Start: 2024-11-27 21:22:10 GMT [sid] Package: shasta Source: shasta (0.12.0-1) Version: 0.12.0-1+b1 Installed-Size: 2591 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 (>= 13.1), python3-shasta (= 0.12.0-1+b1) 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+b1_amd64.deb Size: 625032 MD5sum: 13cb51e69ea66c095f03d5caa0c102d5 SHA256: bb344b03a7f52a2716a4a594e1beb1bd88eee1144e30431c1bb680f3712aa1e3 [experimental] Package: shasta Version: 0.12.0-2 Installed-Size: 2598 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 (= 0.12.0-2) 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_0.12.0-2_amd64.deb Size: 625124 MD5sum: d107990bd4f83921893ecacc7b07f96c SHA256: baf466b5ed990b3783849331ab81d15db257bd69893c75b76f2d04f7bd4fa7a0 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt shasta=0.12.0-2 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt shasta=0.12.0-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpe_1gs_c5 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpe_1gs_c5 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/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/tmpe_1gs_c5/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/tmpe_1gs_c5/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpe_1gs_c5/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', 'update'] 0m3.4s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7341 kB] Fetched 17.6 MB in 2s (8153 kB/s) Reading package lists... 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', 'update'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', '-yf', 'dist-upgrade'] 0m4.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libseccomp2 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 47.8 kB of archives. After this operation, 3072 B of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-2 [47.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.8 kB in 0s (1670 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 ... 5150 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-2_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-2) over (2.5.5-1+b3) ... Setting up libseccomp2:amd64 (2.5.5-2) ... Processing triggers for libc-bin (2.40-4) ... 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', '-yf', 'dist-upgrade'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.1s DUMP: 7c4274058c1ab94a9552136cbac7a794 - 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.1s INFO: Running scripts post_setup 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_setup_dummy_users'] 0m6.0s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_setup_dummy_users'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_setup_forbid_home'] 0m6.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_setup_forbid_home'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.0s 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' 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_setup_minimize'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_setup_minimize'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_setup_zz_backports'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_setup_zz_backports'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.0s DUMP: install ok installed apt apt 2.9.14 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc2-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257~rc2-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-11 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl-base perl-base 5.40.0-8 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat 0m6.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m6.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m6.4s INFO: Running scripts is_testable 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/is_testable_uninstallable'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/is_testable_uninstallable'] 0m6.4s INFO: Running scripts pre_test 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_test_exceptions'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_test_exceptions'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_test_root_password'] 0m6.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_test_root_password'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'show', '--no-all-versions', 'shasta'] 0m6.6s DUMP: Package: shasta Source: shasta (0.12.0-1) Version: 0.12.0-1+b1 Installed-Size: 2591 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 (>= 13.1), python3-shasta (= 0.12.0-1+b1) 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+b1_amd64.deb Size: 625032 MD5sum: 13cb51e69ea66c095f03d5caa0c102d5 SHA256: bb344b03a7f52a2716a4a594e1beb1bd88eee1144e30431c1bb680f3712aa1e3 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'show', '--no-all-versions', 'shasta'] 0m6.6s INFO: apt-cache knows about the following packages: shasta 0m6.6s INFO: Running scripts pre_install 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_database-server'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_database-server'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_exceptions'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_exceptions'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_extras'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_extras'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'policy'] 0m6.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'policy'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'policy', 'shasta'] 0m6.7s DUMP: shasta: Installed: (none) Candidate: 0.12.0-1+b1 Version table: 0.12.0-1+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'policy', 'shasta'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', '-y', 'install', 'shasta'] 0m15.2s 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 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgomp1 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncursesw6 libnghttp2-14 libnsl2 libperl5.40 libpng16-16t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libreadline8t64 libspoa7.0.0 libsqlite3-0 libtirpc-common libtirpc3t64 libuv1t64 media-types ncbi-blast+ ncbi-data netbase perl perl-modules-5.40 python3 python3-minimal python3-shasta python3.12 python3.12-minimal readline-common Suggested packages: gdbm-l10n krb5-doc krb5-user sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python3.12-venv python3.12-doc binutils binfmt-support readline-doc Recommended packages: krb5-locales 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 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgomp1 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncursesw6 libnghttp2-14 libnsl2 libperl5.40 libpng16-16t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libreadline8t64 libspoa7.0.0 libsqlite3-0 libtirpc-common libtirpc3t64 libuv1t64 media-types ncbi-blast+ ncbi-data netbase perl perl-modules-5.40 python3 python3-minimal python3-shasta python3.12 python3.12-minimal readline-common shasta 0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded. 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Preparing to unpack .../25-shasta_0.12.0-1+b1_amd64.deb ... Unpacking shasta (0.12.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up liblmdb0:amd64 (0.9.31-1+b2) ... Setting up ncbi-data (6.1.20170106+dfsg2-5) ... Setting up libboost-program-options1.83.0:amd64 (1.83.0-3.2+b1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libuv1t64:amd64 (1.48.0-7) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libgomp1:amd64 (14.2.0-8) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libboost-serialization1.83.0:amd64 (1.83.0-3.2+b1) ... Setting up libblas3:amd64 (3.12.0-4) ... 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 (1.83.0-3.2+b1) ... Setting up libspoa7.0.0:amd64 (4.1.4-2+b1) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up libncursesw6:amd64 (6.5-2+b1) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up perl-modules-5.40 (5.40.0-8) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libmbedcrypto16:amd64 (3.6.2-3) ... Setting up readline-common (8.2-5) ... Setting up liblapack3:amd64 (3.12.0-4) ... 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 (5.40.0-8) ... Setting up perl (5.40.0-8) ... Setting up libmbedx509-7:amd64 (3.6.2-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... Setting up libpython3.12t64:amd64 (3.12.7-3) ... Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up python3-shasta (0.12.0-1+b1) ... Setting up shasta (0.12.0-1+b1) ... Processing triggers for libc-bin (2.40-4) ... 0m15.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', '-y', 'install', 'shasta'] 0m15.2s INFO: Running scripts post_install 0m15.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_install_exceptions'] 0m15.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_install_exceptions'] 0m15.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m15.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m15.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpe_1gs_c5 to experimental 0m15.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main deb http://deb.debian.org/debian/ experimental main 0m15.6s INFO: Running scripts pre_distupgrade 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_distupgrade_exceptions'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_distupgrade_exceptions'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', 'update'] 0m17.1s DUMP: Hit:1 http://deb.debian.org/debian sid InRelease Get:2 http://deb.debian.org/debian experimental InRelease [101 kB] Get:3 http://deb.debian.org/debian experimental/main amd64 Packages [504 kB] Get:4 http://deb.debian.org/debian experimental/main Translation-en [305 kB] Fetched 910 kB in 1s (1406 kB/s) Reading package lists... 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', 'update'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', '-yf', 'dist-upgrade'] 0m17.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', '-yf', 'dist-upgrade'] 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.1s DUMP: 000978097eb1a60a299d454e8b880299 - 0m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'show', '--no-all-versions', 'shasta'] 0m18.4s DUMP: Package: shasta Source: shasta (0.12.0-1) Version: 0.12.0-1+b1 Installed-Size: 2591 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 (>= 13.1), python3-shasta (= 0.12.0-1+b1) 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+b1_amd64.deb Size: 625032 MD5sum: 13cb51e69ea66c095f03d5caa0c102d5 SHA256: bb344b03a7f52a2716a4a594e1beb1bd88eee1144e30431c1bb680f3712aa1e3 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'show', '--no-all-versions', 'shasta'] 0m18.4s INFO: apt-cache knows about the following packages: shasta 0m18.4s INFO: Running scripts pre_install 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_database-server'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_database-server'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_exceptions'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_exceptions'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_extras'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_extras'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'policy'] 0m18.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 1 http://deb.debian.org/debian experimental/main amd64 Packages release o=Debian,a=experimental,n=rc-buggy,l=Debian,c=main,b=amd64 origin deb.debian.org 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: 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'policy'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'policy', 'shasta'] 0m18.6s DUMP: shasta: Installed: 0.12.0-1+b1 Candidate: 0.12.0-1+b1 Version table: 0.12.0-2 1 1 http://deb.debian.org/debian experimental/main amd64 Packages *** 0.12.0-1+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'policy', 'shasta'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', '-y', '-t', 'experimental', 'install', 'shasta'] 0m19.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: python3-shasta The following packages will be upgraded: python3-shasta shasta 2 upgraded, 0 newly installed, 0 to remove and 12 not upgraded. Need to get 2876 kB of archives. After this operation, 159 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian experimental/main amd64 shasta amd64 0.12.0-2 [625 kB] Get:2 http://deb.debian.org/debian experimental/main amd64 python3-shasta amd64 0.12.0-2 [2251 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2876 kB in 0s (39.4 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 ... 8731 files and directories currently installed.) Preparing to unpack .../shasta_0.12.0-2_amd64.deb ... Unpacking shasta (0.12.0-2) over (0.12.0-1+b1) ... Preparing to unpack .../python3-shasta_0.12.0-2_amd64.deb ... Unpacking python3-shasta (0.12.0-2) over (0.12.0-1+b1) ... Setting up python3-shasta (0.12.0-2) ... Setting up shasta (0.12.0-2) ... 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', '-y', '-t', 'experimental', 'install', 'shasta'] 0m19.9s INFO: Running scripts post_install 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_install_exceptions'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_install_exceptions'] 0m19.9s INFO: Running scripts post_distupgrade 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m20.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m20.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m20.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m20.9s INFO: Running scripts pre_install 0m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_database-server'] 0m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_database-server'] 0m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_exceptions'] 0m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_exceptions'] 0m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_extras'] 0m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_extras'] 0m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'policy'] 0m21.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 1 http://deb.debian.org/debian experimental/main amd64 Packages release o=Debian,a=experimental,n=rc-buggy,l=Debian,c=main,b=amd64 origin deb.debian.org 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: 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'policy'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'policy', 'shasta'] 0m21.0s DUMP: shasta: Installed: 0.12.0-2 Candidate: 0.12.0-2 Version table: *** 0.12.0-2 100 1 http://deb.debian.org/debian experimental/main amd64 Packages 100 /var/lib/dpkg/status 0.12.0-1+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-cache', 'policy', 'shasta'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', '-y', '-t', 'experimental', 'install', 'shasta=0.12.0-2'] 0m21.6s DUMP: Reading package lists... Building dependency tree... Reading state information... shasta is already the newest version (0.12.0-2). 0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded. 0m21.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', '-y', '-t', 'experimental', 'install', 'shasta=0.12.0-2'] 0m21.6s INFO: Running scripts post_install 0m21.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_install_exceptions'] 0m21.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_install_exceptions'] 0m21.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m22.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m22.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', '-ac', '--ignore-obsolete'] 0m24.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', '-ac', '--ignore-obsolete'] 0m24.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m24.2s DUMP: 0.15.6 0m24.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m24.2s INFO: Running adequate version 0.15.6 now. 0m24.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'shasta'] 0m24.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'shasta'] 0m24.3s INFO: Running scripts pre_remove 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m25.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m25.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m25.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m25.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_remove_exceptions'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/pre_remove_exceptions'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m25.3s DUMP: install ok installed apt apt 2.9.14 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblas3:amd64 libblas3 3.12.0-4 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 install ok installed libboost-chrono1.83.0t64:amd64 libboost-chrono1.83.0t64 1.83.0-3.2+b1 install ok installed libboost-program-options1.83.0:amd64 libboost-program-options1.83.0 1.83.0-3.2+b1 install ok installed libboost-serialization1.83.0:amd64 libboost-serialization1.83.0 1.83.0-3.2+b1 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-8 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-8 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-4 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.2-3 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.2-3 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.2-3 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libncursesw6:amd64 libncursesw6 6.5-2+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-4 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-8 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.44-2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.7-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.7-3 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.7-3 install ok installed libpython3.12t64:amd64 libpython3.12t64 3.12.7-3 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libspoa7.0.0:amd64 libspoa7.0.0 4.1.4-2+b1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc2-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3+b1 install ok installed libudev1:amd64 libudev1 257~rc2-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libuv1t64:amd64 libuv1t64 1.48.0-7 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-11 install ok installed ncbi-blast+ ncbi-blast+ 2.16.0+ds-6+b1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-5 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed netbase netbase 6.4 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl perl 5.40.0-8 install ok installed perl-base perl-base 5.40.0-8 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.0-8 install ok installed python3 python3 3.12.7-1 install ok installed python3-minimal python3-minimal 3.12.7-1 install ok installed python3-shasta python3-shasta 0.12.0-2 install ok installed python3.12 python3.12 3.12.7-3 install ok installed python3.12-minimal python3.12-minimal 3.12.7-3 install ok installed readline-common readline-common 8.2-5 install ok installed sed sed 4.9-2 install ok installed shasta shasta 0.12.0-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', 'remove', 'libblas3:amd64', 'libboost-chrono1.83.0t64:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-serialization1.83.0:amd64', 'libexpat1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libperl5.40:amd64', 'libpng16-16t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libreadline8t64:amd64', 'libspoa7.0.0:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libuv1t64:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'perl', 'perl-modules-5.40', 'python3', 'python3-minimal', 'python3-shasta', 'python3.12', 'python3.12-minimal', 'readline-common', 'shasta'] 0m26.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libblas3 libboost-chrono1.83.0t64 libboost-program-options1.83.0 libboost-serialization1.83.0 libexpat1 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgomp1 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblmdb0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncursesw6 libnghttp2-14 libnsl2 libperl5.40 libpng16-16t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libreadline8t64 libspoa7.0.0 libsqlite3-0 libtirpc-common libtirpc3t64 libuv1t64 media-types ncbi-blast+ ncbi-data netbase perl perl-modules-5.40 python3 python3-minimal python3-shasta python3.12 python3.12-minimal readline-common shasta 0 upgraded, 0 newly installed, 47 to remove and 0 not upgraded. After this operation, 217 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 ... 8729 files and directories currently installed.) Removing shasta (0.12.0-2) ... Removing python3-shasta (0.12.0-2) ... Removing liblapack3:amd64 (3.12.0-4) ... Removing libblas3:amd64 (3.12.0-4) ... Removing libboost-chrono1.83.0t64:amd64 (1.83.0-3.2+b1) ... Removing libboost-program-options1.83.0:amd64 (1.83.0-3.2+b1) ... Removing libboost-serialization1.83.0:amd64 (1.83.0-3.2+b1) ... Removing ncbi-blast+ (2.16.0+ds-6+b1) ... Removing python3 (3.12.7-1) ... Removing python3.12 (3.12.7-3) ... Removing python3-minimal (3.12.7-1) ... Removing python3.12-minimal (3.12.7-3) ... Removing libpython3.12t64:amd64 (3.12.7-3) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing perl (5.40.0-8) ... Removing libperl5.40:amd64 (5.40.0-8) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgfortran5:amd64 (14.2.0-8) ... Removing libgomp1:amd64 (14.2.0-8) ... Removing libpython3-stdlib:amd64 (3.12.7-1) ... Removing libpython3.12-stdlib:amd64 (3.12.7-3) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b3) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing liblmdb0:amd64 (0.9.31-1+b2) ... Removing libmbedtls21:amd64 (3.6.2-3) ... Removing libmbedx509-7:amd64 (3.6.2-3) ... Removing libmbedcrypto16:amd64 (3.6.2-3) ... Removing libncursesw6:amd64 (6.5-2+b1) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libpng16-16t64:amd64 (1.6.44-2) ... Removing libpython3.12-minimal:amd64 (3.12.7-3) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libspoa7.0.0:amd64 (4.1.4-2+b1) ... Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing libuv1t64:amd64 (1.48.0-7) ... Removing media-types (10.1.0) ... Removing ncbi-data (6.1.20170106+dfsg2-5) ... Removing netbase (6.4) ... Removing perl-modules-5.40 (5.40.0-8) ... Removing readline-common (8.2-5) ... Processing triggers for libc-bin (2.40-4) ... 0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', 'remove', 'libblas3:amd64', 'libboost-chrono1.83.0t64:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-serialization1.83.0:amd64', 'libexpat1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libperl5.40:amd64', 'libpng16-16t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libreadline8t64:amd64', 'libspoa7.0.0:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libuv1t64:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'perl', 'perl-modules-5.40', 'python3', 'python3-minimal', 'python3-shasta', 'python3.12', 'python3.12-minimal', 'readline-common', 'shasta'] 0m26.7s INFO: Running scripts post_remove 0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_remove_exceptions'] 0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_remove_exceptions'] 0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg', '--purge', 'libblas3:amd64', 'libboost-chrono1.83.0t64:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-serialization1.83.0:amd64', 'libexpat1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libperl5.40:amd64', 'libpng16-16t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libreadline8t64:amd64', 'libspoa7.0.0:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libuv1t64:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'perl', 'perl-modules-5.40', 'python3', 'python3-minimal', 'python3-shasta', 'python3.12', 'python3.12-minimal', 'readline-common'] 0m26.7s DUMP: dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-chrono1.83.0t64 which isn't installed dpkg: warning: ignoring request to remove libboost-program-options1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-serialization1.83.0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed (Reading database ... 5167 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto16 which isn't installed dpkg: warning: ignoring request to remove libmbedtls21 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-7 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.7-3) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.12t64 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... dpkg: warning: ignoring request to remove libspoa7.0.0 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... dpkg: warning: ignoring request to remove libuv1t64 which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-5) ... Purging configuration files for netbase (6.4) ... Purging configuration files for perl (5.40.0-8) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed Purging configuration files for python3 (3.12.7-1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-shasta which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.7-3) ... Purging configuration files for readline-common (8.2-5) ... 0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg', '--purge', 'libblas3:amd64', 'libboost-chrono1.83.0t64:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-serialization1.83.0:amd64', 'libexpat1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libperl5.40:amd64', 'libpng16-16t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libreadline8t64:amd64', 'libspoa7.0.0:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libuv1t64:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'perl', 'perl-modules-5.40', 'python3', 'python3-minimal', 'python3-shasta', 'python3.12', 'python3.12-minimal', 'readline-common'] 0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg', '--purge', 'shasta'] 0m26.7s DUMP: dpkg: warning: ignoring request to remove shasta which isn't installed 0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg', '--purge', 'shasta'] 0m26.7s INFO: Running scripts post_purge 0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_purge_exceptions'] 0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_purge_exceptions'] 0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg', '--purge', '--pending'] 0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg', '--purge', '--pending'] 0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg', '--remove', '--pending'] 0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg', '--remove', '--pending'] 0m26.7s INFO: Running scripts post_test 0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_test_exceptions'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'tmp/scripts/post_test_exceptions'] 0m26.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m27.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg-divert', '--list'] 0m27.1s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'dpkg-divert', '--list'] 0m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', 'clean'] 0m27.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5', 'apt-get', 'clean'] 0m27.2s DEBUG: Recording chroot state 0m28.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/shm'] 0m28.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/shm'] 0m28.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/console'] 0m28.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/console'] 0m28.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/ptmx'] 0m28.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/ptmx'] 0m28.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/pts'] 0m28.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/dev/pts'] 0m28.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/proc'] 0m28.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5/proc'] 0m28.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m28.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpe_1gs_c5'] 0m28.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpe_1gs_c5 0m28.2s INFO: PASS: Upgrading between Debian distributions. 0m28.2s INFO: PASS: All tests. 0m28.2s INFO: piuparts run ends. ret=0 End: 2024-11-27 21:22:38 GMT