Start: 2023-11-29 02:50:23 GMT [testing] Package: kraken2 Version: 2.1.2-2 Installed-Size: 1787 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libstdc++6 (>= 11), 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_2.1.2-2_amd64.deb Size: 831588 MD5sum: 861f3560973bc8f1f108370d764526f5 SHA256: 88d764c767f9ade07d3325bc5bc95a3574d7d3fe7804947fd897f3c603045b3c [sid] 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/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/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 1.2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt kraken2=2.1.3-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-26-amd64 #1 SMP Debian 5.10.197-1 (2023-09-29) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp5n6yzve7 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp5n6yzve7 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m1.7s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/proc'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/proc'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/pts'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/pts'] 0m1.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/ptmx'] 0m1.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/ptmx'] 0m1.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/console'] 0m1.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/console'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/shm'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/shm'] 0m1.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m1.8s DEBUG: Created policy-rc.d and chmodded it. 0m1.8s DEBUG: Created resolv.conf. 0m1.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp5n6yzve7/tmp/scripts/ 0m1.8s INFO: Running scripts post_chroot_unpack 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', 'update'] 0m3.0s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', 'update'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', '-yf', 'dist-upgrade'] 0m3.6s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', '-yf', 'dist-upgrade'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.8s DUMP: 6deb31383f0b3f5ce38f822020ad491f - 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.8s INFO: Running scripts post_setup 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_setup_dummy_users'] 0m5.0s 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 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_setup_dummy_users'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_setup_forbid_home'] 0m5.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_setup_forbid_home'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_setup_minimize'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_setup_minimize'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_setup_zz_backports'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_setup_zz_backports'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.1s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u2 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u2 install ok installed libc6:amd64 libc6 2.36-9+deb12u2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.17-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.17-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-5 install ok installed usr-is-merged usr-is-merged 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m5.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m5.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m5.4s INFO: Running scripts is_testable 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/is_testable_uninstallable'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/is_testable_uninstallable'] 0m5.5s INFO: Running scripts pre_test 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_test_exceptions'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_test_exceptions'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_test_root_password'] 0m5.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_test_root_password'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'show', '--no-all-versions', 'kraken2'] 0m5.8s DUMP: Package: kraken2 Version: 2.1.2-2 Installed-Size: 1787 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libstdc++6 (>= 11), 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_2.1.2-2_amd64.deb Size: 831588 MD5sum: 861f3560973bc8f1f108370d764526f5 SHA256: 88d764c767f9ade07d3325bc5bc95a3574d7d3fe7804947fd897f3c603045b3c 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'show', '--no-all-versions', 'kraken2'] 0m5.8s INFO: apt-cache knows about the following packages: kraken2 0m5.8s INFO: Running scripts pre_install 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_database-server'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_database-server'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_exceptions'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_exceptions'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_extras'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_extras'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'policy'] 0m5.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.2,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'policy'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'policy', 'kraken2'] 0m5.9s DUMP: kraken2: Installed: (none) Candidate: 2.1.2-2 Version table: 2.1.2-2 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'policy', 'kraken2'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', '-y', 'install', 'kraken2'] 0m13.9s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libexpat1 libgdbm-compat4 libgdbm6 libgomp1 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblmdb0 libmbedcrypto7 libmbedtls14 libmbedx509-1 libncursesw6 libnsl2 libpcre3 libperl5.36 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 media-types ncbi-blast+ ncbi-data perl perl-modules-5.36 python3 python3-minimal python3.11 python3.11-minimal readline-common Suggested packages: gdbm-l10n krb5-doc krb5-user sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binutils binfmt-support readline-doc Recommended packages: krb5-locales libgpm2 netbase ca-certificates The following NEW packages will be installed: kraken2 libexpat1 libgdbm-compat4 libgdbm6 libgomp1 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblmdb0 libmbedcrypto7 libmbedtls14 libmbedx509-1 libncursesw6 libnsl2 libpcre3 libperl5.36 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 media-types ncbi-blast+ ncbi-data perl perl-modules-5.36 python3 python3-minimal python3.11 python3.11-minimal readline-common 0 upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 34.2 MB of archives. After this operation, 163 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7 [2815 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7 [4218 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7 [239 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.11-1~deb12u1 [2018 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:16 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:27 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+ amd64 2.12.0+ds-3+b1 [11.9 MB] Get:36 http://deb.debian.org/debian bookworm/main amd64 kraken2 amd64 2.1.2-2 [832 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 34.2 MB in 0s (83.8 MB/s) Selecting previously unselected package perl-modules-5.36. (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 ... 6100 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.36_5.36.0-7_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.23-3_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-3) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.23-3_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-3) ... Selecting previously unselected package libperl5.36:amd64. Preparing to unpack .../3-libperl5.36_5.36.0-7_amd64.deb ... Unpacking libperl5.36:amd64 (5.36.0-7) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.36.0-7_amd64.deb ... Unpacking perl (5.36.0-7) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../5-libssl3_3.0.11-1~deb12u1_amd64.deb ... Unpacking libssl3:amd64 (3.0.11-1~deb12u1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../6-libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../7-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../8-python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libssl3:amd64 (3.0.11-1~deb12u1) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (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 ... 8432 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.11.2-1+b1_amd64.deb ... 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Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... Selecting previously unselected package liblmdb0:amd64. Preparing to unpack .../3-liblmdb0_0.9.24-1_amd64.deb ... Unpacking liblmdb0:amd64 (0.9.24-1) ... Selecting previously unselected package libmbedcrypto7:amd64. Preparing to unpack .../4-libmbedcrypto7_2.28.3-1_amd64.deb ... Unpacking libmbedcrypto7:amd64 (2.28.3-1) ... Selecting previously unselected package libmbedx509-1:amd64. Preparing to unpack .../5-libmbedx509-1_2.28.3-1_amd64.deb ... Unpacking libmbedx509-1:amd64 (2.28.3-1) ... Selecting previously unselected package libmbedtls14:amd64. Preparing to unpack .../6-libmbedtls14_2.28.3-1_amd64.deb ... Unpacking libmbedtls14:amd64 (2.28.3-1) ... Selecting previously unselected package libpcre3:amd64. Preparing to unpack .../7-libpcre3_2%3a8.39-15_amd64.deb ... Unpacking libpcre3:amd64 (2:8.39-15) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../8-ncbi-blast+_2.12.0+ds-3+b1_amd64.deb ... Unpacking ncbi-blast+ (2.12.0+ds-3+b1) ... Selecting previously unselected package kraken2. Preparing to unpack .../9-kraken2_2.1.2-2_amd64.deb ... Unpacking kraken2 (2.1.2-2) ... Setting up media-types (10.0.0) ... Setting up liblmdb0:amd64 (0.9.24-1) ... Setting up ncbi-data (6.1.20170106+dfsg1-10) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libtirpc-common (1.3.3+ds-1) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libpcre3:amd64 (2:8.39-15) ... Setting up perl-modules-5.36 (5.36.0-7) ... Setting up libmbedcrypto7:amd64 (2.28.3-1) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up readline-common (8.2-1.3) ... Setting up libgdbm6:amd64 (1.23-3) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up libperl5.36:amd64 (5.36.0-7) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up perl (5.36.0-7) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up python3 (3.11.2-1+b1) ... Setting up ncbi-blast+ (2.12.0+ds-3+b1) ... Setting up kraken2 (2.1.2-2) ... Processing triggers for libc-bin (2.36-9+deb12u2) ... 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', '-y', 'install', 'kraken2'] 0m13.9s INFO: Running scripts post_install 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_install_exceptions'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_install_exceptions'] 0m13.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m14.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m14.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp5n6yzve7 to sid 0m14.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m14.3s INFO: Running scripts pre_distupgrade 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', 'update'] 0m18.4s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9616 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7079 kB] Fetched 16.9 MB in 3s (5431 kB/s) Reading package lists... 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', 'update'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', '-yf', 'dist-upgrade'] 0m40.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libpcre3 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: gcc-13-base libunistring5 The following packages will be upgraded: adduser apt base-files base-passwd bash bsdutils coreutils dash debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils gcc-12-base grep init-system-helpers kraken2 libapt-pkg6.0 libaudit-common libaudit1 libblkid1 libc-bin libc6 libcom-err2 libcrypt1 libdb5.3 libdebconfclient0 libexpat1 libext2fs2 libffi8 libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libhogweed6 libidn2-0 libk5crypto3 libkrb5-3 libkrb5support0 liblmdb0 liblzma5 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmd0 libmount1 libncursesw6 libnettle8 libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtirpc-common libtirpc3 libudev1 libuuid1 libxxhash0 libzstd1 login logsave mawk media-types mount ncbi-blast+ ncurses-base ncurses-bin passwd perl perl-base perl-modules-5.36 python3 python3-minimal python3.11 python3.11-minimal readline-common sysvinit-utils tzdata usr-is-merged util-linux util-linux-extra zlib1g 108 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 60.9 MB of archives. After this operation, 6333 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.14 [88.3 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.2-6 [96.7 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-12 [2753 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-12 [601 kB] Get:7 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.2.0-7 [40.8 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 13.2.0-7 [57.7 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2 [557 kB] Get:10 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-2+b1 [2948 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 13.2.0-7 [696 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.2-3 [704 kB] Get:15 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.4.5-0.1 [239 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255~rc3-2 [359 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255~rc3-2 [121 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2 [26.4 kB] Get:19 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3 [87.5 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.7.7 [946 kB] Get:21 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.1 [1561 kB] Get:22 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:23 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:24 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:25 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-3 [431 kB] Get:26 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-3 [616 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20231121-1 [135 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20231121-1 [341 kB] Get:29 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20231121-1 [429 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libperl5.36 amd64 5.36.0-10 [4221 kB] Get:31 http://deb.debian.org/debian sid/main amd64 perl amd64 5.36.0-10 [239 kB] Get:32 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.36.0-10 [1602 kB] Get:33 http://deb.debian.org/debian sid/main amd64 perl-modules-5.36 all 5.36.0-10 [2815 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-2 [89.7 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4 [697 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.23-5 [72.5 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.23-5 [48.3 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.2-6 [159 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4 [261 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-1 [73.9 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.2-6 [190 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.1-1 [10.8 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.1-1 [47.3 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.2-6 [116 kB] Get:45 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.39.2-6 [154 kB] Get:46 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.2-6 [1225 kB] Get:47 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libsemanage-common all 3.5-1 [9908 B] Get:59 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1 [89.7 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.2-9.1 [49.9 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.2-9.1 [264 kB] Get:63 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-3 [972 kB] Get:64 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:65 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.4-2 [46.8 kB] Get:67 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.7 [1362 kB] Get:68 http://deb.debian.org/debian sid/main amd64 usr-is-merged all 38 [5504 B] Get:69 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:70 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amd64 libkrb5-3 amd64 1.20.1-5 [332 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5 [79.6 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5 [32.9 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2+b1 [20.1 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.1.4-2 [2058 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:88 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.2-3 [167 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.44.2-1 [882 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.2-6 [29.6 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.6-3 [1812 kB] Get:93 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.6-3 [2030 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.6-3 [815 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.5.0-2 [99.0 kB] Get:96 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.4-5+b1 [26.5 kB] Get:97 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.4-5+b1 [26.5 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.4-5+b1 [9492 B] Get:99 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.2-9.1 [134 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-1 [35.5 kB] Get:101 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20231102-1 [135 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 13.2.0-7 [131 kB] Get:103 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-11 [40.7 kB] Get:104 http://deb.debian.org/debian sid/main amd64 liblmdb0 amd64 0.9.31-1 [44.3 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libmbedcrypto7 amd64 2.28.5-1 [279 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libmbedx509-1 amd64 2.28.5-1 [129 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libmbedtls14 amd64 2.28.5-1 [165 kB] Get:108 http://deb.debian.org/debian sid/main amd64 ncbi-blast+ amd64 2.12.0+ds-4 [12.5 MB] Get:109 http://deb.debian.org/debian sid/main amd64 kraken2 amd64 2.1.3-1 [868 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.0-2+b1 [24.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 60.9 MB in 2s (30.8 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 ... 9317 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.47-3_amd64.deb ... Unpacking libgpg-error0:amd64 (1.47-3) over (1.46-1) ... Setting up libgpg-error0:amd64 (1.47-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9317 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.2-3_amd64.deb ... Unpacking libgcrypt20:amd64 (1.10.2-3) over (1.10.1-3) ... Setting up libgcrypt20:amd64 (1.10.2-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9317 files and directories currently installed.) Preparing to unpack .../liblzma5_5.4.5-0.1_amd64.deb ... Unpacking liblzma5:amd64 (5.4.5-0.1) over (5.4.1-0.2) ... Setting up liblzma5:amd64 (5.4.5-0.1) ... (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 ... 9317 files and directories currently installed.) Preparing to unpack .../libudev1_255~rc3-2_amd64.deb ... Unpacking libudev1:amd64 (255~rc3-2) over (252.17-1~deb12u1) ... Setting up libudev1:amd64 (255~rc3-2) ... (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 ... 9317 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.2-2_amd64.deb ... Unpacking libxxhash0:amd64 (0.8.2-2) over (0.8.1-1) ... Setting up libxxhash0:amd64 (0.8.2-2) ... (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 ... 9317 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.7.7_amd64.deb ... Unpacking libapt-pkg6.0:amd64 (2.7.7) over (2.6.1) ... Setting up libapt-pkg6.0:amd64 (2.7.7) ... (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 ... 9317 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.22.1_amd64.deb ... Unpacking dpkg (1.22.1) over (1.21.22) ... Setting up dpkg (1.22.1) ... (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 ... 9312 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-6_amd64.deb ... Unpacking dash (0.5.12-6) over (0.5.12-2) ... Setting up dash (0.5.12-6) ... Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' (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 ... 9311 files and directories currently installed.) Preparing to unpack .../libperl5.36_5.36.0-10_amd64.deb ... Unpacking libperl5.36:amd64 (5.36.0-10) over (5.36.0-7) ... Preparing to unpack .../perl_5.36.0-10_amd64.deb ... Unpacking perl (5.36.0-10) over (5.36.0-7) ... Preparing to unpack .../perl-base_5.36.0-10_amd64.deb ... Unpacking perl-base (5.36.0-10) over (5.36.0-7) ... Setting up perl-base (5.36.0-10) ... (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 ... 9311 files and directories currently installed.) Preparing to unpack .../libgdbm6_1.23-5_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-5) over (1.23-3) ... Preparing to unpack .../libgdbm-compat4_1.23-5_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-5) over (1.23-3) ... Preparing to unpack .../libblkid1_2.39.2-6_amd64.deb ... Unpacking libblkid1:amd64 (2.39.2-6) over (2.38.1-5+b1) ... Setting up libblkid1:amd64 (2.39.2-6) ... (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 ... 9310 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.42-4_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-4) over (10.42-1) ... Setting up libpcre2-8-0:amd64 (10.42-4) ... (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 ... 9310 files and directories currently installed.) Preparing to unpack .../libselinux1_3.5-1_amd64.deb ... Unpacking libselinux1:amd64 (3.5-1) over (3.4-1+b6) ... Setting up libselinux1:amd64 (3.5-1) ... (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 ... 9309 files and directories currently installed.) Preparing to unpack .../libmount1_2.39.2-6_amd64.deb ... Unpacking libmount1:amd64 (2.39.2-6) over (2.38.1-5+b1) ... Setting up libmount1:amd64 (2.39.2-6) ... (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 ... 9308 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.1-1_all.deb ... Unpacking libaudit-common (1:3.1.1-1) over (1:3.0.9-1) ... Setting up libaudit-common (1:3.1.1-1) ... (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 ... 9308 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.1-1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.1.1-1) over (1:3.0.9-1) ... Setting up libaudit1:amd64 (1:3.1.1-1) ... (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 ... 9308 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.39.2-6_amd64.deb ... Unpacking libsmartcols1:amd64 (2.39.2-6) over (2.38.1-5+b1) ... Setting up libsmartcols1:amd64 (2.39.2-6) ... (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 ... 9307 files and directories currently installed.) Preparing to unpack .../util-linux-extra_2.39.2-6_amd64.deb ... Unpacking util-linux-extra (2.39.2-6) over (2.38.1-5+b1) ... dpkg: warning: unable to delete old directory '/usr/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/usr/lib/udev': Directory not empty dpkg: warning: unable to delete old directory '/etc/init.d': Directory not empty Setting up util-linux-extra (2.39.2-6) ... (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 ... 9311 files and directories currently installed.) Preparing to unpack .../util-linux_2.39.2-6_amd64.deb ... Unpacking util-linux (2.39.2-6) over (2.38.1-5+b1) ... Setting up util-linux (2.39.2-6) ... (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 ... 9312 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.4-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.4-2) over (3.4.4-1) ... Setting up libffi8:amd64 (3.4.4-2) ... (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 ... 9312 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.0-5_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.0-5) over (0.24.1-2) ... Setting up libp11-kit0:amd64 (0.25.0-5) ... Selecting previously unselected package libunistring5:amd64. (Reading database ... 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Setting up libtirpc-common (1.3.4+ds-1) ... Setting up libsqlite3-0:amd64 (3.44.2-1) ... Setting up libcom-err2:amd64 (1.47.0-2+b1) ... Setting up libgomp1:amd64 (13.2.0-7) ... Setting up libkrb5support0:amd64 (1.20.1-5) ... Setting up gcc-12-base:amd64 (12.3.0-11) ... Setting up tzdata (2023c-11) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Nov 29 02:51:02 UTC 2023. Universal Time is now: Wed Nov 29 02:51:02 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up perl-modules-5.36 (5.36.0-10) ... Setting up libmbedcrypto7:amd64 (2.28.5-1) ... Setting up libss2:amd64 (1.47.0-2+b1) ... Setting up libncursesw6:amd64 (6.4+20231121-1) ... Setting up libk5crypto3:amd64 (1.20.1-5) ... Setting up logsave (1.47.0-2+b1) ... Setting up mount (2.39.2-6) ... Setting up mawk (1.3.4.20231102-1) ... Setting up libkrb5-3:amd64 (1.20.1-5) ... Setting up readline-common (8.2-3) ... Setting up libgdbm6:amd64 (1.23-5) ... Setting up libmbedx509-1:amd64 (2.28.5-1) ... Setting up libmbedtls14:amd64 (2.28.5-1) ... Setting up libreadline8:amd64 (8.2-3) ... Setting up e2fsprogs (1.47.0-2+b1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5) ... Setting up libgdbm-compat4:amd64 (1.23-5) ... Setting up libperl5.36:amd64 (5.36.0-10) ... Setting up libtirpc3:amd64 (1.3.4+ds-1) ... Setting up perl (5.36.0-10) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.6-3) ... Setting up libpython3-stdlib:amd64 (3.11.4-5+b1) ... Setting up python3.11 (3.11.6-3) ... Setting up python3 (3.11.4-5+b1) ... Setting up ncbi-blast+ (2.12.0+ds-4) ... Setting up kraken2 (2.1.3-1) ... Processing triggers for debianutils (5.14) ... Processing triggers for libc-bin (2.37-12) ... 0m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', '-yf', 'dist-upgrade'] 0m40.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m41.9s DUMP: b6702f6c675fc9f9a0d747673300aed9 - 0m41.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m41.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'show', '--no-all-versions', 'kraken2'] 0m42.2s 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 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'show', '--no-all-versions', 'kraken2'] 0m42.2s INFO: apt-cache knows about the following packages: kraken2 0m42.2s INFO: Running scripts pre_install 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_database-server'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_database-server'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_exceptions'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_exceptions'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_extras'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_extras'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'policy'] 0m42.3s 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: 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'policy'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'policy', 'kraken2'] 0m42.4s 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 sid/main amd64 Packages 100 /var/lib/dpkg/status 0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'policy', 'kraken2'] 0m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', '-y', 'install', 'kraken2'] 0m43.0s DUMP: Reading package lists... Building dependency tree... Reading state information... kraken2 is already the newest version (2.1.3-1). The following package was automatically installed and is no longer required: libpcre3 Use 'sudo apt autoremove' to remove it. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', '-y', 'install', 'kraken2'] 0m43.0s INFO: Running scripts post_install 0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_install_exceptions'] 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_install_exceptions'] 0m43.0s INFO: Running scripts post_distupgrade 0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_distupgrade_exceptions'] 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_distupgrade_exceptions'] 0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_distupgrade_zz_backports'] 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_distupgrade_zz_backports'] 0m43.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m43.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m43.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m43.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m43.8s INFO: Running scripts pre_install 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_database-server'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_database-server'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_exceptions'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_exceptions'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_extras'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_extras'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_foreign_architecture'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_foreign_architecture'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'policy'] 0m43.9s 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: 0m43.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'policy'] 0m43.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'policy', 'kraken2'] 0m43.9s 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 sid/main amd64 Packages 100 /var/lib/dpkg/status 0m43.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-cache', 'policy', 'kraken2'] 0m43.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', '-y', 'install', 'kraken2=2.1.3-1'] 0m44.6s DUMP: Reading package lists... Building dependency tree... Reading state information... kraken2 is already the newest version (2.1.3-1). The following package was automatically installed and is no longer required: libpcre3 Use 'sudo apt autoremove' to remove it. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m44.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', '-y', 'install', 'kraken2=2.1.3-1'] 0m44.6s INFO: Running scripts post_install 0m44.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_install_exceptions'] 0m44.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_install_exceptions'] 0m44.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m45.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m45.0s INFO: /bin converted to /usr/bin by /usr merge 0m45.0s INFO: /lib converted to /usr/lib by /usr merge 0m45.0s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m45.0s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m45.0s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m45.0s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m45.0s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m45.0s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m45.0s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m45.0s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m45.0s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m45.0s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m45.0s INFO: /sbin converted to /usr/sbin by /usr merge 0m45.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', '-ac', '--ignore-obsolete'] 0m46.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', '-ac', '--ignore-obsolete'] 0m46.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m46.6s DUMP: 0.15.6 0m46.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m46.6s INFO: Running adequate version 0.15.6 now. 0m46.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'kraken2'] 0m46.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'kraken2'] 0m46.8s INFO: Running scripts pre_remove 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_remove_exceptions'] 0m49.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/pre_remove_exceptions'] 0m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m49.0s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.7 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.2 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.39.2-6 install ok installed coreutils coreutils 9.4-2+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.14 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.1 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-11 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-7 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.11-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed kraken2 kraken2 2.1.3-1 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.7 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.1.1-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.1-1 install ok installed libblkid1:amd64 libblkid1 2.39.2-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.37-12 install ok installed libc6:amd64 libc6 2.37-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libexpat1:amd64 libexpat1 2.5.0-2 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libffi8:amd64 libffi8 3.4.4-2 install ok installed libgcc-s1:amd64 libgcc-s1 13.2.0-7 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.2-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-5 install ok installed libgdbm6:amd64 libgdbm6 1.23-5 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.1-4+b1 install ok installed libgomp1:amd64 libgomp1 13.2.0-7 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-5 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.5-0.1 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.5-1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.5-1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-1 install ok installed libmount1:amd64 libmount1 2.39.2-6 install ok installed libncursesw6:amd64 libncursesw6 6.4+20231121-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.0-5 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libpcre3:amd64 libpcre3 2:8.39-15 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-10 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.4-5+b1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.6-3 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.6-3 install ok installed libreadline8:amd64 libreadline8 8.2-3 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-2 install ok installed libselinux1:amd64 libselinux1 3.5-1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.2-6 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.44.2-1 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssl3:amd64 libssl3 3.1.4-2 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-7 install ok installed libsystemd0:amd64 libsystemd0 255~rc3-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.4+20231121-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.4+ds-1 install ok installed libudev1:amd64 libudev1 255~rc3-2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.2-6 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-3 install ok installed logsave logsave 1.47.0-2+b1 install ok installed mawk mawk 1.3.4.20231102-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.39.2-6 install ok installed ncbi-blast+ ncbi-blast+ 2.12.0+ds-4 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-10 install ok installed ncurses-base ncurses-base 6.4+20231121-1 install ok installed ncurses-bin ncurses-bin 6.4+20231121-1 install ok installed passwd passwd 1:4.13+dfsg1-3 install ok installed perl perl 5.36.0-10 install ok installed perl-base perl-base 5.36.0-10 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-10 install ok installed python3 python3 3.11.4-5+b1 install ok installed python3-minimal python3-minimal 3.11.4-5+b1 install ok installed python3.11 python3.11 3.11.6-3 install ok installed python3.11-minimal python3.11-minimal 3.11.6-3 install ok installed readline-common readline-common 8.2-3 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.08-3 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-11 install ok installed usr-is-merged usr-is-merged 38 install ok installed util-linux util-linux 2.39.2-6 install ok installed util-linux-extra util-linux-extra 2.39.2-6 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3 0m49.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', 'remove', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblmdb0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpcre3:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common', 'kraken2'] 0m50.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: kraken2 libexpat1 libgdbm-compat4 libgdbm6 libgomp1 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblmdb0 libmbedcrypto7 libmbedtls14 libmbedx509-1 libncursesw6 libnsl2 libpcre3 libperl5.36 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libsqlite3-0 libtirpc-common libtirpc3 media-types ncbi-blast+ ncbi-data perl perl-modules-5.36 python3 python3-minimal python3.11 python3.11-minimal readline-common 0 upgraded, 0 newly installed, 35 to remove and 0 not upgraded. After this operation, 160 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 ... 8533 files and directories currently installed.) Removing kraken2 (2.1.3-1) ... Removing ncbi-blast+ (2.12.0+ds-4) ... Removing python3 (3.11.4-5+b1) ... Removing python3.11 (3.11.6-3) ... Removing python3-minimal (3.11.4-5+b1) ... Removing python3.11-minimal (3.11.6-3) ... Removing libexpat1:amd64 (2.5.0-2) ... Removing perl (5.36.0-10) ... Removing libperl5.36:amd64 (5.36.0-10) ... Removing libgdbm-compat4:amd64 (1.23-5) ... Removing libgdbm6:amd64 (1.23-5) ... Removing libgomp1:amd64 (13.2.0-7) ... Removing libpython3-stdlib:amd64 (3.11.4-5+b1) ... Removing libpython3.11-stdlib:amd64 (3.11.6-3) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3) ... Removing libtirpc3:amd64 (1.3.4+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-5) ... Removing libkrb5-3:amd64 (1.20.1-5) ... Removing libk5crypto3:amd64 (1.20.1-5) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-5) ... Removing liblmdb0:amd64 (0.9.31-1) ... Removing libmbedtls14:amd64 (2.28.5-1) ... Removing libmbedx509-1:amd64 (2.28.5-1) ... Removing libmbedcrypto7:amd64 (2.28.5-1) ... Removing libncursesw6:amd64 (6.4+20231121-1) ... Removing libpcre3:amd64 (2:8.39-15) ... Removing libpython3.11-minimal:amd64 (3.11.6-3) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.2-3) ... Removing libsqlite3-0:amd64 (3.44.2-1) ... Removing libtirpc-common (1.3.4+ds-1) ... Removing media-types (10.1.0) ... Removing ncbi-data (6.1.20170106+dfsg1-10) ... Removing perl-modules-5.36 (5.36.0-10) ... Removing readline-common (8.2-3) ... Processing triggers for libc-bin (2.37-12) ... 0m50.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', 'remove', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblmdb0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpcre3:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common', 'kraken2'] 0m50.7s INFO: Running scripts post_remove 0m50.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_remove_exceptions'] 0m50.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_remove_exceptions'] 0m50.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg', '--purge', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblmdb0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpcre3:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common'] 0m50.8s DUMP: dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed (Reading database ... 5335 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-5) ... 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 liblmdb0 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1 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 libpcre3 which isn't installed dpkg: warning: ignoring request to remove libperl5.36 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.6-3) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1) ... dpkg: warning: ignoring request to remove libtirpc3 which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-10) ... Purging configuration files for perl (5.36.0-10) ... dpkg: warning: ignoring request to remove perl-modules-5.36 which isn't installed Purging configuration files for python3 (3.11.4-5+b1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.6-3) ... Purging configuration files for readline-common (8.2-3) ... 0m50.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg', '--purge', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblmdb0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpcre3:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common'] 0m50.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg', '--purge', 'kraken2'] 0m50.8s DUMP: dpkg: warning: ignoring request to remove kraken2 which isn't installed 0m50.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg', '--purge', 'kraken2'] 0m50.8s INFO: Running scripts post_purge 0m50.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_purge_exceptions'] 0m50.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_purge_exceptions'] 0m50.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg', '--purge', '--pending'] 0m50.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg', '--purge', '--pending'] 0m50.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg', '--remove', '--pending'] 0m50.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg', '--remove', '--pending'] 0m50.8s INFO: Running scripts post_test 0m50.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_test_exceptions'] 0m50.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'tmp/scripts/post_test_exceptions'] 0m50.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m51.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m51.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg-divert', '--list'] 0m51.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 0m51.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'dpkg-divert', '--list'] 0m51.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', 'clean'] 0m51.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7', 'apt-get', 'clean'] 0m51.2s DEBUG: Recording chroot state 0m52.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/shm'] 0m52.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/shm'] 0m52.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/console'] 0m52.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/console'] 0m52.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/ptmx'] 0m52.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/ptmx'] 0m52.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/pts'] 0m52.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/dev/pts'] 0m52.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/proc'] 0m52.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7/proc'] 0m52.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m52.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5n6yzve7'] 0m52.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp5n6yzve7 0m52.3s INFO: PASS: Upgrading between Debian distributions. 0m52.3s INFO: PASS: All tests. 0m52.3s INFO: piuparts run ends. ret=0 End: 2023-11-29 02:51:16 GMT