Start: 2024-11-28 04:02:10 GMT [testing] Package: pyfastx Version: 2.1.0-2 Installed-Size: 168 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3, python3-pyfastx Description: fast random access to sequences from FASTA/Q file - command Homepage: https://github.com/lmdu/pyfastx Description-md5: 499b00909ee985a2ddfd9ac4ba066bd5 Section: science Priority: optional Filename: pool/main/p/pyfastx/pyfastx_2.1.0-2_amd64.deb Size: 127152 MD5sum: 5e3fbbeb9bc630cdde8f9894b6b36183 SHA256: 16ed491ece8742b917e7bed89c40d066cf004cdcbee2eea1f0fe744deb5079f6 [sid] Package: pyfastx Version: 2.1.0-3 Installed-Size: 171 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, python3-pyfastx Description: fast random access to sequences from FASTA/Q file - command Homepage: https://github.com/lmdu/pyfastx Description-md5: 499b00909ee985a2ddfd9ac4ba066bd5 Section: science Priority: optional Filename: pool/main/p/pyfastx/pyfastx_2.1.0-3_amd64.deb Size: 127504 MD5sum: b1f05a253edefb696a43ebcf791f8658 SHA256: 5abb7f25da1d387a9479aae3dce56abb18894e413ffe1ee4739b8edc1045acb8 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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt pyfastx=2.1.0-3 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 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt pyfastx=2.1.0-3 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpo5_1_7qp 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpo5_1_7qp 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.3s DEBUG: Created policy-rc.d and chmodded it. 0m0.3s DEBUG: Created resolv.conf. 0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpo5_1_7qp/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', 'update'] 0m1.6s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9375 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6273 kB] Fetched 15.8 MB in 1s (18.2 MB/s) Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: apt base-files libapt-pkg6.0t64 libpcre2-8-0 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2846 kB of archives. After this operation, 67.6 kB disk space will be freed. Get:1 http://deb.debian.org/debian trixie/main amd64 base-files amd64 13.6 [72.8 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libapt-pkg6.0t64 amd64 2.9.14 [1103 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.14 [1395 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libpcre2-8-0 amd64 10.44-4 [275 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2846 kB in 0s (88.9 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 ... 5154 files and directories currently installed.) Preparing to unpack .../base-files_13.6_amd64.deb ... Unpacking base-files (13.6) over (13.5) ... Setting up base-files (13.6) ... Updating /root/.profile to current default. (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 ... 5154 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.14_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.14) over (2.9.10) ... Setting up libapt-pkg6.0t64:amd64 (2.9.14) ... (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 ... 5154 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.14_amd64.deb ... Unpacking apt (2.9.14) over (2.9.10) ... Setting up apt (2.9.14) ... (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 ... 5151 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.44-4_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.44-4) over (10.42-4+b2) ... Setting up libpcre2-8-0:amd64 (10.44-4) ... Processing triggers for libc-bin (2.40-3) ... 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.1s DUMP: 74ca845aaf638b9d51e082ddbbccaf53 - 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.1s INFO: Running scripts post_setup 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s 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 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s 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' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DUMP: install ok installed apt apt 2.9.14 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 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 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b3 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc2-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257~rc2-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-11 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl-base perl-base 5.40.0-7 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m3.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m3.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m3.8s INFO: Running scripts is_testable 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/is_testable_uninstallable'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/is_testable_uninstallable'] 0m3.8s INFO: Running scripts pre_test 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_test_exceptions'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_test_exceptions'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_test_root_password'] 0m3.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_test_root_password'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'show', '--no-all-versions', 'pyfastx'] 0m3.9s DUMP: Package: pyfastx Version: 2.1.0-2 Installed-Size: 168 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3, python3-pyfastx Description-en: fast random access to sequences from FASTA/Q file - command The pyfastx is a lightweight Python C extension that enables users to randomly access to sequences from plain and gzipped FASTA/Q files. This module aims to provide simple APIs for users to extract sequence from FASTA and reads from FASTQ by identifier and index number. The pyfastx will build indexes stored in a sqlite3 database file for random access to avoid consuming excessive amount of memory. In addition, the pyfastx can parse standard (sequence is spread into multiple lines with same length) and nonstandard (sequence is spread into one or more lines with different length) FASTA format. . It features: . * a single file for the Python extension; * lightweight, memory efficient FASTA/Q file parsing; * fast random access to sequences from gzipped FASTA/Q file; * sequences reading from FASTA file line by line; * N50 and L50 calculation of sequences in FASTA file; * GC content and nucleotides composition calculation; * reverse, complement and antisense sequences extraction; * excellent compatibility: support for parsing nonstandard FASTA file; * support for FASTQ quality score conversion; * a command line interface for splitting FASTA/Q file. . This package provides the command line interface. Description-md5: 499b00909ee985a2ddfd9ac4ba066bd5 Homepage: https://github.com/lmdu/pyfastx Section: science Priority: optional Filename: pool/main/p/pyfastx/pyfastx_2.1.0-2_amd64.deb Size: 127152 MD5sum: 5e3fbbeb9bc630cdde8f9894b6b36183 SHA256: 16ed491ece8742b917e7bed89c40d066cf004cdcbee2eea1f0fe744deb5079f6 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'show', '--no-all-versions', 'pyfastx'] 0m3.9s INFO: apt-cache knows about the following packages: pyfastx 0m3.9s INFO: Running scripts pre_install 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_database-server'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_database-server'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_exceptions'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_exceptions'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_extras'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_extras'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'policy'] 0m3.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'policy'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'policy', 'pyfastx'] 0m3.9s DUMP: pyfastx: Installed: (none) Candidate: 2.1.0-2 Version table: 2.1.0-2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'policy', 'pyfastx'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', '-y', 'install', 'pyfastx'] 0m6.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libexpat1 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libncursesw6 libnsl2 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 libsqlite3-0 libtirpc-common libtirpc3t64 media-types netbase python3 python3-importlib-metadata python3-minimal python3-packaging python3-pyfaidx python3-pyfastx python3-zipp python3.12 python3.12-minimal readline-common Suggested packages: krb5-doc krb5-user python3-doc python3-tk python3-venv python3.12-venv python3.12-doc binutils binfmt-support readline-doc Recommended packages: krb5-locales libgpm2 python3-biopython ca-certificates The following NEW packages will be installed: libexpat1 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libncursesw6 libnsl2 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 libsqlite3-0 libtirpc-common libtirpc3t64 media-types netbase pyfastx python3 python3-importlib-metadata python3-minimal python3-packaging python3-pyfaidx python3-pyfastx python3-zipp python3.12 python3.12-minimal readline-common 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. Need to get 8126 kB of archives. After this operation, 30.4 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:11 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get:22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 python3-importlib-metadata all 8.5.0-1 [21.0 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 python3-pyfaidx all 0.8.1.3-1 [29.1 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 python3-pyfastx amd64 2.1.0-2 [57.2 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 pyfastx amd64 2.1.0-2 [127 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8126 kB in 0s (36.3 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5154 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../14-libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... 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Processing triggers for libc-bin (2.40-3) ... 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', '-y', 'install', 'pyfastx'] 0m6.7s INFO: Running scripts post_install 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_install_exceptions'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_install_exceptions'] 0m6.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m7.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m7.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpo5_1_7qp to sid 0m7.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m7.0s INFO: Running scripts pre_distupgrade 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', 'update'] 0m9.0s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7342 kB] Fetched 17.6 MB in 2s (11.5 MB/s) Reading package lists... 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', 'update'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', '-yf', 'dist-upgrade'] 0m10.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc6 libcap-ng0 libpython3-stdlib libseccomp2 libsystemd0 libudev1 perl-base pyfastx python3 python3-minimal python3-pyfastx 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6022 kB of archives. After this operation, 136 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.40.0-8 [1675 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.40-4 [2804 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.40-4 [626 kB] Get:4 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get:5 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get:7 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.5-4 [17.3 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-2 [47.8 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 257~rc3-1 [448 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 257~rc3-1 [147 kB] Get:11 http://deb.debian.org/debian sid/main amd64 python3-pyfastx amd64 2.1.0-3 [64.7 kB] Get:12 http://deb.debian.org/debian sid/main amd64 pyfastx amd64 2.1.0-3 [128 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6022 kB in 0s (28.8 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6174 files and directories currently installed.) Preparing to unpack .../libc-bin_2.40-4_amd64.deb ... Unpacking libc-bin (2.40-4) over (2.40-3) ... Setting up libc-bin (2.40-4) ... (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 ... 6174 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... Unpacking python3-minimal (3.12.7-1) over (3.12.6-1) ... Setting up python3-minimal (3.12.7-1) ... (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 ... 6174 files and directories currently installed.) Preparing to unpack .../python3_3.12.7-1_amd64.deb ... Unpacking python3 (3.12.7-1) over (3.12.6-1) ... Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-1) ... Preparing to unpack .../libcap-ng0_0.8.5-4_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.5-4) over (0.8.5-3+b1) ... Setting up libcap-ng0:amd64 (0.8.5-4) ... (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 ... 6173 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-2_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-2) over (2.5.5-1+b3) ... Setting up libseccomp2:amd64 (2.5.5-2) ... (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 ... 6172 files and directories currently installed.) Preparing to unpack .../libsystemd0_257~rc3-1_amd64.deb ... Unpacking libsystemd0:amd64 (257~rc3-1) over (257~rc2-3) ... Setting up libsystemd0:amd64 (257~rc3-1) ... (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 ... 6172 files and directories currently installed.) Preparing to unpack .../libudev1_257~rc3-1_amd64.deb ... Unpacking libudev1:amd64 (257~rc3-1) over (257~rc2-3) ... Setting up libudev1:amd64 (257~rc3-1) ... (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 ... 6172 files and directories currently installed.) Preparing to unpack .../python3-pyfastx_2.1.0-3_amd64.deb ... Unpacking python3-pyfastx (2.1.0-3) over (2.1.0-2) ... Preparing to unpack .../pyfastx_2.1.0-3_amd64.deb ... Unpacking pyfastx (2.1.0-3) over (2.1.0-2) ... Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up python3-pyfastx (2.1.0-3) ... Setting up pyfastx (2.1.0-3) ... Processing triggers for libc-bin (2.40-4) ... 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', '-yf', 'dist-upgrade'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m10.8s DUMP: bfc323afe666bc9f63366a818ca3f7a2 - 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'show', '--no-all-versions', 'pyfastx'] 0m10.9s DUMP: Package: pyfastx Version: 2.1.0-3 Installed-Size: 171 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, python3-pyfastx Description-en: fast random access to sequences from FASTA/Q file - command The pyfastx is a lightweight Python C extension that enables users to randomly access to sequences from plain and gzipped FASTA/Q files. This module aims to provide simple APIs for users to extract sequence from FASTA and reads from FASTQ by identifier and index number. The pyfastx will build indexes stored in a sqlite3 database file for random access to avoid consuming excessive amount of memory. In addition, the pyfastx can parse standard (sequence is spread into multiple lines with same length) and nonstandard (sequence is spread into one or more lines with different length) FASTA format. . It features: . * a single file for the Python extension; * lightweight, memory efficient FASTA/Q file parsing; * fast random access to sequences from gzipped FASTA/Q file; * sequences reading from FASTA file line by line; * N50 and L50 calculation of sequences in FASTA file; * GC content and nucleotides composition calculation; * reverse, complement and antisense sequences extraction; * excellent compatibility: support for parsing nonstandard FASTA file; * support for FASTQ quality score conversion; * a command line interface for splitting FASTA/Q file. . This package provides the command line interface. Description-md5: 499b00909ee985a2ddfd9ac4ba066bd5 Homepage: https://github.com/lmdu/pyfastx Section: science Priority: optional Filename: pool/main/p/pyfastx/pyfastx_2.1.0-3_amd64.deb Size: 127504 MD5sum: b1f05a253edefb696a43ebcf791f8658 SHA256: 5abb7f25da1d387a9479aae3dce56abb18894e413ffe1ee4739b8edc1045acb8 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'show', '--no-all-versions', 'pyfastx'] 0m10.9s INFO: apt-cache knows about the following packages: pyfastx 0m10.9s INFO: Running scripts pre_install 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_database-server'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_database-server'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_exceptions'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_exceptions'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_extras'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_extras'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'policy'] 0m11.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'policy'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'policy', 'pyfastx'] 0m11.0s DUMP: pyfastx: Installed: 2.1.0-3 Candidate: 2.1.0-3 Version table: *** 2.1.0-3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'policy', 'pyfastx'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', '-y', 'install', 'pyfastx'] 0m11.3s DUMP: Reading package lists... Building dependency tree... Reading state information... pyfastx is already the newest version (2.1.0-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', '-y', 'install', 'pyfastx'] 0m11.3s INFO: Running scripts post_install 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_install_exceptions'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_install_exceptions'] 0m11.3s INFO: Running scripts post_distupgrade 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_distupgrade_exceptions'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_distupgrade_exceptions'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_distupgrade_zz_backports'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_distupgrade_zz_backports'] 0m11.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m11.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m11.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m11.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m11.8s INFO: Running scripts pre_install 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_database-server'] 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_database-server'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_exceptions'] 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_exceptions'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_extras'] 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_extras'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'policy'] 0m11.9s 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: 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'policy'] 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'policy', 'pyfastx'] 0m11.9s DUMP: pyfastx: Installed: 2.1.0-3 Candidate: 2.1.0-3 Version table: *** 2.1.0-3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-cache', 'policy', 'pyfastx'] 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', '-y', 'install', 'pyfastx=2.1.0-3'] 0m12.1s DUMP: Reading package lists... Building dependency tree... Reading state information... pyfastx is already the newest version (2.1.0-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', '-y', 'install', 'pyfastx=2.1.0-3'] 0m12.1s INFO: Running scripts post_install 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_install_exceptions'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_install_exceptions'] 0m12.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m12.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m12.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', '-ac', '--ignore-obsolete'] 0m13.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', '-ac', '--ignore-obsolete'] 0m13.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m13.0s DUMP: 0.15.6 0m13.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m13.0s INFO: Running adequate version 0.15.6 now. 0m13.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'pyfastx'] 0m13.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'pyfastx'] 0m13.1s INFO: Running scripts pre_remove 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_remove_exceptions'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/pre_remove_exceptions'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m13.6s DUMP: install ok installed apt apt 2.9.14 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 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 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libncursesw6:amd64 libncursesw6 6.5-2+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-4 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.7-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.7-3 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.7-3 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc3-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3+b1 install ok installed libudev1:amd64 libudev1 257~rc3-1 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-11 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed netbase netbase 6.4 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl-base perl-base 5.40.0-8 install ok installed pyfastx pyfastx 2.1.0-3 install ok installed python3 python3 3.12.7-1 install ok installed python3-importlib-metadata python3-importlib-metadata 8.5.0-1 install ok installed python3-minimal python3-minimal 3.12.7-1 install ok installed python3-packaging python3-packaging 24.2-1 install ok installed python3-pyfaidx python3-pyfaidx 0.8.1.3-1 install ok installed python3-pyfastx python3-pyfastx 2.1.0-3 install ok installed python3-zipp python3-zipp 3.21.0-1 install ok installed python3.12 python3.12 3.12.7-3 install ok installed python3.12-minimal python3.12-minimal 3.12.7-3 install ok installed readline-common readline-common 8.2-5 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', 'remove', 'libexpat1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'python3', 'python3-importlib-metadata', 'python3-minimal', 'python3-packaging', 'python3-pyfaidx', 'python3-pyfastx', 'python3-zipp', 'python3.12', 'python3.12-minimal', 'readline-common', 'pyfastx'] 0m14.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libexpat1 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libncursesw6 libnsl2 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 libsqlite3-0 libtirpc-common libtirpc3t64 media-types netbase pyfastx python3 python3-importlib-metadata python3-minimal python3-packaging python3-pyfaidx python3-pyfastx python3-zipp python3.12 python3.12-minimal readline-common 0 upgraded, 0 newly installed, 28 to remove and 0 not upgraded. After this operation, 30.5 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 ... 6173 files and directories currently installed.) Removing pyfastx (2.1.0-3) ... Removing python3-pyfastx (2.1.0-3) ... Removing python3-pyfaidx (0.8.1.3-1) ... Removing python3-importlib-metadata (8.5.0-1) ... Removing python3-zipp (3.21.0-1) ... Removing python3-packaging (24.2-1) ... Removing python3 (3.12.7-1) ... Removing python3.12 (3.12.7-3) ... Removing python3-minimal (3.12.7-1) ... Removing python3.12-minimal (3.12.7-3) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libpython3-stdlib:amd64 (3.12.7-1) ... Removing libpython3.12-stdlib:amd64 (3.12.7-3) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b3) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libncursesw6:amd64 (6.5-2+b1) ... Removing libpython3.12-minimal:amd64 (3.12.7-3) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-5) ... Processing triggers for libc-bin (2.40-4) ... 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', 'remove', 'libexpat1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'python3', 'python3-importlib-metadata', 'python3-minimal', 'python3-packaging', 'python3-pyfaidx', 'python3-pyfastx', 'python3-zipp', 'python3.12', 'python3.12-minimal', 'readline-common', 'pyfastx'] 0m14.4s INFO: Running scripts post_remove 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_remove_exceptions'] 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_remove_exceptions'] 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg', '--purge', 'libexpat1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'python3', 'python3-importlib-metadata', 'python3-minimal', 'python3-packaging', 'python3-pyfaidx', 'python3-pyfastx', 'python3-zipp', 'python3.12', 'python3.12-minimal', 'readline-common'] 0m14.5s DUMP: dpkg: warning: ignoring request to remove libexpat1 which isn't installed (Reading database ... 5160 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.7-3) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for python3 (3.12.7-1) ... dpkg: warning: ignoring request to remove python3-importlib-metadata which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pyfaidx which isn't installed dpkg: warning: ignoring request to remove python3-pyfastx which isn't installed dpkg: warning: ignoring request to remove python3-zipp which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.7-3) ... Purging configuration files for readline-common (8.2-5) ... 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg', '--purge', 'libexpat1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'python3', 'python3-importlib-metadata', 'python3-minimal', 'python3-packaging', 'python3-pyfaidx', 'python3-pyfastx', 'python3-zipp', 'python3.12', 'python3.12-minimal', 'readline-common'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg', '--purge', 'pyfastx'] 0m14.5s DUMP: dpkg: warning: ignoring request to remove pyfastx which isn't installed 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg', '--purge', 'pyfastx'] 0m14.5s INFO: Running scripts post_purge 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_purge_exceptions'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_purge_exceptions'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg', '--purge', '--pending'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg', '--purge', '--pending'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg', '--remove', '--pending'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg', '--remove', '--pending'] 0m14.5s INFO: Running scripts post_test 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_test_exceptions'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'tmp/scripts/post_test_exceptions'] 0m14.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m14.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg-divert', '--list'] 0m14.7s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 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 /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 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 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'dpkg-divert', '--list'] 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', 'clean'] 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp', 'apt-get', 'clean'] 0m14.7s DEBUG: Recording chroot state 0m15.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/shm'] 0m15.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/shm'] 0m15.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/console'] 0m15.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/console'] 0m15.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/ptmx'] 0m15.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/ptmx'] 0m15.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/pts'] 0m15.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/dev/pts'] 0m15.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/proc'] 0m15.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp/proc'] 0m15.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m15.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpo5_1_7qp'] 0m15.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpo5_1_7qp 0m15.4s INFO: PASS: Upgrading between Debian distributions. 0m15.4s INFO: PASS: All tests. 0m15.4s INFO: piuparts run ends. ret=0 End: 2024-11-28 04:02:26 GMT