16.0s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [165 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9125 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6768 kB] Fetched 16.1 MB in 3s (6312 kB/s) Reading package lists... 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', 'update'] 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', '-yf', 'dist-upgrade'] 0m18.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: dpkg pftools zlib1g 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 27.4 MB of archives. After this operation, 17.4 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.21.4 [2551 kB] Get:2 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.2.11.dfsg-4 [91.6 kB] Get:3 http://deb.debian.org/debian sid/main amd64 pftools amd64 3.2.12-1 [24.8 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 27.4 MB in 0s (108 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 ... 8815 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.21.4_amd64.deb ... Unpacking dpkg (1.21.4) over (1.21.2) ... Setting up dpkg (1.21.4) ... (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 ... 8815 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-4_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.11.dfsg-4) over (1:1.2.11.dfsg-2) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-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 ... 8815 files and directories currently installed.) Preparing to unpack .../pftools_3.2.12-1_amd64.deb ... Unpacking pftools (3.2.12-1) over (3.2.11-2+b1) ... Setting up pftools (3.2.12-1) ... Processing triggers for libc-bin (2.33-7) ... 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', '-yf', 'dist-upgrade'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m19.2s DUMP: 3110eb18d8e64db2c9b8e0be4df345d0 - 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'show', '--no-all-versions', 'pftools'] 0m19.5s 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 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'show', '--no-all-versions', 'pftools'] 0m19.5s INFO: apt-cache knows about the following packages: pftools 0m19.5s INFO: Running scripts pre_install 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_database-server'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_database-server'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_exceptions'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_exceptions'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_extras'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_extras'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'policy'] 0m19.6s 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: 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'policy'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'policy', 'pftools'] 0m19.6s 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 sid/main amd64 Packages 100 /var/lib/dpkg/status 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'policy', 'pftools'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', '-y', 'install', 'pftools'] 0m20.0s 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. 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', '-y', 'install', 'pftools'] 0m20.0s INFO: Running scripts post_install 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_install_exceptions'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_install_exceptions'] 0m20.1s INFO: Running scripts post_distupgrade 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_distupgrade_exceptions'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_distupgrade_exceptions'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_distupgrade_zz_backports'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_distupgrade_zz_backports'] 0m20.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m20.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m20.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m20.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m20.6s INFO: Running scripts pre_install 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_database-server'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_database-server'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_exceptions'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_exceptions'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_extras'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_extras'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'policy'] 0m20.7s 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: 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'policy'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'policy', 'pftools'] 0m20.7s 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 sid/main amd64 Packages 100 /var/lib/dpkg/status 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-cache', 'policy', 'pftools'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', '-y', 'install', 'pftools=3.2.12-1'] 0m21.1s 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. 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', '-y', 'install', 'pftools=3.2.12-1'] 0m21.1s INFO: Running scripts post_install 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_install_exceptions'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_install_exceptions'] 0m21.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m21.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m21.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', '-ac', '--ignore-obsolete'] 0m22.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', '-ac', '--ignore-obsolete'] 0m22.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m22.8s DUMP: 0.15.2 0m22.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m22.8s INFO: Running adequate version 0.15.2 now. 0m22.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'pftools'] 0m23.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'pftools'] 0m23.0s INFO: Running scripts pre_remove 0m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_remove_exceptions'] 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/pre_remove_exceptions'] 0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.9s DUMP: install ok installed adduser adduser 3.121 install ok installed apt apt 2.4.3 install ok installed base-files base-files 12.2 install ok installed base-passwd base-passwd 3.5.52 install ok installed bash bash 5.1-6 install ok installed bsdutils bsdutils 1:2.37.3-1+b1 install ok installed coreutils coreutils 8.32-4.1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-8 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.1 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.21.4 install ok installed e2fsprogs e2fsprogs 1.46.5-2 install ok installed findutils findutils 4.9.0-2 install ok installed gcc-12-base:amd64 gcc-12-base 12-20220319-1 install ok installed gpgv gpgv 2.2.27-3+b1 install ok installed grep grep 3.7-1 install ok installed gzip gzip 1.10-4 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.62 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.4.3 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1+b1 install ok installed libblkid1:amd64 libblkid1 2.37.3-1+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5 install ok installed libc-bin libc-bin 2.33-7 install ok installed libc6:amd64 libc6 2.33-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.5-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.27-1.1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.261 install ok installed libext2fs2:amd64 libext2fs2 1.46.5-2 install ok installed libffi8:amd64 libffi8 3.4.2-4 install ok installed libfile-slurp-perl libfile-slurp-perl 9999.32-1 install ok installed libgcc-s1:amd64 libgcc-s1 12-20220319-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.9.4-5 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-1 install ok installed libgdbm6:amd64 libgdbm6 1.23-1 install ok installed libgfortran5:amd64 libgfortran5 12-20220319-1 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-3 install ok installed libgnutls30:amd64 libgnutls30 3.7.3-4+b1 install ok installed libgpg-error0:amd64 libgpg-error0 1.43-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.19.2-2+b1 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.2-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.19.2-2+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.19.2-2+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.19.2-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2 install ok installed libmount1:amd64 libmount1 2.37.3-1+b1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.0-6 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-11 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-11 install ok installed libpam-runtime libpam-runtime 1.4.0-11 install ok installed libpam0g:amd64 libpam0g 1.4.0-11 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.39-3 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libperl5.34:amd64 libperl5.34 5.34.0-3 install ok installed libquadmath0:amd64 libquadmath0 12-20220319-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.3-2 install ok installed libselinux1:amd64 libselinux1 3.3-1+b2 install ok installed libsemanage-common libsemanage-common 3.3-1 install ok installed libsemanage2:amd64 libsemanage2 3.3-1+b2 install ok installed libsepol2:amd64 libsepol2 3.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.37.3-1+b1 install ok installed libss2:amd64 libss2 1.46.5-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1n-1 install ok installed libstdc++6:amd64 libstdc++6 12-20220319-1 install ok installed libsystemd0:amd64 libsystemd0 250.4-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.18.0-4 install ok installed libtinfo6:amd64 libtinfo6 6.3-2 install ok installed libtirpc-common libtirpc-common 1.3.2-2 install ok installed libtirpc3:amd64 libtirpc3 1.3.2-2 install ok installed libudev1:amd64 libudev1 250.4-1 install ok installed libunistring2:amd64 libunistring2 1.0-1 install ok installed libuuid1:amd64 libuuid1 2.37.3-1+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.4.9+dfsg-1 install ok installed login login 1:4.11.1+dfsg1-2 install ok installed logsave logsave 1.46.5-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-3+b1 install ok installed mount mount 2.37.3-1+b1 install ok installed ncurses-base ncurses-base 6.3-2 install ok installed ncurses-bin ncurses-bin 6.3-2 install ok installed passwd passwd 1:4.11.1+dfsg1-2 install ok installed perl perl 5.34.0-3 install ok installed perl-base perl-base 5.34.0-3 install ok installed perl-modules-5.34 perl-modules-5.34 5.34.0-3 install ok installed pftools pftools 3.2.12-1 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.01-1 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022a-1 install ok installed util-linux util-linux 2.37.3-1+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', 'remove', 'libfile-slurp-perl', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libperl5.34:amd64', 'libquadmath0:amd64', 'perl', 'perl-modules-5.34', 'pftools'] 0m24.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libfile-slurp-perl libgdbm-compat4 libgdbm6 libgfortran5 libperl5.34 libquadmath0 perl perl-modules-5.34 pftools 0 upgraded, 0 newly installed, 9 to remove and 0 not upgraded. After this operation, 105 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 ... 8826 files and directories currently installed.) Removing pftools (3.2.12-1) ... Removing libfile-slurp-perl (9999.32-1) ... Removing perl (5.34.0-3) ... Removing libperl5.34:amd64 (5.34.0-3) ... Removing libgdbm-compat4:amd64 (1.23-1) ... Removing libgdbm6:amd64 (1.23-1) ... Removing libgfortran5:amd64 (12-20220319-1) ... Removing libquadmath0:amd64 (12-20220319-1) ... Removing perl-modules-5.34 (5.34.0-3) ... Processing triggers for libc-bin (2.33-7) ... 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', 'remove', 'libfile-slurp-perl', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libperl5.34:amd64', 'libquadmath0:amd64', 'perl', 'perl-modules-5.34', 'pftools'] 0m24.6s INFO: Running scripts post_remove 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_remove_exceptions'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_remove_exceptions'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg', '--purge', 'libfile-slurp-perl', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libperl5.34:amd64', 'libquadmath0:amd64', 'perl', 'perl-modules-5.34'] 0m24.6s DUMP: dpkg: warning: ignoring request to remove libfile-slurp-perl which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libperl5.34 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed (Reading database ... 6692 files and directories currently installed.) Purging configuration files for perl (5.34.0-3) ... dpkg: warning: ignoring request to remove perl-modules-5.34 which isn't installed 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg', '--purge', 'libfile-slurp-perl', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libperl5.34:amd64', 'libquadmath0:amd64', 'perl', 'perl-modules-5.34'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg', '--purge', 'pftools'] 0m24.7s DUMP: dpkg: warning: ignoring request to remove pftools which isn't installed 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg', '--purge', 'pftools'] 0m24.7s INFO: Running scripts post_purge 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_purge_exceptions'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_purge_exceptions'] 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg', '--purge', '--pending'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg', '--purge', '--pending'] 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg', '--remove', '--pending'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg', '--remove', '--pending'] 0m24.7s INFO: Running scripts post_test 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_test_exceptions'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'tmp/scripts/post_test_exceptions'] 0m24.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m24.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg-divert', '--list'] 0m24.9s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'dpkg-divert', '--list'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', 'clean'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj', 'apt-get', 'clean'] 0m24.9s DEBUG: Recording chroot state 0m25.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/shm'] 0m25.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/shm'] 0m25.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/console'] 0m25.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/console'] 0m25.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/ptmx'] 0m25.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/ptmx'] 0m25.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/pts'] 0m25.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/dev/pts'] 0m25.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/proc'] 0m25.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj/proc'] 0m25.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m25.7s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpqrybm0nj'] 0m25.7s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpqrybm0nj 0m25.7s INFO: PASS: Upgrading between Debian distributions. 0m25.7s INFO: PASS: All tests. 0m25.7s INFO: piuparts run ends. ret=0 End: 2022-03-26 23:51:07 GMT