Start: 2026-01-24 22:59:33 GMT [stable] Package: shasta Source: shasta (0.12.0-1) Version: 0.12.0-1+b2 Installed-Size: 2599 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-chrono1.83.0t64 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 14), python3-shasta (= 0.12.0-1+b2) Description: nanopore whole genome assembly (binaries and scripts) Homepage: https://github.com/chanzuckerberg/shasta Description-md5: 7bb8ac3039d8e82623b175abb8ab2e67 Section: science Priority: optional Filename: pool/main/s/shasta/shasta_0.12.0-1+b2_amd64.deb Size: 625376 MD5sum: 975300cffd2ee20c3926a83daebf1ef8 SHA256: 62cd7c134c785739c3327404b9a71edad73da7616538967109c8e7d533f1510d [sid] Package: shasta Version: 0.14.0-1 Installed-Size: 2752 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-chrono1.83.0t64 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 14), python3-shasta (= 0.14.0-1) Description: nanopore whole genome assembly (binaries and scripts) Homepage: https://paoloshasta.github.io/shasta/ Description-md5: 7bb8ac3039d8e82623b175abb8ab2e67 Section: science Priority: optional Filename: pool/main/s/shasta/shasta_0.14.0-1_amd64.deb Size: 642020 MD5sum: 4ef6b19e4917580d77693b163ab5f980 SHA256: b0c4ef234b75b14917136d09d60bd500a10fe5dbd5df7c4228caa9c07714715c Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt shasta=0.14.0-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.6.1~202508211856~1.6.0-10-gffba2cce starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt shasta=0.14.0-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 6.1.0-42-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.159-1 (2025-12-30) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpxqkljo91 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpxqkljo91 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpxqkljo91/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', 'update'] 0m3.5s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [140 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9670 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6484 kB] Fetched 16.3 MB in 2s (7354 kB/s) Reading package lists... 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', 'update'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', '-yf', 'dist-upgrade'] 0m6.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: base-files bash libc-bin libc6 libcap2 sqv 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5752 kB of archives. After this operation, 3072 B disk space will be freed. Get:1 http://deb.debian.org/debian trixie/main amd64 libc6 amd64 2.41-12+deb13u1 [2851 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 base-files amd64 13.8+deb13u3 [73.3 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 bash amd64 5.2.37-2+b7 [1501 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libc-bin amd64 2.41-12+deb13u1 [637 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libcap2 amd64 1:2.75-10+b3 [28.8 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 sqv amd64 1.3.0-3+b2 [661 kB] Preconfiguring packages ... Fetched 5752 kB in 1s (9013 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4935 files and directories currently installed.) Preparing to unpack .../libc6_2.41-12+deb13u1_amd64.deb ... Unpacking libc6:amd64 (2.41-12+deb13u1) over (2.41-12) ... Setting up libc6:amd64 (2.41-12+deb13u1) ... (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 ... 4935 files and directories currently installed.) Preparing to unpack .../base-files_13.8+deb13u3_amd64.deb ... Unpacking base-files (13.8+deb13u3) over (13.8+deb13u2) ... Setting up base-files (13.8+deb13u3) ... Installing new version of config file /etc/debian_version ... (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 ... 4935 files and directories currently installed.) Preparing to unpack .../bash_5.2.37-2+b7_amd64.deb ... Unpacking bash (5.2.37-2+b7) over (5.2.37-2+b5) ... Setting up bash (5.2.37-2+b7) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (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 ... 4935 files and directories currently installed.) Preparing to unpack .../libc-bin_2.41-12+deb13u1_amd64.deb ... Unpacking libc-bin (2.41-12+deb13u1) over (2.41-12) ... Setting up libc-bin (2.41-12+deb13u1) ... (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 ... 4935 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.75-10+b3_amd64.deb ... Unpacking libcap2:amd64 (1:2.75-10+b3) over (1:2.75-10+b1) ... Setting up libcap2:amd64 (1:2.75-10+b3) ... (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 ... 4935 files and directories currently installed.) Preparing to unpack .../sqv_1.3.0-3+b2_amd64.deb ... Unpacking sqv (1.3.0-3+b2) over (1.3.0-3) ... Setting up sqv (1.3.0-3+b2) ... Processing triggers for debianutils (5.23.2) ... Processing triggers for libc-bin (2.41-12+deb13u1) ... 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', '-yf', 'dist-upgrade'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.4s DUMP: 6d53b35ca35697b2767d0c31d63fde0a - 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.4s INFO: Running scripts post_setup 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_setup_dummy_users'] 0m7.3s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_setup_dummy_users'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_setup_forbid_home'] 0m7.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_setup_forbid_home'] 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.4s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_setup_minimize'] 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_setup_minimize'] 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_setup_zz_backports'] 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_setup_zz_backports'] 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.4s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8+deb13u3 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b7 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69~deb13u1 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12+deb13u1 install ok installed libc6:amd64 libc6 2.41-12+deb13u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b3 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1~deb13u1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.4-1~deb13u1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.9-1~deb13u1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.9-1~deb13u1 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-5 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.4-1~deb13u1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3+b2 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-4+deb13u1 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat 0m7.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m7.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m7.9s INFO: Running scripts is_testable 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/is_testable_uninstallable'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/is_testable_uninstallable'] 0m7.9s INFO: Running scripts pre_test 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_test_exceptions'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_test_exceptions'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_test_root_password'] 0m7.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_test_root_password'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'show', '--no-all-versions', 'shasta'] 0m8.1s DUMP: Package: shasta Source: shasta (0.12.0-1) Version: 0.12.0-1+b2 Installed-Size: 2599 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-chrono1.83.0t64 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 14), python3-shasta (= 0.12.0-1+b2) Description-en: nanopore whole genome assembly (binaries and scripts) De novo assembly from Oxford Nanopore reads. The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. . Computational methods used by the Shasta assembler include: . * Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads. . * Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ?? 10). . Shasta assembly quality is comparable or better than assembly quality achieved by other long read assemblers. . This package contains the executable binaries (tools) and accommodating scripts. Description-md5: 7bb8ac3039d8e82623b175abb8ab2e67 Homepage: https://github.com/chanzuckerberg/shasta Section: science Priority: optional Filename: pool/main/s/shasta/shasta_0.12.0-1+b2_amd64.deb Size: 625376 MD5sum: 975300cffd2ee20c3926a83daebf1ef8 SHA256: 62cd7c134c785739c3327404b9a71edad73da7616538967109c8e7d533f1510d 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'show', '--no-all-versions', 'shasta'] 0m8.1s INFO: apt-cache knows about the following packages: shasta 0m8.1s INFO: Running scripts pre_install 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_database-server'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_database-server'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_exceptions'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_exceptions'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_extras'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_extras'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'policy'] 0m8.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.3,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'policy'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'policy', 'shasta'] 0m8.2s DUMP: shasta: Installed: (none) Candidate: 0.12.0-1+b2 Version table: 0.12.0-1+b2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'policy', 'shasta'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', '-y', 'install', 'shasta'] 0m16.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libblas3 libboost-chrono1.83.0t64 libboost-program-options1.83.0 libboost-serialization1.83.0 libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgomp1 liblapack3 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncursesw6 libnghttp2-14 libperl5.40 libpng16-16t64 libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libspoa7.0.0 libuv1t64 media-types ncbi-blast+ ncbi-data ncbi-vdb-data netbase perl perl-modules-5.40 python3 python3-minimal python3-shasta python3.13 python3.13-minimal readline-common Suggested packages: gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binutils binfmt-support readline-doc Recommended packages: libgpm2 ca-certificates The following NEW packages will be installed: libblas3 libboost-chrono1.83.0t64 libboost-program-options1.83.0 libboost-serialization1.83.0 libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgomp1 liblapack3 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncursesw6 libnghttp2-14 libperl5.40 libpng16-16t64 libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libspoa7.0.0 libuv1t64 media-types ncbi-blast+ ncbi-data ncbi-vdb-data netbase perl perl-modules-5.40 python3 python3-minimal python3-shasta python3.13 python3.13-minimal readline-common shasta 0 upgraded, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 45.9 MB of archives. After this operation, 219 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.1-6 [3019 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.1-6 [4341 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.1-6 [267 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-6 [160 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-4.2 [240 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.2 [347 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4.2 [333 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-6 [2447 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.5-0.1~deb13u1 [361 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.5-0.1~deb13u1 [152 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.5-0.1~deb13u1 [243 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.48-1+deb13u1 [283 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libpython3.13 amd64 3.13.5-2 [2160 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libspoa7.0.0 amd64 4.1.4-2+b1 [74.1 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] Get:40 http://deb.debian.org/debian trixie/main amd64 python3-shasta amd64 0.12.0-1+b2 [2253 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 shasta amd64 0.12.0-1+b2 [625 kB] Fetched 45.9 MB in 1s (31.4 MB/s) Selecting previously unselected package libexpat1:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.5-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.5-2_amd64.deb ... Unpacking python3.13 (3.13.5-2) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Unpacking libuv1t64:amd64 (1.50.0-2) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../24-ncbi-data_6.1.20170106+dfsg2-6_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg2-6) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../25-ncbi-blast+_2.16.0+ds-7_amd64.deb ... Unpacking ncbi-blast+ (2.16.0+ds-7) ... Selecting previously unselected package python3-shasta. Preparing to unpack .../26-python3-shasta_0.12.0-1+b2_amd64.deb ... Unpacking python3-shasta (0.12.0-1+b2) ... Selecting previously unselected package shasta. Preparing to unpack .../27-shasta_0.12.0-1+b2_amd64.deb ... Unpacking shasta (0.12.0-1+b2) ... Setting up media-types (13.0.0) ... Setting up liblmdb0:amd64 (0.9.31-1+b2) ... Setting up ncbi-data (6.1.20170106+dfsg2-6) ... Setting up libboost-program-options1.83.0:amd64 (1.83.0-4.2) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up libuv1t64:amd64 (1.50.0-2) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1) ... Setting up libgomp1:amd64 (14.2.0-19) ... Setting up libboost-serialization1.83.0:amd64 (1.83.0-4.2) ... Setting up libblas3:amd64 (3.12.1-6) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libboost-chrono1.83.0t64:amd64 (1.83.0-4.2) ... Setting up libspoa7.0.0:amd64 (4.1.4-2+b1) ... Setting up libpng16-16t64:amd64 (1.6.48-1+deb13u1) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up perl-modules-5.40 (5.40.1-6) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up netbase (6.5) ... Setting up libmbedcrypto16:amd64 (3.6.5-0.1~deb13u1) ... Setting up readline-common (8.2-6) ... Setting up liblapack3:amd64 (3.12.1-6) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libperl5.40:amd64 (5.40.1-6) ... Setting up perl (5.40.1-6) ... Setting up libmbedx509-7:amd64 (3.6.5-0.1~deb13u1) ... Setting up libmbedtls21:amd64 (3.6.5-0.1~deb13u1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up libpython3.13:amd64 (3.13.5-2) ... Setting up python3.13 (3.13.5-2) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Setting up python3 (3.13.5-1) ... Setting up ncbi-blast+ (2.16.0+ds-7) ... Setting up python3-shasta (0.12.0-1+b2) ... Setting up shasta (0.12.0-1+b2) ... Processing triggers for libc-bin (2.41-12+deb13u1) ... 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', '-y', 'install', 'shasta'] 0m16.3s INFO: Running scripts post_install 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_install_exceptions'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_install_exceptions'] 0m16.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m17.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m17.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpxqkljo91 to sid 0m17.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m17.0s INFO: Running scripts pre_distupgrade 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_distupgrade_exceptions'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_distupgrade_exceptions'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', 'update'] 0m21.1s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [187 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.2 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7421 kB] Fetched 17.8 MB in 3s (5525 kB/s) Reading package lists... 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', 'update'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', '-yf', 'dist-upgrade'] 0m38.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-15-base isa-support libc-gconv-modules-extra sse4.2-support The following packages will be upgraded: apt base-files base-passwd bash bsdutils diffutils dpkg gcc-14-base grep init-system-helpers libacl1 libapt-pkg7.0 libattr1 libaudit-common libaudit1 libblas3 libblkid1 libboost-chrono1.83.0t64 libboost-program-options1.83.0 libboost-serialization1.83.0 libbsd0 libbz2-1.0 libc-bin libc6 libcap-ng0 libcap2 libcrypt1 libdb5.3t64 libdebconfclient0 libexpat1 libffi8 libgcc-s1 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgmp10 libgomp1 libhogweed6t64 liblapack3 liblastlog2-2 liblmdb0 liblz4-1 liblzma5 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmd0 libmount1 libncbi-vdb3 libncursesw6 libnettle8t64 libnghttp2-14 libpam-modules libpam-modules-bin libpam0g libpcre2-8-0 libperl5.40 libpng16-16t64 libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libspoa7.0.0 libsqlite3-0 libssl3t64 libstdc++6 libsystemd0 libtinfo6 libudev1 libuuid1 libuv1t64 libxxhash0 libzstd1 login login.defs mawk media-types mount ncbi-blast+ ncbi-data ncurses-base ncurses-bin openssl-provider-legacy passwd perl perl-base perl-modules-5.40 python3 python3-minimal python3-shasta python3.13 python3.13-minimal readline-common shasta sqv sysvinit-utils tzdata util-linux zlib1g 106 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 75.1 MB of archives. After this operation, 4791 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libc-gconv-modules-extra amd64 2.42-10+b1 [1123 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.42-10+b1 [1811 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.42-10+b1 [643 kB] Get:4 http://deb.debian.org/debian sid/main amd64 gcc-15-base amd64 15.2.0-12 [54.1 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 15.2.0-12 [71.5 kB] Get:6 http://deb.debian.org/debian sid/main amd64 base-files amd64 14 [72.9 kB] Get:7 http://deb.debian.org/debian sid/main amd64 bash amd64 5.3-1 [1556 kB] Get:8 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.12-1 [405 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-6+b1 [40.4 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.3-2+b1 [28.1 kB] Get:11 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.10.0-6 [70.5 kB] Get:12 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.8.2-2 [327 kB] Get:13 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.5.4-1+b1 [308 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.7+dfsg-3+b1 [308 kB] Get:15 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b2 [89.0 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.5.4-1+b1 [2446 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 15.2.0-12 [737 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 259-1 [470 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 259-1 [157 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libapt-pkg7.0 amd64 3.1.14 [1232 kB] Get:21 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.23.5 [1527 kB] Get:22 http://deb.debian.org/debian sid/main amd64 grep amd64 3.12-1 [443 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.6+20251231-1 [137 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.6+20251231-1 [354 kB] Get:25 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.6+20251231-1 [445 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libperl5.40 amd64 5.40.1-7 [4317 kB] Get:27 http://deb.debian.org/debian sid/main amd64 perl amd64 5.40.1-7 [267 kB] Get:28 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.40.1-7 [1679 kB] Get:29 http://deb.debian.org/debian sid/main amd64 perl-modules-5.40 all 5.40.1-7 [3012 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.5.1-1 [98.0 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11 [710 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.26-1+b1 [78.9 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.26-1+b1 [53.1 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.41.3-3 [39.0 kB] Get:35 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.41.3-3 [94.3 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.41.3-3 [174 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.41.3-3 [212 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.41.3-3 [145 kB] Get:39 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.41.3-3 [1167 kB] Get:40 http://deb.debian.org/debian sid/main amd64 mount amd64 2.41.3-3 [164 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.46-1+b1 [298 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.9-4+b1 [86.1 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.282+b2 [11.2 kB] Get:44 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.8 [54.6 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5+b1 [561 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libnettle8t64 amd64 3.10.2-1 [307 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libhogweed6t64 amd64 3.10.2-1 [336 kB] Get:48 http://deb.debian.org/debian sid/main amd64 sqv amd64 1.3.0-5 [648 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.6.0-2+b1 [52.2 kB] Get:50 http://deb.debian.org/debian sid/main amd64 apt amd64 3.1.14 [1524 kB] Get:51 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.69 [39.3 kB] Get:52 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.6+20251231-1 [277 kB] Get:53 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.15-6 [35.0 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.1.2-1 [14.3 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.5-4+b2 [17.5 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.1.2-1+b1 [60.2 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.7.0-5+b1 [70.4 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.7.0-5+b1 [49.8 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.7.0-5+b1 [179 kB] Get:60 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.41.3-3 [106 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.7.3-2 [112 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libpython3.13 amd64 3.13.11-1+b1 [2185 kB] Get:63 http://deb.debian.org/debian sid/main amd64 media-types all 14.0.0 [30.8 kB] Get:64 http://deb.debian.org/debian sid/main amd64 tzdata all 2025c-3 [263 kB] Get:65 http://deb.debian.org/debian sid/main amd64 python3.13 amd64 3.13.11-1+b1 [770 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.5.2-3+b1 [26.4 kB] Get:67 http://deb.debian.org/debian sid/main amd64 readline-common all 8.3-3 [74.8 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.3-3+b1 [181 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.46.1-9 [920 kB] Get:70 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.11-1+b1 [2254 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.11-1+b1 [866 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libpython3.13-stdlib amd64 3.13.11-1+b1 [1968 kB] Get:73 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.13.9-3 [27.6 kB] Get:74 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.13.9-3 [27.6 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.13.9-3 [10.5 kB] Get:76 http://deb.debian.org/debian sid/main amd64 isa-support amd64 27+b1 [15.5 kB] Get:77 http://deb.debian.org/debian sid/main amd64 sse4.2-support amd64 27+b1 [3692 B] Get:78 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-2+b2 [33.0 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-3+b1 [23.2 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.75-10+b5 [28.8 kB] Get:81 http://deb.debian.org/debian sid/main amd64 liblastlog2-2 amd64 2.41.3-3 [29.8 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2+b2 [36.2 kB] Get:83 http://deb.debian.org/debian sid/main amd64 login.defs all 1:4.19.0-4 [211 kB] Get:84 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20250131-2 [142 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.12.2-2+b1 [132 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.9-1 [7888 B] Get:87 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.9-2 [300 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.9-1+b1 [96.9 kB] Get:89 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.19.0-4 [1289 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 15.2.0-12 [140 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 15.2.0-12 [862 kB] Get:92 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.3.0-11 [52.8 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.1-7+b1 [209 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-5+b1 [241 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libboost-program-options1.83.0 amd64 1.83.0-5+b1 [349 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libboost-serialization1.83.0 amd64 1.83.0-5+b1 [335 kB] Get:97 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.1-7+b1 [2550 kB] Get:98 http://deb.debian.org/debian sid/main amd64 liblmdb0 amd64 0.9.31-1+b3 [46.1 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libmbedcrypto16 amd64 3.6.5-0.1 [363 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libmbedx509-7 amd64 3.6.5-0.1 [152 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libmbedtls21 amd64 3.6.5-0.1 [246 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2+b1 [1180 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.54-1 [288 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libspoa7.0.0 amd64 4.1.5-1 [75.6 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libuv1t64 amd64 1.51.0-2+b1 [156 kB] Get:107 http://deb.debian.org/debian sid/main amd64 ncbi-data all 6.1.20170106+dfsg2-7 [3540 kB] Get:108 http://deb.debian.org/debian sid/main amd64 ncbi-blast+ amd64 2.17.0+ds-6 [17.0 MB] Get:109 http://deb.debian.org/debian sid/main amd64 shasta amd64 0.14.0-1 [642 kB] Get:110 http://deb.debian.org/debian sid/main amd64 python3-shasta amd64 0.14.0-1 [2695 kB] Preconfiguring packages ... Fetched 75.1 MB in 3s (24.4 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8543 files and directories currently installed.) Preparing to unpack .../libc6_2.42-10+b1_amd64.deb ... Unpacking libc6:amd64 (2.42-10+b1) over (2.41-12+deb13u1) ... Selecting previously unselected package libc-gconv-modules-extra:amd64. Preparing to unpack .../libc-gconv-modules-extra_2.42-10+b1_amd64.deb ... Unpacking libc-gconv-modules-extra:amd64 (2.42-10+b1) ... Setting up libc-gconv-modules-extra:amd64 (2.42-10+b1) ... (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 ... 8550 files and directories currently installed.) Preparing to unpack .../libc-bin_2.42-10+b1_amd64.deb ... Unpacking libc-bin (2.42-10+b1) over (2.41-12+deb13u1) ... Setting up libc6:amd64 (2.42-10+b1) ... Installing new version of config file /etc/ld.so.conf.d/x86_64-linux-gnu.conf ... Setting up libc-bin (2.42-10+b1) ... Selecting previously unselected package gcc-15-base:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8551 files and directories currently installed.) Preparing to unpack .../gcc-15-base_15.2.0-12_amd64.deb ... Unpacking gcc-15-base:amd64 (15.2.0-12) ... Setting up gcc-15-base:amd64 (15.2.0-12) ... (Reading database ... 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(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 ... 8567 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.41.3-3_amd64.deb ... Unpacking bsdutils (1:2.41.3-3) over (1:2.41-5) ... Setting up bsdutils (1:2.41.3-3) ... (Reading database ... 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Leaving 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Leaving 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Leaving 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Leaving 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3+b1) over (8.2-6) ... Preparing to unpack .../9-libsqlite3-0_3.46.1-9_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-9) over (3.46.1-7) ... Setting up libsqlite3-0:amd64 (3.46.1-9) ... (Reading database ... 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Unpacking libmbedx509-7:amd64 (3.6.5-0.1) over (3.6.5-0.1~deb13u1) ... Preparing to unpack .../18-libmbedtls21_3.6.5-0.1_amd64.deb ... Unpacking libmbedtls21:amd64 (3.6.5-0.1) over (3.6.5-0.1~deb13u1) ... Preparing to unpack .../19-libncbi-vdb3_3.2.1+dfsg-2+b1_amd64.deb ... Unpacking libncbi-vdb3:amd64 (3.2.1+dfsg-2+b1) over (3.2.1+dfsg-2) ... Preparing to unpack .../20-libnghttp2-14_1.64.0-1.1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1+b1) over (1.64.0-1.1) ... Preparing to unpack .../21-libpng16-16t64_1.6.54-1_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.54-1) over (1.6.48-1+deb13u1) ... Preparing to unpack .../22-libspoa7.0.0_4.1.5-1_amd64.deb ... Unpacking libspoa7.0.0:amd64 (4.1.5-1) over (4.1.4-2+b1) ... Preparing to unpack .../23-libuv1t64_1.51.0-2+b1_amd64.deb ... Unpacking libuv1t64:amd64 (1.51.0-2+b1) over (1.50.0-2) ... Preparing to unpack .../24-ncbi-data_6.1.20170106+dfsg2-7_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg2-7) over (6.1.20170106+dfsg2-6) ... Preparing to unpack .../25-ncbi-blast+_2.17.0+ds-6_amd64.deb ... Unpacking ncbi-blast+ (2.17.0+ds-6) over (2.16.0+ds-7) ... Preparing to unpack .../26-shasta_0.14.0-1_amd64.deb ... Unpacking shasta (0.14.0-1) over (0.12.0-1+b2) ... Preparing to unpack .../27-python3-shasta_0.14.0-1_amd64.deb ... Unpacking python3-shasta (0.14.0-1) over (0.12.0-1+b2) ... Setting up media-types (14.0.0) ... Installing new version of config file /etc/mime.types ... Setting up liblmdb0:amd64 (0.9.31-1+b3) ... Setting up ncbi-data (6.1.20170106+dfsg2-7) ... Installing new version of config file /etc/ncbi/.ncbirc ... Setting up libboost-program-options1.83.0:amd64 (1.83.0-5+b1) ... Setting up libgdbm6t64:amd64 (1.26-1+b1) ... Setting up libgdbm-compat4t64:amd64 (1.26-1+b1) ... Setting up gcc-14-base:amd64 (14.3.0-11) ... Setting up login.defs (1:4.19.0-4) ... Installing new version of config file /etc/login.defs ... Setting up libuv1t64:amd64 (1.51.0-2+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up libgomp1:amd64 (15.2.0-12) ... Setting up libsemanage-common (3.9-1) ... Setting up tzdata (2025c-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jan 24 23:00:10 UTC 2026. Universal Time is now: Sat Jan 24 23:00:10 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-serialization1.83.0:amd64 (1.83.0-5+b1) ... Setting up libblas3:amd64 (3.12.1-7+b1) ... Setting up libboost-chrono1.83.0t64:amd64 (1.83.0-5+b1) ... Setting up libspoa7.0.0:amd64 (4.1.5-1) ... Setting up libpng16-16t64:amd64 (1.6.54-1) ... Setting up libsepol2:amd64 (3.9-2) ... Setting up libncursesw6:amd64 (6.6+20251231-1) ... Setting up libgfortran5:amd64 (15.2.0-12) ... Setting up libffi8:amd64 (3.5.2-3+b1) ... Setting up mount (2.41.3-3) ... Setting up perl-modules-5.40 (5.40.1-7) ... Setting up sse4.2-support (27+b1) ... Setting up libsemanage2:amd64 (3.9-1+b1) ... Setting up mawk (1.3.4.20250131-2) ... Setting up libmbedcrypto16:amd64 (3.6.5-0.1) ... Setting up libbsd0:amd64 (0.12.2-2+b1) ... Setting up readline-common (8.3-3) ... Setting up login (1:4.16.0-2+really2.41.3-3) ... Setting up liblapack3:amd64 (3.12.1-7+b1) ... Setting up libperl5.40:amd64 (5.40.1-7) ... Setting up perl (5.40.1-7) ... Setting up libmbedx509-7:amd64 (3.6.5-0.1) ... Setting up libmbedtls21:amd64 (3.6.5-0.1) ... Setting up libreadline8t64:amd64 (8.3-3+b1) ... Setting up passwd (1:4.19.0-4) ... Setting up libpython3.13-stdlib:amd64 (3.13.11-1+b1) ... Setting up libpython3-stdlib:amd64 (3.13.9-3) ... Setting up libpython3.13:amd64 (3.13.11-1+b1) ... Setting up python3.13 (3.13.11-1+b1) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2+b1) ... Setting up python3 (3.13.9-3) ... Setting up ncbi-blast+ (2.17.0+ds-6) ... Setting up python3-shasta (0.14.0-1) ... Setting up shasta (0.14.0-1) ... Processing triggers for debianutils (5.23.2) ... Processing triggers for libc-bin (2.42-10+b1) ... 0m38.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', '-yf', 'dist-upgrade'] 0m38.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m39.7s DUMP: e333a88d296c565aea9c7921ba8de23c - 0m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'show', '--no-all-versions', 'shasta'] 0m39.9s DUMP: Package: shasta Version: 0.14.0-1 Installed-Size: 2752 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-chrono1.83.0t64 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 14), python3-shasta (= 0.14.0-1) Description-en: nanopore whole genome assembly (binaries and scripts) De novo assembly from Oxford Nanopore reads. The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. . Computational methods used by the Shasta assembler include: . * Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads. . * Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ?? 10). . Shasta assembly quality is comparable or better than assembly quality achieved by other long read assemblers. . This package contains the executable binaries (tools) and accommodating scripts. Description-md5: 7bb8ac3039d8e82623b175abb8ab2e67 Homepage: https://paoloshasta.github.io/shasta/ Section: science Priority: optional Filename: pool/main/s/shasta/shasta_0.14.0-1_amd64.deb Size: 642020 MD5sum: 4ef6b19e4917580d77693b163ab5f980 SHA256: b0c4ef234b75b14917136d09d60bd500a10fe5dbd5df7c4228caa9c07714715c 0m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'show', '--no-all-versions', 'shasta'] 0m39.9s INFO: apt-cache knows about the following packages: shasta 0m39.9s INFO: Running scripts pre_install 0m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_database-server'] 0m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_database-server'] 0m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_exceptions'] 0m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_exceptions'] 0m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_extras'] 0m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_extras'] 0m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_foreign_architecture'] 0m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_foreign_architecture'] 0m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'policy'] 0m40.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'policy'] 0m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'policy', 'shasta'] 0m40.0s DUMP: shasta: Installed: 0.14.0-1 Candidate: 0.14.0-1 Version table: *** 0.14.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'policy', 'shasta'] 0m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', '-y', 'install', 'shasta'] 0m40.4s DUMP: Reading package lists... Building dependency tree... Reading state information... shasta is already the newest version (0.14.0-1). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m40.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', '-y', 'install', 'shasta'] 0m40.4s INFO: Running scripts post_install 0m40.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_install_exceptions'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_install_exceptions'] 0m40.5s INFO: Running scripts post_distupgrade 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_distupgrade_exceptions'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_distupgrade_exceptions'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_distupgrade_zz_backports'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_distupgrade_zz_backports'] 0m40.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m41.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m41.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m41.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m41.8s INFO: Running scripts pre_install 0m41.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_database-server'] 0m41.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_database-server'] 0m41.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_exceptions'] 0m41.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_exceptions'] 0m41.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_extras'] 0m41.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_extras'] 0m41.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_foreign_architecture'] 0m41.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_foreign_architecture'] 0m41.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m41.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m41.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'policy'] 0m41.9s 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: 0m41.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'policy'] 0m41.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'policy', 'shasta'] 0m41.9s DUMP: shasta: Installed: 0.14.0-1 Candidate: 0.14.0-1 Version table: *** 0.14.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m41.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-cache', 'policy', 'shasta'] 0m41.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', '-y', 'install', 'shasta=0.14.0-1'] 0m42.4s DUMP: Reading package lists... Building dependency tree... Reading state information... shasta is already the newest version (0.14.0-1). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', '-y', 'install', 'shasta=0.14.0-1'] 0m42.4s INFO: Running scripts post_install 0m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_install_exceptions'] 0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_install_exceptions'] 0m42.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m43.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m43.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', '-ac', '--ignore-obsolete'] 0m45.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', '-ac', '--ignore-obsolete'] 0m45.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m45.0s DUMP: 0.15.9~deb12u1 0m45.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m45.0s INFO: Running adequate version 0.15.9~deb12u1 now. 0m45.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'shasta'] 0m45.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'shasta'] 0m45.1s INFO: Running scripts pre_remove 0m45.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m45.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m45.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m45.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m45.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m46.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m46.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m46.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m46.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m46.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m46.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_remove_exceptions'] 0m46.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/pre_remove_exceptions'] 0m46.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m46.4s DUMP: install ok installed apt apt 3.1.14 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.8 install ok installed bash bash 5.3-1 install ok installed bsdutils bsdutils 1:2.41.3-3 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.12-1 install ok installed dpkg dpkg 1.23.5 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.3.0-11 install ok installed gcc-15-base:amd64 gcc-15-base 15.2.0-12 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69 install ok installed isa-support:amd64 isa-support 27+b1 install ok installed libacl1:amd64 libacl1 2.3.2-2+b2 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.1.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-3+b1 install ok installed libaudit-common libaudit-common 1:4.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.2-1+b1 install ok installed libblas3:amd64 libblas3 3.12.1-7+b1 install ok installed libblkid1:amd64 libblkid1 2.41.3-3 install ok installed libboost-chrono1.83.0t64:amd64 libboost-chrono1.83.0t64 1.83.0-5+b1 install ok installed libboost-program-options1.83.0:amd64 libboost-program-options1.83.0 1.83.0-5+b1 install ok installed libboost-serialization1.83.0:amd64 libboost-serialization1.83.0 1.83.0-5+b1 install ok installed libbsd0:amd64 libbsd0 0.12.2-2+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6+b1 install ok installed libc-bin libc-bin 2.42-10+b1 install ok installed libc-gconv-modules-extra:amd64 libc-gconv-modules-extra 2.42-10+b1 install ok installed libc6:amd64 libc6 2.42-10+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b2 install ok installed libcap2:amd64 libcap2 1:2.75-10+b5 install ok installed libcrypt1:amd64 libcrypt1 1:4.5.1-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-11 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.282+b2 install ok installed libexpat1:amd64 libexpat1 2.7.3-2 install ok installed libffi8:amd64 libffi8 3.5.2-3+b1 install ok installed libgcc-s1:amd64 libgcc-s1 15.2.0-12 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.26-1+b1 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.26-1+b1 install ok installed libgfortran5:amd64 libgfortran5 15.2.0-12 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5+b1 install ok installed libgomp1:amd64 libgomp1 15.2.0-12 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1 install ok installed liblapack3:amd64 liblapack3 3.12.1-7+b1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41.3-3 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b3 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-6 install ok installed liblzma5:amd64 liblzma5 5.8.2-2 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.5-0.1 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.5-0.1 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.5-0.1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b2 install ok installed libmount1:amd64 libmount1 2.41.3-3 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.2.1+dfsg-2+b1 install ok installed libncursesw6:amd64 libncursesw6 6.6+20251231-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1.1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5+b1 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1+b1 install ok installed libperl5.40:amd64 libperl5.40 5.40.1-7 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.54-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.9-3 install ok installed libpython3.13:amd64 libpython3.13 3.13.11-1+b1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.11-1+b1 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.11-1+b1 install ok installed libreadline8t64:amd64 libreadline8t64 8.3-3+b1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2+b1 install ok installed libselinux1:amd64 libselinux1 3.9-4+b1 install ok installed libsemanage-common libsemanage-common 3.9-1 install ok installed libsemanage2:amd64 libsemanage2 3.9-1+b1 install ok installed libsepol2:amd64 libsepol2 3.9-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.41.3-3 install ok installed libspoa7.0.0:amd64 libspoa7.0.0 4.1.5-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-9 install ok installed libssl3t64:amd64 libssl3t64 3.5.4-1+b1 install ok installed libstdc++6:amd64 libstdc++6 15.2.0-12 install ok installed libsystemd0:amd64 libsystemd0 259-1 install ok installed libtinfo6:amd64 libtinfo6 6.6+20251231-1 install ok installed libudev1:amd64 libudev1 259-1 install ok installed libuuid1:amd64 libuuid1 2.41.3-3 install ok installed libuv1t64:amd64 libuv1t64 1.51.0-2+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-3+b1 install ok installed login login 1:4.16.0-2+really2.41.3-3 install ok installed login.defs login.defs 1:4.19.0-4 install ok installed mawk mawk 1.3.4.20250131-2 install ok installed media-types media-types 14.0.0 install ok installed mount mount 2.41.3-3 install ok installed ncbi-blast+ ncbi-blast+ 2.17.0+ds-6 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-7 install ok installed ncbi-vdb-data ncbi-vdb-data 3.2.1+dfsg-2 install ok installed ncurses-base ncurses-base 6.6+20251231-1 install ok installed ncurses-bin ncurses-bin 6.6+20251231-1 install ok installed netbase netbase 6.5 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.4-1+b1 install ok installed passwd passwd 1:4.19.0-4 install ok installed perl perl 5.40.1-7 install ok installed perl-base perl-base 5.40.1-7 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.1-7 install ok installed python3 python3 3.13.9-3 install ok installed python3-minimal python3-minimal 3.13.9-3 install ok installed python3-shasta python3-shasta 0.14.0-1 install ok installed python3.13 python3.13 3.13.11-1+b1 install ok installed python3.13-minimal python3.13-minimal 3.13.11-1+b1 install ok installed readline-common readline-common 8.3-3 install ok installed sed sed 4.9-2 install ok installed shasta shasta 0.14.0-1 install ok installed sqv sqv 1.3.0-5 install ok installed sse4.2-support sse4.2-support 27+b1 install ok installed sysvinit-utils sysvinit-utils 3.15-6 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025c-3 install ok installed util-linux util-linux 2.41.3-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b2 0m46.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m46.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', 'remove', '--allow-remove-essential', 'isa-support:amd64', 'libblas3:amd64', 'libboost-chrono1.83.0t64:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-serialization1.83.0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpng16-16t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libspoa7.0.0:amd64', 'libuv1t64:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'ncbi-vdb-data', 'netbase', 'perl', 'perl-modules-5.40', 'python3', 'python3-minimal', 'python3-shasta', 'python3.13', 'python3.13-minimal', 'readline-common', 'sse4.2-support', 'shasta'] 0m47.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following packages will be REMOVED: isa-support libblas3 libboost-chrono1.83.0t64 libboost-program-options1.83.0 libboost-serialization1.83.0 libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgomp1 liblapack3 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncursesw6 libnghttp2-14 libperl5.40 libpng16-16t64 libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libspoa7.0.0 libuv1t64 media-types ncbi-blast+ ncbi-data ncbi-vdb-data netbase perl perl-modules-5.40 python3 python3-minimal python3-shasta python3.13 python3.13-minimal readline-common shasta sse4.2-support 0 upgraded, 0 newly installed, 43 to remove and 0 not upgraded. After this operation, 223 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 ... 8583 files and directories currently installed.) Removing shasta (0.14.0-1) ... Removing python3-shasta (0.14.0-1) ... Removing ncbi-blast+ (2.17.0+ds-6) ... Removing sse4.2-support (27+b1) ... Removing isa-support:amd64 (27+b1) ... Removing liblapack3:amd64 (3.12.1-7+b1) ... Removing libblas3:amd64 (3.12.1-7+b1) ... Removing libboost-chrono1.83.0t64:amd64 (1.83.0-5+b1) ... Removing libboost-program-options1.83.0:amd64 (1.83.0-5+b1) ... Removing libboost-serialization1.83.0:amd64 (1.83.0-5+b1) ... Removing python3 (3.13.9-3) ... Removing python3.13 (3.13.11-1+b1) ... Removing python3-minimal (3.13.9-3) ... Removing python3.13-minimal (3.13.11-1+b1) ... Removing libpython3.13:amd64 (3.13.11-1+b1) ... Removing libexpat1:amd64 (2.7.3-2) ... Removing libpython3-stdlib:amd64 (3.13.9-3) ... Removing libpython3.13-stdlib:amd64 (3.13.11-1+b1) ... Removing libffi8:amd64 (3.5.2-3+b1) ... Removing perl (5.40.1-7) ... Removing libperl5.40:amd64 (5.40.1-7) ... Removing libgdbm-compat4t64:amd64 (1.26-1+b1) ... Removing libgdbm6t64:amd64 (1.26-1+b1) ... Removing libgfortran5:amd64 (15.2.0-12) ... Removing libgomp1:amd64 (15.2.0-12) ... Removing liblmdb0:amd64 (0.9.31-1+b3) ... Removing libncbi-vdb3:amd64 (3.2.1+dfsg-2+b1) ... Removing libmbedtls21:amd64 (3.6.5-0.1) ... Removing libmbedx509-7:amd64 (3.6.5-0.1) ... Removing libmbedcrypto16:amd64 (3.6.5-0.1) ... Removing libncursesw6:amd64 (6.6+20251231-1) ... Removing libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Removing libpng16-16t64:amd64 (1.6.54-1) ... Removing libpython3.13-minimal:amd64 (3.13.11-1+b1) ... Removing libreadline8t64:amd64 (8.3-3+b1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libspoa7.0.0:amd64 (4.1.5-1) ... Removing libuv1t64:amd64 (1.51.0-2+b1) ... Removing media-types (14.0.0) ... Removing ncbi-data (6.1.20170106+dfsg2-7) ... Removing ncbi-vdb-data (3.2.1+dfsg-2) ... Removing netbase (6.5) ... Removing perl-modules-5.40 (5.40.1-7) ... Removing readline-common (8.3-3) ... Processing triggers for libc-bin (2.42-10+b1) ... 0m47.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', 'remove', '--allow-remove-essential', 'isa-support:amd64', 'libblas3:amd64', 'libboost-chrono1.83.0t64:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-serialization1.83.0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpng16-16t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libspoa7.0.0:amd64', 'libuv1t64:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'ncbi-vdb-data', 'netbase', 'perl', 'perl-modules-5.40', 'python3', 'python3-minimal', 'python3-shasta', 'python3.13', 'python3.13-minimal', 'readline-common', 'sse4.2-support', 'shasta'] 0m47.8s INFO: Running scripts post_remove 0m47.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_remove_exceptions'] 0m47.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_remove_exceptions'] 0m47.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg', '--purge', 'isa-support:amd64', 'libblas3:amd64', 'libboost-chrono1.83.0t64:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-serialization1.83.0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpng16-16t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libspoa7.0.0:amd64', 'libuv1t64:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'ncbi-vdb-data', 'netbase', 'perl', 'perl-modules-5.40', 'python3', 'python3-minimal', 'python3-shasta', 'python3.13', 'python3.13-minimal', 'readline-common', 'sse4.2-support'] 0m48.1s DUMP: dpkg: warning: ignoring request to remove isa-support which is not installed dpkg: warning: ignoring request to remove libblas3 which is not installed dpkg: warning: ignoring request to remove libboost-chrono1.83.0t64 which is not installed dpkg: warning: ignoring request to remove libboost-program-options1.83.0 which is not installed dpkg: warning: ignoring request to remove libboost-serialization1.83.0 which is not installed dpkg: warning: ignoring request to remove libexpat1 which is not installed dpkg: warning: ignoring request to remove libffi8 which is not installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which is not installed dpkg: warning: ignoring request to remove libgdbm6t64 which is not installed dpkg: warning: ignoring request to remove libgfortran5 which is not installed dpkg: warning: ignoring request to remove libgomp1 which is not installed dpkg: warning: ignoring request to remove liblapack3 which is not installed dpkg: warning: ignoring request to remove liblmdb0 which is not installed dpkg: warning: ignoring request to remove libmbedcrypto16 which is not installed dpkg: warning: ignoring request to remove libmbedtls21 which is not installed dpkg: warning: ignoring request to remove libmbedx509-7 which is not installed dpkg: warning: ignoring request to remove libncbi-vdb3 which is not installed dpkg: warning: ignoring request to remove libncursesw6 which is not installed dpkg: warning: ignoring request to remove libnghttp2-14 which is not installed dpkg: warning: ignoring request to remove libperl5.40 which is not installed dpkg: warning: ignoring request to remove libpng16-16t64 which is not installed dpkg: warning: ignoring request to remove libpython3-stdlib which is not installed dpkg: warning: ignoring request to remove libpython3.13 which is not installed (Reading database ... 4949 files and directories currently installed.) Purging configuration files for libpython3.13-minimal:amd64 (3.13.11-1+b1) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which is not installed Purging configuration files for libreadline8t64:amd64 (8.3-3+b1) ... dpkg: warning: ignoring request to remove libspoa7.0.0 which is not installed dpkg: warning: ignoring request to remove libuv1t64 which is not installed Purging configuration files for media-types (14.0.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which is not installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-7) ... Purging configuration files for ncbi-vdb-data (3.2.1+dfsg-2) ... Purging configuration files for netbase (6.5) ... Purging configuration files for perl (5.40.1-7) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which is not installed Purging configuration files for python3 (3.13.9-3) ... dpkg: warning: ignoring request to remove python3-minimal which is not installed dpkg: warning: ignoring request to remove python3-shasta which is not installed dpkg: warning: ignoring request to remove python3.13 which is not installed Purging configuration files for python3.13-minimal (3.13.11-1+b1) ... Purging configuration files for readline-common (8.3-3) ... Purging configuration files for sse4.2-support (27+b1) ... 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg', '--purge', 'isa-support:amd64', 'libblas3:amd64', 'libboost-chrono1.83.0t64:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-serialization1.83.0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libperl5.40:amd64', 'libpng16-16t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libspoa7.0.0:amd64', 'libuv1t64:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'ncbi-vdb-data', 'netbase', 'perl', 'perl-modules-5.40', 'python3', 'python3-minimal', 'python3-shasta', 'python3.13', 'python3.13-minimal', 'readline-common', 'sse4.2-support'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg', '--purge', 'shasta'] 0m48.2s DUMP: dpkg: warning: ignoring request to remove shasta which is not installed 0m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg', '--purge', 'shasta'] 0m48.2s INFO: Running scripts post_purge 0m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_purge_exceptions'] 0m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_purge_exceptions'] 0m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg', '--purge', '--pending'] 0m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg', '--purge', '--pending'] 0m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg', '--remove', '--pending'] 0m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg', '--remove', '--pending'] 0m48.2s INFO: Running scripts post_test 0m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_test_exceptions'] 0m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'tmp/scripts/post_test_exceptions'] 0m48.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m48.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m48.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg-divert', '--list'] 0m48.7s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'dpkg-divert', '--list'] 0m48.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', 'clean'] 0m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxqkljo91', 'apt-get', 'clean'] 0m48.7s DEBUG: Recording chroot state 0m49.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/shm'] 0m49.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/shm'] 0m49.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/console'] 0m49.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/console'] 0m49.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/ptmx'] 0m49.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/ptmx'] 0m49.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/pts'] 0m49.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/dev/pts'] 0m49.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/proc'] 0m50.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpxqkljo91/proc'] 0m50.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m50.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpxqkljo91'] 0m50.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpxqkljo91 0m50.1s INFO: PASS: Upgrading between Debian distributions. 0m50.1s INFO: PASS: All tests. 0m50.1s INFO: piuparts run ends. ret=0 End: 2026-01-24 23:00:23 GMT