Start: 2025-08-13 07:51:16 GMT [trixie] Package: kraken2 Version: 2.1.3-1 Installed-Size: 1971 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.6), python3, ncbi-blast+ Description: taxonomic classification system using exact k-mer matches Homepage: https://www.ccb.jhu.edu/software/kraken2/ Description-md5: 70f2ff9ad084534e552c6c2118d2a186 Section: science Priority: optional Filename: pool/main/k/kraken2/kraken2_2.1.3-1_amd64.deb Size: 868196 MD5sum: dc9df4488dae6523c2e94534ecf2a08e SHA256: 6bf53c46f2adc3a8e24f66f43bb151444c35f2b3baa3c3365721b9133eb086d7 [trixie-next] Package: kraken2 Version: 2.1.3-1 Installed-Size: 1971 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.6), python3, ncbi-blast+ Description: taxonomic classification system using exact k-mer matches Homepage: https://www.ccb.jhu.edu/software/kraken2/ Description-md5: 70f2ff9ad084534e552c6c2118d2a186 Section: science Priority: optional Filename: pool/main/k/kraken2/kraken2_2.1.3-1_amd64.deb Size: 868196 MD5sum: dc9df4488dae6523c2e94534ecf2a08e SHA256: 6bf53c46f2adc3a8e24f66f43bb151444c35f2b3baa3c3365721b9133eb086d7 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d trixie -d trixie-next -B /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat --apt kraken2=2.1.3-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.6.1~202508101417~1.6.0-7-g17c4ea32 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d trixie -d trixie-next -B /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat --apt kraken2=2.1.3-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpuxygb_21 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpuxygb_21 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', '--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/tmpuxygb_21', '--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/tmpuxygb_21/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/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/tmpuxygb_21/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/tmpuxygb_21/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpuxygb_21/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', 'update'] 0m1.4s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [138 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9668 kB] Fetched 9805 kB in 1s (13.7 MB/s) Reading package lists... 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', 'update'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', '-yf', 'dist-upgrade'] 0m1.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', '-yf', 'dist-upgrade'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.9s DUMP: 8fc0def95551deb38dc214d6c9cce720 - 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.9s INFO: Running scripts post_setup 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_setup_dummy_users'] 0m2.3s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_setup_dummy_users'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_setup_forbid_home'] 0m2.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_setup_forbid_home'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.3s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_setup_minimize'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_setup_minimize'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_setup_zz_backports'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_setup_zz_backports'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.3s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-5 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-4 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat 0m2.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m2.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m2.6s INFO: Running scripts is_testable 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/is_testable_uninstallable'] 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/is_testable_uninstallable'] 0m2.6s INFO: Running scripts pre_test 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_test_exceptions'] 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_test_exceptions'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_test_root_password'] 0m2.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_test_root_password'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'show', '--no-all-versions', 'kraken2'] 0m2.7s DUMP: Package: kraken2 Version: 2.1.3-1 Installed-Size: 1971 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.6), python3, ncbi-blast+ Description-en: taxonomic classification system using exact k-mer matches Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. [see: Kraken 1's Webpage for more details]. . Kraken 2 provides significant improvements to Kraken 1, with faster database build times, smaller database sizes, and faster classification speeds. These improvements were achieved by the following updates to the Kraken classification program: . 1. Storage of Minimizers: Instead of storing/querying entire k-mers, Kraken 2 stores minimizers (l-mers) of each k-mer. The length of each l-mer must be ?? the k-mer length. Each k-mer is treated by Kraken 2 as if its LCA is the same as its minimizer's LCA. 2. Introduction of Spaced Seeds: Kraken 2 also uses spaced seeds to store and query minimizers to improve classification accuracy. 3. Database Structure: While Kraken 1 saved an indexed and sorted list of k-mer/LCA pairs, Kraken 2 uses a compact hash table. This hash table is a probabilistic data structure that allows for faster queries and lower memory requirements. However, this data structure does have a <1% chance of returning the incorrect LCA or returning an LCA for a non-inserted minimizer. Users can compensate for this possibility by using Kraken's confidence scoring thresholds. 4. Protein Databases: Kraken 2 allows for databases built from amino acid sequences. When queried, Kraken 2 performs a six-frame translated search of the query sequences against the database. 5. 16S Databases: Kraken 2 also provides support for databases not based on NCBI's taxonomy. Currently, these include the 16S databases: Greengenes, SILVA, and RDP. Description-md5: 70f2ff9ad084534e552c6c2118d2a186 Homepage: https://www.ccb.jhu.edu/software/kraken2/ Section: science Priority: optional Filename: pool/main/k/kraken2/kraken2_2.1.3-1_amd64.deb Size: 868196 MD5sum: dc9df4488dae6523c2e94534ecf2a08e SHA256: 6bf53c46f2adc3a8e24f66f43bb151444c35f2b3baa3c3365721b9133eb086d7 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'show', '--no-all-versions', 'kraken2'] 0m2.7s INFO: apt-cache knows about the following packages: kraken2 0m2.7s INFO: Running scripts pre_install 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_database-server'] 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_database-server'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_exceptions'] 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_exceptions'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_extras'] 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_extras'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'policy'] 0m2.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'policy'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'policy', 'kraken2'] 0m2.7s DUMP: kraken2: Installed: (none) Candidate: 2.1.3-1 Version table: 2.1.3-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'policy', 'kraken2'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', '-y', 'install', 'kraken2'] 0m6.2s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgomp1 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncursesw6 libnghttp2-14 libperl5.40 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libuv1t64 media-types ncbi-blast+ ncbi-data ncbi-vdb-data netbase perl perl-modules-5.40 python3 python3-minimal python3.13 python3.13-minimal readline-common Suggested packages: gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binutils binfmt-support readline-doc Recommended packages: libgpm2 ca-certificates The following NEW packages will be installed: kraken2 libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgomp1 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncursesw6 libnghttp2-14 libperl5.40 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libuv1t64 media-types ncbi-blast+ ncbi-data ncbi-vdb-data netbase perl perl-modules-5.40 python3 python3-minimal python3.13 python3.13-minimal readline-common 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 37.0 MB of archives. After this operation, 182 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.1-6 [3019 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.1-6 [4341 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.1-6 [267 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.4-2 [360 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.4-2 [151 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.4-2 [242 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] Get:31 http://deb.debian.org/debian trixie/main amd64 kraken2 amd64 2.1.3-1 [868 kB] Fetched 37.0 MB in 0s (83.2 MB/s) Selecting previously unselected package libexpat1: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 ... 4938 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.5-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13-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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.5-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.5-2_amd64.deb ... Unpacking python3.13 (3.13.5-2) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up libuv1t64:amd64 (1.50.0-2) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1) ... Setting up libgomp1:amd64 (14.2.0-19) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up perl-modules-5.40 (5.40.1-6) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up netbase (6.5) ... Setting up libmbedcrypto16:amd64 (3.6.4-2) ... Setting up readline-common (8.2-6) ... Setting up libperl5.40:amd64 (5.40.1-6) ... Setting up perl (5.40.1-6) ... Setting up libmbedx509-7:amd64 (3.6.4-2) ... Setting up libmbedtls21:amd64 (3.6.4-2) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up python3.13 (3.13.5-2) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Setting up python3 (3.13.5-1) ... Setting up ncbi-blast+ (2.16.0+ds-7) ... Setting up kraken2 (2.1.3-1) ... Processing triggers for libc-bin (2.41-12) ... 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', '-y', 'install', 'kraken2'] 0m6.2s INFO: Running scripts post_install 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_install_exceptions'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_install_exceptions'] 0m6.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m6.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m6.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpuxygb_21 to trixie-next 0m6.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main deb http://security.debian.org trixie-security main deb http://deb.debian.org/debian/ trixie-updates main deb http://deb.debian.org/debian/ trixie-proposed-updates main 0m6.5s INFO: Running scripts pre_distupgrade 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_distupgrade_exceptions'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_distupgrade_exceptions'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', 'update'] 0m7.2s DUMP: Hit:1 http://deb.debian.org/debian trixie InRelease Get:2 http://deb.debian.org/debian trixie-updates InRelease [47.1 kB] Get:3 http://deb.debian.org/debian trixie-proposed-updates InRelease [55.8 kB] Get:4 http://deb.debian.org/debian trixie-updates/main amd64 Packages [2432 B] Get:5 http://deb.debian.org/debian trixie-updates/main Translation-en [396 B] Get:6 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages [7300 B] Get:7 http://deb.debian.org/debian trixie-proposed-updates/main Translation-en [3288 B] Get:8 http://security.debian.org trixie-security InRelease [43.4 kB] Get:9 http://security.debian.org trixie-security/main amd64 Packages [5304 B] Get:10 http://security.debian.org trixie-security/main Translation-en [6724 B] Fetched 172 kB in 0s (699 kB/s) Reading package lists... 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', 'update'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', '-yf', 'dist-upgrade'] 0m7.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', '-yf', 'dist-upgrade'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.7s DUMP: 5c6a884f0339ba51c78a9d3f50b19f1b - 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'show', '--no-all-versions', 'kraken2'] 0m7.8s DUMP: Package: kraken2 Version: 2.1.3-1 Installed-Size: 1971 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.6), python3, ncbi-blast+ Description-en: taxonomic classification system using exact k-mer matches Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. [see: Kraken 1's Webpage for more details]. . Kraken 2 provides significant improvements to Kraken 1, with faster database build times, smaller database sizes, and faster classification speeds. These improvements were achieved by the following updates to the Kraken classification program: . 1. Storage of Minimizers: Instead of storing/querying entire k-mers, Kraken 2 stores minimizers (l-mers) of each k-mer. The length of each l-mer must be ?? the k-mer length. Each k-mer is treated by Kraken 2 as if its LCA is the same as its minimizer's LCA. 2. Introduction of Spaced Seeds: Kraken 2 also uses spaced seeds to store and query minimizers to improve classification accuracy. 3. Database Structure: While Kraken 1 saved an indexed and sorted list of k-mer/LCA pairs, Kraken 2 uses a compact hash table. This hash table is a probabilistic data structure that allows for faster queries and lower memory requirements. However, this data structure does have a <1% chance of returning the incorrect LCA or returning an LCA for a non-inserted minimizer. Users can compensate for this possibility by using Kraken's confidence scoring thresholds. 4. Protein Databases: Kraken 2 allows for databases built from amino acid sequences. When queried, Kraken 2 performs a six-frame translated search of the query sequences against the database. 5. 16S Databases: Kraken 2 also provides support for databases not based on NCBI's taxonomy. Currently, these include the 16S databases: Greengenes, SILVA, and RDP. Description-md5: 70f2ff9ad084534e552c6c2118d2a186 Homepage: https://www.ccb.jhu.edu/software/kraken2/ Section: science Priority: optional Filename: pool/main/k/kraken2/kraken2_2.1.3-1_amd64.deb Size: 868196 MD5sum: dc9df4488dae6523c2e94534ecf2a08e SHA256: 6bf53c46f2adc3a8e24f66f43bb151444c35f2b3baa3c3365721b9133eb086d7 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'show', '--no-all-versions', 'kraken2'] 0m7.8s INFO: apt-cache knows about the following packages: kraken2 0m7.8s INFO: Running scripts pre_install 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_database-server'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_database-server'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_exceptions'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_exceptions'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_extras'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_extras'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'policy'] 0m7.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages release v=13-updates,o=Debian,a=proposed-updates,n=trixie-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian trixie-updates/main amd64 Packages release v=13-updates,o=Debian,a=stable-updates,n=trixie-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org trixie-security/main amd64 Packages release v=13,o=Debian,a=stable-security,n=trixie-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'policy'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'policy', 'kraken2'] 0m7.9s DUMP: kraken2: Installed: 2.1.3-1 Candidate: 2.1.3-1 Version table: *** 2.1.3-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'policy', 'kraken2'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', '-y', 'install', 'kraken2'] 0m8.1s DUMP: Reading package lists... Building dependency tree... Reading state information... kraken2 is already the newest version (2.1.3-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', '-y', 'install', 'kraken2'] 0m8.1s INFO: Running scripts post_install 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_install_exceptions'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_install_exceptions'] 0m8.1s INFO: Running scripts post_distupgrade 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_distupgrade_exceptions'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_distupgrade_exceptions'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_distupgrade_zz_backports'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_distupgrade_zz_backports'] 0m8.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m8.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m8.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m8.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m8.7s INFO: Running scripts pre_install 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_database-server'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_database-server'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_exceptions'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_exceptions'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_extras'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_extras'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'policy'] 0m8.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages release v=13-updates,o=Debian,a=proposed-updates,n=trixie-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian trixie-updates/main amd64 Packages release v=13-updates,o=Debian,a=stable-updates,n=trixie-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org trixie-security/main amd64 Packages release v=13,o=Debian,a=stable-security,n=trixie-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'policy'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'policy', 'kraken2'] 0m8.8s DUMP: kraken2: Installed: 2.1.3-1 Candidate: 2.1.3-1 Version table: *** 2.1.3-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-cache', 'policy', 'kraken2'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', '-y', 'install', 'kraken2=2.1.3-1'] 0m9.0s DUMP: Reading package lists... Building dependency tree... Reading state information... kraken2 is already the newest version (2.1.3-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', '-y', 'install', 'kraken2=2.1.3-1'] 0m9.0s INFO: Running scripts post_install 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_install_exceptions'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_install_exceptions'] 0m9.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m9.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m9.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', '-ac', '--ignore-obsolete'] 0m10.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', '-ac', '--ignore-obsolete'] 0m10.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m10.3s DUMP: 0.15.9~deb12u1 0m10.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m10.3s INFO: Running adequate version 0.15.9~deb12u1 now. 0m10.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'kraken2'] 0m10.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'kraken2'] 0m10.3s INFO: Running scripts pre_remove 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_remove_exceptions'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/pre_remove_exceptions'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.9s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed kraken2 kraken2 2.1.3-1 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libexpat1:amd64 libexpat1 2.7.1-2 install ok installed libffi8:amd64 libffi8 3.4.8-2 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgomp1:amd64 libgomp1 14.2.0-19 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b2 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.4-2 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.4-2 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.4-2 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.2.1+dfsg-2 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1.1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libperl5.40:amd64 libperl5.40 5.40.1-6 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.5-1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.5-2 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.5-2 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libuv1t64:amd64 libuv1t64 1.50.0-2 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed media-types media-types 13.0.0 install ok installed mount mount 2.41-5 install ok installed ncbi-blast+ ncbi-blast+ 2.16.0+ds-7 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-6 install ok installed ncbi-vdb-data ncbi-vdb-data 3.2.1+dfsg-2 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed netbase netbase 6.5 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl perl 5.40.1-6 install ok installed perl-base perl-base 5.40.1-6 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.1-6 install ok installed python3 python3 3.13.5-1 install ok installed python3-minimal python3-minimal 3.13.5-1 install ok installed python3.13 python3.13 3.13.5-2 install ok installed python3.13-minimal python3.13-minimal 3.13.5-2 install ok installed readline-common readline-common 8.2-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-4 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', 'remove', '--allow-remove-essential', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgomp1:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libuv1t64:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'ncbi-vdb-data', 'netbase', 'perl', 'perl-modules-5.40', 'python3', 'python3-minimal', 'python3.13', 'python3.13-minimal', 'readline-common', 'kraken2'] 0m11.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: kraken2 libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgomp1 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncursesw6 libnghttp2-14 libperl5.40 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libuv1t64 media-types ncbi-blast+ ncbi-data ncbi-vdb-data netbase perl perl-modules-5.40 python3 python3-minimal python3.13 python3.13-minimal readline-common 0 upgraded, 0 newly installed, 31 to remove and 0 not upgraded. After this operation, 182 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 ... 8384 files and directories currently installed.) Removing kraken2 (2.1.3-1) ... Removing ncbi-blast+ (2.16.0+ds-7) ... Removing python3 (3.13.5-1) ... Removing python3.13 (3.13.5-2) ... Removing python3-minimal (3.13.5-1) ... Removing python3.13-minimal (3.13.5-2) ... Removing libexpat1:amd64 (2.7.1-2) ... Removing libpython3-stdlib:amd64 (3.13.5-1) ... Removing libpython3.13-stdlib:amd64 (3.13.5-2) ... Removing libffi8:amd64 (3.4.8-2) ... Removing perl (5.40.1-6) ... Removing libperl5.40:amd64 (5.40.1-6) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgomp1:amd64 (14.2.0-19) ... Removing liblmdb0:amd64 (0.9.31-1+b2) ... Removing libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Removing libmbedtls21:amd64 (3.6.4-2) ... Removing libmbedx509-7:amd64 (3.6.4-2) ... Removing libmbedcrypto16:amd64 (3.6.4-2) ... Removing libncursesw6:amd64 (6.5+20250216-2) ... Removing libnghttp2-14:amd64 (1.64.0-1.1) ... Removing libpython3.13-minimal:amd64 (3.13.5-2) ... Removing libreadline8t64:amd64 (8.2-6) ... 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 libuv1t64:amd64 (1.50.0-2) ... Removing media-types (13.0.0) ... Removing ncbi-data (6.1.20170106+dfsg2-6) ... Removing ncbi-vdb-data (3.2.1+dfsg-2) ... Removing netbase (6.5) ... Removing perl-modules-5.40 (5.40.1-6) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.41-12) ... 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', 'remove', '--allow-remove-essential', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgomp1:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libuv1t64:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'ncbi-vdb-data', 'netbase', 'perl', 'perl-modules-5.40', 'python3', 'python3-minimal', 'python3.13', 'python3.13-minimal', 'readline-common', 'kraken2'] 0m11.5s INFO: Running scripts post_remove 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_remove_exceptions'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_remove_exceptions'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg', '--purge', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgomp1:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libuv1t64:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'ncbi-vdb-data', 'netbase', 'perl', 'perl-modules-5.40', 'python3', 'python3-minimal', 'python3.13', 'python3.13-minimal', 'readline-common'] 0m11.6s DUMP: dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libffi8 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto16 which isn't installed dpkg: warning: ignoring request to remove libmbedtls21 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-7 which isn't installed dpkg: warning: ignoring request to remove libncbi-vdb3 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed (Reading database ... 4952 files and directories currently installed.) Purging configuration files for libpython3.13-minimal:amd64 (3.13.5-2) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove libuv1t64 which isn't installed Purging configuration files for media-types (13.0.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-6) ... Purging configuration files for ncbi-vdb-data (3.2.1+dfsg-2) ... Purging configuration files for netbase (6.5) ... Purging configuration files for perl (5.40.1-6) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed Purging configuration files for python3 (3.13.5-1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.5-2) ... Purging configuration files for readline-common (8.2-6) ... 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg', '--purge', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgomp1:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libuv1t64:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'ncbi-vdb-data', 'netbase', 'perl', 'perl-modules-5.40', 'python3', 'python3-minimal', 'python3.13', 'python3.13-minimal', 'readline-common'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg', '--purge', 'kraken2'] 0m11.6s DUMP: dpkg: warning: ignoring request to remove kraken2 which isn't installed 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg', '--purge', 'kraken2'] 0m11.6s INFO: Running scripts post_purge 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_purge_exceptions'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_purge_exceptions'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg', '--purge', '--pending'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg', '--purge', '--pending'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg', '--remove', '--pending'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg', '--remove', '--pending'] 0m11.6s INFO: Running scripts post_test 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_test_exceptions'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'tmp/scripts/post_test_exceptions'] 0m11.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m11.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg-divert', '--list'] 0m11.8s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'dpkg-divert', '--list'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', 'clean'] 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuxygb_21', 'apt-get', 'clean'] 0m11.8s DEBUG: Recording chroot state 0m12.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/shm'] 0m12.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/shm'] 0m12.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/console'] 0m12.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/console'] 0m12.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/ptmx'] 0m12.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/ptmx'] 0m12.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/pts'] 0m12.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/dev/pts'] 0m12.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/proc'] 0m12.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuxygb_21/proc'] 0m12.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m12.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpuxygb_21'] 0m12.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpuxygb_21 0m12.6s INFO: PASS: Upgrading between Debian distributions. 0m12.6s INFO: PASS: All tests. 0m12.6s INFO: piuparts run ends. ret=0 End: 2025-08-13 07:51:29 GMT